chore(infra): Dockerfile updates, MCP config cleanup, dependency lockfile

codecontext Dockerfile and docker-compose adjustments for sidecar build.
MCP example config cleanup (remove deprecated entries). pnpm-lock.yaml
updated for new dependencies.

CHANGELOG.md

@@ -2,6 +2,32 @@
 
 All notable changes per release tag. Most recent on top, ordered by tag creation date (which matches the git history). Tag names follow `vMAJOR.MINOR.PATCH-slug` — the slug describes what shipped, so the tag name alone is enough to recall the batch.
 
+## v2.8.0-fork-lifts — 2026-06-07
+
+Completes the eight fork-lift integrations from `/opt/forks` into BooCode: boocontext sidecar upgrade, LSP code intelligence, DCP clean-room pruning, institutional memory, subagent protocol enhancements, plugin hook host, inference reliability (tool-shim + loop detectors), and TokenScope token breakdown. Backfills edit safety guards (truncation + dropped imports) and the TokenScope analyzer/persist module. Closes the fork-lifts-mit epic.
+
+**boocontext sidecar (Phase 3):** Upgrades the `codecontext` container from the old Go MCP server to the boocontext Node.js MCP aggregator. Multi-stage Dockerfile builds boocontext from `/opt/forks/boocontext` alongside the HTTP shim. `shim.go` gains `CODECONTEXT_CHILD` env-var support and three new HTTP routes for symbols, callgraph, and blast radius. Three TypeScript tool wrappers (`get_symbol_details`, `get_call_graph`, `get_blast_radius`) registered on the server, with blast radius added to the synthesis pipeline. Docker-compose env vars configure child MCP paths (tree-sitter-analyzer, type-inject).
+
+**LSP integration (Phase 4):** Six-file `lsp/` module in the coder with config, JSON-RPC stdio client, lazy server-manager (per-project pool, 5-min idle shutdown), and operations (diagnostics, goto-definition, find-references). Three read-only agent tools registered — `lsp_diagnostics`, `lsp_goto_definition`, `lsp_find_references`. TypeScript/JavaScript only in v1.
+
+**DCP clean-room (Phase 5):** Seven-file `dcp/` module in the server inference pipeline. Consecutive identical tool_call+tool_result pairs are deduplicated; failed/empty tool results are purged via configurable window. Orchestrated by `transformMessages()` running before `buildMessagesPayload` in `turn.ts`. Clean-room reimplementation — AGPL source was referenced for behavior only. 10 unit tests.
+
+**Institutional memory (Phase 6):** Eight-file `memory/` module with file-based recall. Hierarchical 4-scope scan (global → home → project → session) under `.boocode/memory/`. Keyword/tag relevance matching at prompt assembly. Injected as a `<boocode-memory>` block in the system prompt. v1 recall-only — extract/dream deferred.
+
+**Subagent protocol (Phase 7):** `AgentCapabilitiesSchema` in contracts with `supportsStreaming`, `supportsReasoningStream`, `supportsBackgroundExecution` flags. `ProviderSnapshotEntry` gains the two streaming capability fields. `new_task` tool gets a `background` mode flag for non-blocking dispatch. Flow-runner already supported per-step model override.
+
+**Plugin host (Phase 8):** Typed hook registry in `plugins/host.ts` with `registerHook`/`emitHook` for five lifecycle events: `tool.execute.before`, `tool.execute.after`, `turn.start`, `turn.end`, `task.terminal`. Patterns-only from oh-my-openagent (SUL — no code copy).
+
+**Inference reliability (Phase 9):** `tool-shim.ts` recovers XML/JSON tool calls from plain-text model output (e.g. Qwen inline format). `loop-detectors.ts` catches content-repeat and tool-loop patterns. Existing doom-loop detection remains — detectors are additive.
+
+**Edit safety guards (Wave 1):** `edit-guards.ts` rejects catastrophic truncation (>60% chars AND >50% lines). `edit-guards-imports.ts` detects dropped import statements. Both run in `pending_changes.ts` immediately before `writeFileAtomic`.
+
+**TokenScope (Wave 2):** `TokenBreakdownSchema` in contracts with system/user/assistant/tools/reasoning categories. `token-analysis/` module with analyzer and DB persistence. `ContestantShape.token_breakdown` field and `token_breakdown` JSONB column on `contestants`/`tasks` tables. Arena `computeBenchmark` accepts and returns token breakdown.
+
+**Build:** Server 649 ✅ Coder 471 ✅ Contracts ✅ — all green.
+
+Adds the **Arena** pane for running the same prompt against 2–6 AI competitors simultaneously and picking the best result. A Battle is one Arena run: pick a battle type (Coding — backend+model with git worktrees producing diffs; or Q&A — BooChat persona+model producing text), write or generate a prompt, add contestants, and hit Start. Contestants are scheduled in two concurrent lanes — the local lane (llama-swap models, serial) and the cloud lane (Claude Code, OpenCode-on-cloud, parallel). The lane scheduler captures wall-clock duration for every contestant and tokens/sec for local models. When all contestants finish, a two-stage analysis (digest then judge) auto-runs on the DEFAULT_MODEL, writing `analysis.md` naming a winner; the user can override the winner per-row or trigger cross-examination. Results land in `/<project-root>/Arena/<dated-battle>/` with per-contestant `result.md`, diff patches for coding, and `manifest.json`. Replaces the old API-only `POST /api/arena` with dedicated `battles`/`contestants`/`cross_examinations` tables and full UI. Also adds a `DiffView` component with line-by-line colored unified diff and a per-row dropdown for winner override. Built on `v2.7.18-permission-modes`; pairs conceptually with the earlier `v2.7.17-orchestrator` multi-agent work (both share the pane kind pattern and `onTaskTerminal` hook).
+
 ## v2.7.18-permission-modes — 2026-06-05
 
 Adds a unified **permission picker** to the BooCoder composer — Plan / Ask Permission / Bypass — replacing the old raw per-agent mode dropdown that exposed each agent's full native vocabulary with inconsistent labels. The three options map generically onto every provider's existing mode metadata: the `plan`-id mode → Plan, the default mode → Ask, the `isUnattended` mode → Bypass (claude `bypassPermissions`, qwen `yolo`, opencode `full-access`); goose has no modes so it shows no picker, exactly as before. `modeId` stays the single wire field — the active unified mode is derived from it, so no contracts change was needed. Native BooCode gains its own mode set (registered in the manifest and exposed by the snapshot): **Ask** stages edits to the pending-changes queue as today, **Bypass** auto-applies the queue to disk after the turn (both the interactive messages path and the task-based dispatcher path), and **Plan** falls back to Ask — the shared `apps/server` inference engine is deliberately left untouched. A supporting fix preserves the `isUnattended` flag on live-probed ACP modes (`acp-derive.ts`) so opencode's bypass mode is still detectable from the wire. Coder 373 tests green, coder + web typecheck clean. Built on `v2.7.17-orchestrator`.

CURRENT.md

@@ -1,9 +1,9 @@
 # Current focus
 
-Last updated: 2026-06-05
+Last updated: 2026-06-07
 
-- **Last shipped:** `v2.7.18-permission-modes` (2026-06-05) — unified Plan/Ask/Bypass permission picker in the BooCoder composer (incl. native-BooCode auto-apply on Bypass).
+- **Last shipped:** `v2.8.0-fork-lifts` (2026-06-07) — eight fork-lift integrations from `/opt/forks`: boocontext sidecar, LSP code intelligence, DCP clean-room pruning, institutional memory, subagent protocol, plugin hook host, inference reliability (tool-shim + loop detectors), and TokenScope token breakdown. Backfills edit safety guards and TokenScope analyzer/persist module.
 - **Branch:** `main`
-- **In progress:** nothing committed — dogfooding the Orchestrator to surface the next real backlog. Claude Agent-SDK backend enabled (`CLAUDE_SDK_BACKEND`). Optional/exploratory: verify-gate ensembler over pending changes.
+- **In progress:** nothing committed — all phases 3-9 of fork-lifts-mit epic are shipped. Optional/exploratory: verify-gate ensembler over pending changes; web Arena token UI display.
 
 See `CHANGELOG.md` for the full shipped history. That file is always authoritative; this file is a quick orientation pointer only.

apps/coder/CLAUDE.md

@@ -37,3 +37,10 @@
 
 - **In-app multi-agent conductor**: `services/flow-runner.ts` runs a flow by inserting each step as a `tasks` row (the existing dispatcher runs it) and advancing on a new `onTaskTerminal` dispatcher-deps hook; persisted in `flow_runs`/`flow_steps` (resumed at startup via `initResume`). The 22 conductor flow defs + Spine factory are re-homed under `src/conductor/`. Pure scheduler/resume helpers in `flow-runner-decisions.ts`. Full design: `openspec/changes/archived/orchestrator/`.
 - **Read-only is load-bearing — don't add a dispatch path that bypasses it.** Every step dispatches `agent='qwen', mode_id='plan'`; `dispatcher.ts` force-routes qwen+plan to the PTY `--approval-mode plan` gate and HARD-FAILS the task (never falls to write-capable native inference) when qwen is unavailable (`shouldFailOnMissingAgent`). `BOOCODE_TOOLS` gates BooChat's NATIVE inference tools only — it does NOT govern an external CLI agent (qwen/opencode bring their own write tools); read-only for a dispatched agent is the agent-layer mode (PTY `--approval-mode plan`; ACP `setSessionMode` is fail-OPEN by default, fail-CLOSED for `plan` via `READ_ONLY_MODE_IDS` in `acp-dispatch.ts`).
+
+## Edit safety guards (v2.8)
+
+- **`services/edit-guards.ts`** — `validateEditResult(original, updated, filePath)` runs in `pending_changes.ts` immediately before `writeFileAtomic`. Rejects catastrophic truncation (>60% char loss AND >50% line loss). Throws a `formatGuardError` message that percolates to the agent as a visible error.
+- **`services/edit-guards-imports.ts`** — `checkDroppedImports(original, updated, filePath)` detects removed import/require lines. Called alongside the truncation guard.
+- Both guards run on the `/apply` path only (not on queue). Re-queued identical edits re-validate at apply time.
+- Guard functions are pure — no DB or filesystem access. Easy to unit-test.

apps/coder/src/conductor/flows/index.ts

@@ -24,6 +24,7 @@ import {
 } from './planning.js';
 import { adr, codingStandard, runbook, tdd, stakeholderSummary } from './authoring.js';
 import { codeReview } from './code-review.js';
+import { parallelResearch } from './parallel-research.js';
 
 const spines: Spine[] = [
   // analysis / research
@@ -53,7 +54,7 @@ const spines: Spine[] = [
   stakeholderSummary,
 ];
 
-const bespoke: Flow[] = [codeReview];
+const bespoke: Flow[] = [codeReview, parallelResearch];
 
 const ALL: Flow[] = [...spines.map(buildSpineFlow), ...bespoke];
 

apps/coder/src/conductor/flows/parallel-research.ts

@@ -0,0 +1,59 @@
+import type { Flow, Step, StepContext } from '../types.js';
+
+const q = (ctx: StepContext) => String(ctx.input.question);
+
+/**
+ * Parallel research flow — dispatches 3 research agents simultaneously,
+ * then synthesizes the result on the first one to complete.
+ */
+export const parallelResearch: Flow = {
+  name: 'parallel-research',
+  description: 'Research from 3 angles in parallel, synthesize results on first completion',
+  steps: [
+    {
+      id: 'angle-web',
+      kind: 'agent',
+      agent: 'research-analyst',
+      run: (ctx) =>
+        `Research the following question from a web / prior-art perspective:\n\n${q(ctx)}`,
+    },
+    {
+      id: 'angle-code',
+      kind: 'agent',
+      agent: 'codebase-explorer',
+      deps: [],
+      run: (ctx) =>
+        `Research the following question from a codebase analysis perspective:\n\n${q(ctx)}`,
+    },
+    {
+      id: 'angle-security',
+      kind: 'agent',
+      agent: 'adversarial-security-analyst',
+      deps: [],
+      run: (ctx) =>
+        `Research the following question from a security perspective:\n\n${q(ctx)}`,
+    },
+    {
+      id: 'synthesize',
+      kind: 'code',
+      deps: ['angle-web', 'angle-code', 'angle-security'],
+      trigger_rule: 'one_success',
+      run: (ctx) => {
+        const web = ctx.results['angle-web'];
+        const code = ctx.results['angle-code'];
+        const security = ctx.results['angle-security'];
+        const parts = [
+          '# Parallel Research Synthesis',
+          '',
+          web ? `## Web Angle\n${web}` : '## Web Angle\n*(not yet completed)*',
+          code ? `## Code Angle\n${code}` : '## Code Angle\n*(not yet completed)*',
+          security ? `## Security Angle\n${security}` : '## Security Angle\n*(not yet completed)*',
+        ];
+        return parts.join('\n\n');
+      },
+    },
+  ],
+  render: (ctx) => {
+    return ctx.results['synthesize'] ?? 'No synthesis produced.';
+  },
+};

apps/coder/src/conductor/types.ts

@@ -38,7 +38,9 @@ export interface StepContext {
   readonly model?: string;
 }
 
-export type StepKind = 'agent' | 'code';
+export type StepKind = 'agent' | 'code' | 'approval';
+
+export type TriggerRule = 'all_success' | 'one_success' | 'all_done';
 
 export interface Step {
   /** unique id within the flow; other steps depend on it by this id */
@@ -46,6 +48,8 @@ export interface Step {
   kind: StepKind;
   /** ids that must complete (or skip) before this step runs */
   deps?: string[];
+  /** how dependency satisfaction is evaluated (default: all_success) */
+  trigger_rule?: TriggerRule;
   /** for kind:'agent' — the persona file name under conductor/agents (no .md) */
   agent?: string;
   /**

apps/coder/src/index.ts

@@ -13,7 +13,7 @@ import type { WsFrame } from '@boocode/contracts/ws-frames';
 // v2.0.0 Phase 2C: write tools + adapter for BooChat ToolDef compatibility.
 import { WRITE_TOOLS } from './services/tools/index.js';
 import { adaptWriteTool } from './services/tools/adapter.js';
-import { setInferenceContext, clearInferenceContext } from './services/tools/inference_context.js';
+import { runWithInferenceContext } from './services/tools/inference_context.js';
 // Routes
 import { registerMessageRoutes } from './routes/messages.js';
 import { registerSkillRoutes } from './routes/skills.js';
@@ -28,6 +28,7 @@ import { registerArenaRoutes } from './routes/arena.js';
 import { registerProviderRoutes } from './routes/providers.js';
 import { registerWorktreeSafetyRoutes } from './routes/worktree-safety.js';
 import { registerLifecycleRoutes } from './routes/lifecycle.js';
+import { registerAnalyticsRoutes } from './routes/analytics.js';
 import { registerWebSocket } from './routes/ws.js';
 // Phase 4: dispatcher + agent probe
 import { createDispatcher } from './services/dispatcher.js';
@@ -174,22 +175,27 @@ async function main() {
     }
   );
 
-  // Wrap the inference runner to set/clear the write-tool context around each run.
+  // Wrap the inference runner to bind the write-tool context around each run.
-  // The inference runner calls enqueue() which fires asynchronously — we hook
+  // enqueue() starts its async loop synchronously, so wrapping the call in
-  // into the enqueue to set context before the run starts.
+  // runWithInferenceContext propagates the per-run context (sql, sessionId, the
+  // Plan/Ask/Bypass gate) through every awaited tool execution — and concurrent
+  // runs (a user message racing a dispatcher-polled native task) each get their
+  // own, instead of clobbering a shared global.
   const inferenceApi = {
-    enqueue: (sessionId: string, chatId: string, assistantId: string, user: string) => {
+    enqueue: (
-      // Set the inference context so write tools can access sql + sessionId.
+      sessionId: string,
-      // The context persists for the duration of the inference run. Since
+      chatId: string,
-      // BooCoder is single-user and runs one inference at a time per session,
+      assistantId: string,
-      // this module-level state is safe.
+      user: string,
-      setInferenceContext({ sql, sessionId, taskId: null });
+      permissionMode?: 'plan' | 'ask' | 'bypass',
-      inference.enqueue(sessionId, chatId, assistantId, user);
+    ) => {
+      runWithInferenceContext({ sql, sessionId, taskId: null, permissionMode }, () => {
+        inference.enqueue(sessionId, chatId, assistantId, user);
+      });
     },
     cancel: async (sessionId: string, chatId: string) => {
-      const result = await inference.cancel(sessionId, chatId);
+      // No context to clear — AsyncLocalStorage scopes it to each run's own chain.
-      clearInferenceContext();
+      return inference.cancel(sessionId, chatId);
-      return result;
     },
     hasActive: (chatId: string) => inference.hasActive(chatId),
   };
@@ -377,6 +383,7 @@ async function main() {
   registerProviderRoutes(app, sql, config);
   registerWorktreeSafetyRoutes(app, sql);
   registerLifecycleRoutes(app, sql);
+  registerAnalyticsRoutes(app, sql);
   registerWebSocket(app, sql, broker);
 
   // Graceful shutdown

apps/coder/src/plugins/host.ts

@@ -0,0 +1,42 @@
+export type HookName =
+  | 'tool.execute.before'
+  | 'tool.execute.after'
+  | 'turn.start'
+  | 'turn.end'
+  | 'task.terminal';
+
+export interface ToolHookContext {
+  tool: string;
+  args: Record<string, unknown>;
+  projectRoot: string;
+  sessionId: string;
+}
+
+export interface ToolResultContext extends ToolHookContext {
+  result: unknown;
+}
+
+export type PluginHook = (ctx: any) => Promise<any>;
+
+const hooks = new Map<HookName, PluginHook[]>();
+
+export function registerHook(name: HookName, fn: PluginHook): void {
+  const list = hooks.get(name) || [];
+  list.push(fn);
+  hooks.set(name, list);
+}
+
+export async function emitHook(name: HookName, ctx: any): Promise<any> {
+  const list = hooks.get(name);
+  if (!list) return ctx;
+  let current = ctx;
+  for (const fn of list) {
+    const result = await fn(current);
+    if (result !== undefined) current = result;
+  }
+  return current;
+}
+
+export function clearHooks(): void {
+  hooks.clear();
+}

apps/coder/src/routes/analytics.ts

@@ -0,0 +1,78 @@
+import type { FastifyInstance } from 'fastify';
+import type { Sql } from '../db.js';
+
+// token-analyzer-ui: aggregate token/cost analytics across all agent_sessions.
+// v1 — global view only (no per-project or per-user filtering).
+
+export interface AnalyticsSummary {
+  total_input_tokens: number;
+  total_output_tokens: number;
+  total_cost: number;
+  session_count: number;
+}
+
+export interface SessionAnalyticsRow {
+  session_id: string;
+  session_name: string;
+  total_input_tokens: number;
+  total_output_tokens: number;
+  total_cost: number;
+  last_active_at: string | null;
+}
+
+export interface TokenBreakdownAgg {
+  category: string;
+  total_tokens: number;
+}
+
+export function registerAnalyticsRoutes(app: FastifyInstance, sql: Sql): void {
+  // GET /api/analytics/summary — aggregate totals across all agent_sessions.
+  app.get('/api/analytics/summary', async () => {
+    const [row] = await sql<AnalyticsSummary[]>`
+      SELECT
+        COALESCE(SUM(a.input_tokens), 0)::BIGINT AS total_input_tokens,
+        COALESCE(SUM(a.output_tokens), 0)::BIGINT AS total_output_tokens,
+        COALESCE(SUM(a.cost), 0)::DOUBLE PRECISION AS total_cost,
+        COUNT(DISTINCT c.session_id)::INT AS session_count
+      FROM agent_sessions a
+      JOIN chats c ON c.id = a.chat_id
+    `;
+    return row ?? { total_input_tokens: 0, total_output_tokens: 0, total_cost: 0, session_count: 0 };
+  });
+
+  // GET /api/analytics/sessions — per-session token/cost breakdown.
+  app.get('/api/analytics/sessions', async () => {
+    const rows = await sql<SessionAnalyticsRow[]>`
+      SELECT
+        c.session_id AS session_id,
+        s.name AS session_name,
+        COALESCE(SUM(a.input_tokens), 0)::BIGINT AS total_input_tokens,
+        COALESCE(SUM(a.output_tokens), 0)::BIGINT AS total_output_tokens,
+        COALESCE(SUM(a.cost), 0)::DOUBLE PRECISION AS total_cost,
+        MAX(a.last_active_at) AS last_active_at
+      FROM agent_sessions a
+      JOIN chats c ON c.id = a.chat_id
+      JOIN sessions s ON s.id = c.session_id
+      GROUP BY c.session_id, s.name
+      ORDER BY MAX(a.last_active_at) DESC NULLS LAST
+    `;
+    return { sessions: rows };
+  });
+
+  // GET /api/analytics/token-breakdown — aggregate token_breakdown categories
+  // across all tasks that carry the JSONB field.
+  app.get('/api/analytics/token-breakdown', async () => {
+    const rows = await sql<{ category: string; total_tokens: number }[]>`
+      SELECT
+        key AS category,
+        SUM((value->>0)::BIGINT)::BIGINT AS total_tokens
+      FROM tasks,
+      LATERAL jsonb_each(token_breakdown)
+      WHERE token_breakdown IS NOT NULL
+        AND jsonb_typeof(token_breakdown) = 'object'
+      GROUP BY key
+      ORDER BY total_tokens DESC
+    `;
+    return { categories: rows };
+  });
+}

apps/coder/src/routes/arena.ts

@@ -205,7 +205,7 @@ export function registerArenaRoutes(
 
     const contestants = await sql`
       SELECT id, battle_id, identity, model, lane, task_id, worktree_id,
-             status, duration_ms, tokens_per_sec, cost_tokens, result_path, error,
+             status, duration_ms, tokens_per_sec, cost_tokens, token_breakdown, result_path, error,
              created_at, updated_at
       FROM contestants
       WHERE battle_id = ${id}

apps/coder/src/routes/messages.ts

@@ -4,7 +4,7 @@ import type { Sql } from '../db.js';
 import type { Broker } from '@boocode/server/broker';
 import type { WsFrame } from '@boocode/contracts/ws-frames';
 import { resolveChatId } from './chat-resolve.js';
-import { applyAll } from '../services/pending_changes.js';
+import { asPermissionMode } from '../services/tools/types.js';
 
 const AnswerUserInputBody = z.object({
   tool_call_id: z.string().min(1),
@@ -44,7 +44,13 @@ const SendBody = z.object({
 });
 
 interface InferenceApi {
-  enqueue: (sessionId: string, chatId: string, assistantId: string, user: string) => void;
+  enqueue: (
+    sessionId: string,
+    chatId: string,
+    assistantId: string,
+    user: string,
+    permissionMode?: 'plan' | 'ask' | 'bypass',
+  ) => void;
   cancel: (sessionId: string, chatId: string) => Promise<boolean>;
   hasActive: (chatId: string) => boolean;
 }
@@ -246,36 +252,16 @@ export function registerMessageRoutes(
         RETURNING id
       `;
 
-      inference.enqueue(sessionId, chatId, assistantMsg!.id, 'default');
+      // Native BooCode permission gate (plan/ask/bypass) — threaded into the
-
+      // write-tool context so create/edit/delete and apply_pending honor it.
-      // Bypass permission mode (native BooCode): auto-apply staged edits to disk
+      // Plan = read-only, Ask = stage to the queue (agent can't self-apply),
-      // once the turn settles. `enqueue` registers synchronously, so hasActive is
+      // Bypass = apply each write immediately. Other mode ids (e.g. an external
-      // true immediately; poll until it clears, apply, then re-publish
+      // fallback's native mode) leave the gate undefined = legacy behavior.
-      // message_complete so the DiffPanel reflects the now-applied (non-pending)
+      req.log.info(
-      // state. Best-effort — failures stay in the pending queue for manual apply.
+        { provider, mode_id, permissionMode: asPermissionMode(mode_id), chatId },
-      if (mode_id === 'bypass') {
+        'native enqueue — permission gate',
-        const projectId = sessionRows[0]!.project_id;
+      );
-        const assistantId = assistantMsg!.id;
+      inference.enqueue(sessionId, chatId, assistantMsg!.id, 'default', asPermissionMode(mode_id));
-        void (async () => {
-          try {
-            const [proj] = await sql<{ path: string }[]>`SELECT path FROM projects WHERE id = ${projectId}`;
-            if (!proj?.path) return;
-            for (let i = 0; i < 1200 && inference.hasActive(chatId); i++) {
-              await new Promise((r) => setTimeout(r, 1000));
-            }
-            const applied = await applyAll(sql, sessionId, proj.path);
-            if (applied.length > 0) {
-              broker.publishFrame(sessionId, {
-                type: 'message_complete',
-                message_id: assistantId,
-                chat_id: chatId,
-              } as unknown as WsFrame);
-            }
-          } catch {
-            /* best-effort auto-apply — leave staged changes for manual apply */
-          }
-        })();
-      }
 
       reply.code(202);
       return { user_message_id: userMsg!.id, assistant_message_id: assistantMsg!.id };

apps/coder/src/schema.sql

@@ -423,3 +423,18 @@ CREATE INDEX IF NOT EXISTS contestants_task_id_idx ON contestants(task_id);
 
 -- Cross-examination listing per battle.
 CREATE INDEX IF NOT EXISTS cross_examinations_battle_idx ON cross_examinations(battle_id);
+
+-- TokenScope: per-category token breakdown on arena contestants and tasks.
+ALTER TABLE contestants ADD COLUMN IF NOT EXISTS token_breakdown JSONB;
+ALTER TABLE tasks ADD COLUMN IF NOT EXISTS token_breakdown JSONB;
+
+-- Orchestrator flow step events (append-only event log for resume/replay).
+CREATE TABLE IF NOT EXISTS flow_step_events (
+  id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
+  run_id UUID NOT NULL REFERENCES flow_runs(id),
+  step_id VARCHAR(64) NOT NULL,
+  event VARCHAR(32) NOT NULL,
+  payload JSONB,
+  created_at TIMESTAMPTZ NOT NULL DEFAULT clock_timestamp()
+);
+CREATE INDEX IF NOT EXISTS flow_step_events_run_idx ON flow_step_events(run_id);

apps/coder/src/services/__tests__/arena-decisions.test.ts

@@ -162,6 +162,24 @@ describe('computeBenchmark', () => {
     expect(bench.durationMs).toBe(0);
     expect(bench.tokensPerSec).toBeNull();
   });
+
+  it('includes token breakdown when provided', () => {
+    const breakdown = {
+      system: 10,
+      user: 20,
+      assistant: 30,
+      tools: 40,
+      reasoning: 5,
+      total: 105,
+    };
+    const bench = computeBenchmark(t0, t1, 500, 'local', breakdown);
+    expect(bench.tokenBreakdown).toEqual(breakdown);
+  });
+
+  it('defaults token breakdown to null when omitted', () => {
+    const bench = computeBenchmark(t0, t1, 500, 'local');
+    expect(bench.tokenBreakdown).toBeNull();
+  });
 });
 
 // ─── sanitizeSlug ────────────────────────────────────────────────────────────

apps/coder/src/services/__tests__/fuzzy-match.test.ts

@@ -161,6 +161,52 @@ describe('locateMatch — strategy 4: Levenshtein', () => {
   });
 });
 
+describe('locateMatch — strategy 4: fail-closed on ambiguity (corruption guard)', () => {
+  it('refuses (ambiguous) when two equally-similar anchored blocks both clear the bar', () => {
+    // The repetitive-file case that duplicated blocks: two blocks share the same
+    // first+last anchor lines and their middle lines are EQUALLY similar to the
+    // (drifted) needle. Tier 4 must refuse rather than splice over one of them.
+    const content = [
+      'const x = {',
+      '  total = aa;',
+      '};',
+      'const x = {',
+      '  total = bb;',
+      '};',
+    ].join('\n');
+    const needle = ['const x = {', '  total = ab;', '};'].join('\n');
+    const result = locateMatch(content, needle);
+    expect(result.kind).toBe('ambiguous');
+  });
+
+  it('refuses a below-threshold near-miss that the old 0.66 floor would have spliced', () => {
+    // ~0.7 similar: under the raised 0.85 floor this is now not_found, so the
+    // caller surfaces a correctable error instead of corrupting the file.
+    const content = 'const grandTotalAmount = a + b;\n';
+    const needle = 'const totalValue = a + b;';
+    const result = locateMatch(content, needle);
+    expect(result).toEqual({ kind: 'not_found' });
+  });
+
+  it('still matches a single genuine high-similarity drift uniquely', () => {
+    const content = 'const total = sum + tax;\n';
+    const needle = 'const totals = sum + tax;'; // one-char typo, ~0.96
+    const result = locateMatch(content, needle);
+    expect(result.kind).toBe('fuzzy');
+    const { start, end } = span(result);
+    expect(content.slice(start, end)).toBe('const total = sum + tax;');
+  });
+
+  it('requires an exact first+last line anchor for multi-line needles', () => {
+    // First line drifted too far to anchor → no window is scored → not_found,
+    // even though the middle lines are identical.
+    const content = ['function compute() {', '  return a + b;', '  return done;', '}'].join('\n');
+    const needle = ['totally different opener', '  return a + b;', '}'].join('\n');
+    const result = locateMatch(content, needle);
+    expect(result).toEqual({ kind: 'not_found' });
+  });
+});
+
 describe('locateMatch — edge cases', () => {
   it('returns not_found for an empty needle', () => {
     expect(locateMatch('anything', '')).toEqual({ kind: 'not_found' });

apps/coder/src/services/__tests__/pending_changes_integration.test.ts

@@ -83,6 +83,53 @@ describe.runIf(!!process.env.DATABASE_URL)('pending_changes integration', () =>
     expect(existsSync(resolve(testDir, 'deleteme.txt'))).toBe(false);
   });
 
+  it('re-emitted identical edits dedupe at queue and never duplicate on apply', async () => {
+    // Regression: the 2-3x block-stamping corruption. An anchored insert queued
+    // three times (a local model re-emitting the same tool call) must collapse to
+    // ONE pending row and apply exactly once.
+    await queueCreate(sql, testSessionId, null, 'dup.js', '<script>\nrender();\n', projectRoot)
+      .then((c) => applyOne(sql, c.id, projectRoot));
+
+    const oldStr = '<script>';
+    const newStr = '<script>\nconst recordFormats = ["gif"];';
+    const a = await queueEdit(sql, testSessionId, null, 'dup.js', oldStr, newStr, projectRoot);
+    const b = await queueEdit(sql, testSessionId, null, 'dup.js', oldStr, newStr, projectRoot);
+    const c = await queueEdit(sql, testSessionId, null, 'dup.js', oldStr, newStr, projectRoot);
+    // All three calls return the SAME pending row (deduped).
+    expect(b.id).toBe(a.id);
+    expect(c.id).toBe(a.id);
+
+    await applyOne(sql, a.id, projectRoot);
+    let content = await readFile(resolve(testDir, 'dup.js'), 'utf8');
+    expect((content.match(/const recordFormats/g) || []).length).toBe(1);
+
+    // Even a fresh, separately-queued identical edit re-applied is a no-op, not a stamp.
+    const again = await queueEdit(sql, testSessionId, null, 'dup.js', oldStr, newStr, projectRoot);
+    const res = await applyOne(sql, again.id, projectRoot);
+    expect(res.success).toBe(true);
+    content = await readFile(resolve(testDir, 'dup.js'), 'utf8');
+    expect((content.match(/const recordFormats/g) || []).length).toBe(1);
+  });
+
+  it('preserves CRLF line endings on edit', async () => {
+    await queueCreate(sql, testSessionId, null, 'crlf.txt', 'line one\r\nline two\r\nline three\r\n', projectRoot)
+      .then((c) => applyOne(sql, c.id, projectRoot));
+    const edit = await queueEdit(sql, testSessionId, null, 'crlf.txt', 'line two', 'line TWO', projectRoot);
+    const res = await applyOne(sql, edit.id, projectRoot);
+    expect(res.success).toBe(true);
+    const content = await readFile(resolve(testDir, 'crlf.txt'), 'utf8');
+    expect(content).toBe('line one\r\nline TWO\r\nline three\r\n');
+  });
+
+  it('refuses an edit that matches multiple locations instead of corrupting', async () => {
+    await queueCreate(sql, testSessionId, null, 'ambig.js', 'x=1;\ny=2;\nx=1;\n', projectRoot)
+      .then((ch) => applyOne(sql, ch.id, projectRoot));
+    const edit = await queueEdit(sql, testSessionId, null, 'ambig.js', 'x=1;', 'x=9;', projectRoot);
+    const res = await applyOne(sql, edit.id, projectRoot);
+    expect(res.success).toBe(false);
+    expect(res.error).toMatch(/matches 2 locations/);
+  });
+
   it('rewindOne → verify reverted', async () => {
     // Setup: create and apply a file
     const createChange = await queueCreate(sql, testSessionId, null, 'rewindable.txt', 'initial', projectRoot);

apps/coder/src/services/__tests__/plan-edit.test.ts

@@ -0,0 +1,69 @@
+import { describe, it, expect } from 'vitest';
+import { planEdit } from '../pending_changes.js';
+
+// planEdit is the pure core of applyOne's edit splice. These tests pin the
+// idempotency guards that stop the "block stamped 2-3x" corruption: applying the
+// same queued edit more than once must be a no-op, never a duplicate.
+
+describe('planEdit — normal application', () => {
+  it('applies a unique exact edit', () => {
+    const content = 'a\nfoo\nb\n';
+    const plan = planEdit(content, 'foo', 'bar');
+    expect(plan).toEqual({ kind: 'apply', updated: 'a\nbar\nb\n' });
+  });
+
+  it('reports ambiguous when old_string occurs more than once', () => {
+    const content = 'foo\nx\nfoo\n';
+    const plan = planEdit(content, 'foo', 'bar');
+    expect(plan).toEqual({ kind: 'ambiguous', count: 2 });
+  });
+
+  it('reports not_found when old_string is absent and new is not present', () => {
+    const content = 'alpha\nbeta\n';
+    const plan = planEdit(content, 'gamma that is clearly nowhere', 'delta');
+    expect(plan).toEqual({ kind: 'not_found' });
+  });
+});
+
+describe('planEdit — idempotency (the corruption guard)', () => {
+  it('treats a re-applied anchored insert as already-applied (no duplicate)', () => {
+    // The exact mechanism that tripled `const recordFormats` in settings.html:
+    // an anchored insert (old=anchor, new=anchor+block) where the anchor still
+    // matches uniquely after the first apply.
+    const oldStr = '<script>';
+    const newStr = '<script>\nconst recordFormats = ["gif","mp4"];';
+    const before = '<script>\nfunction render() {}\n</script>\n';
+
+    const first = planEdit(before, oldStr, newStr);
+    expect(first.kind).toBe('apply');
+    const after = first.kind === 'apply' ? first.updated : '';
+    expect((after.match(/const recordFormats/g) || []).length).toBe(1);
+
+    // Re-applying the identical edit to the already-edited content is a no-op.
+    const second = planEdit(after, oldStr, newStr);
+    expect(second).toEqual({ kind: 'noop', reason: 'already-applied' });
+  });
+
+  it('treats an edit whose old_string is gone but new_string is present as already-applied', () => {
+    const content = 'const total = sum + tax;\n';
+    const plan = planEdit(content, 'const subtotal = sum;', 'const total = sum + tax;');
+    expect(plan).toEqual({ kind: 'noop', reason: 'already-applied' });
+  });
+
+  it('treats a no-change splice as a noop', () => {
+    const content = 'a\nfoo\nb\n';
+    const plan = planEdit(content, 'foo', 'foo');
+    expect(plan).toEqual({ kind: 'noop', reason: 'identical' });
+  });
+
+  it('does not duplicate across three repeated applications', () => {
+    const oldStr = 'function f() {';
+    const newStr = 'function f() {\n  const x = 1;';
+    let content = 'function f() {\n  return x;\n}\n';
+    for (let i = 0; i < 3; i++) {
+      const plan = planEdit(content, oldStr, newStr);
+      if (plan.kind === 'apply') content = plan.updated;
+    }
+    expect((content.match(/const x = 1;/g) || []).length).toBe(1);
+  });
+});

apps/coder/src/services/__tests__/trigger-rules.test.ts

@@ -0,0 +1,31 @@
+import { describe, it, expect } from 'vitest';
+import { evaluateTriggerRule } from '../flow-runner-decisions.js';
+
+describe('evaluateTriggerRule', () => {
+  it('all_success requires all deps done', () => {
+    expect(evaluateTriggerRule(['a', 'b'], new Set(['a', 'b']), new Set(), new Set())).toBe(true);
+    expect(evaluateTriggerRule(['a', 'b'], new Set(['a']), new Set(), new Set())).toBe(false);
+  });
+
+  it('one_success fires on first completion', () => {
+    expect(evaluateTriggerRule(['a', 'b'], new Set(['a']), new Set(), new Set(), 'one_success')).toBe(true);
+    expect(evaluateTriggerRule(['a', 'b'], new Set(), new Set(), new Set(), 'one_success')).toBe(false);
+  });
+
+  it('all_done includes skipped deps', () => {
+    expect(evaluateTriggerRule(['a', 'b'], new Set(['a']), new Set(['b']), new Set(), 'all_done')).toBe(true);
+  });
+
+  it('all_success treats excluded deps as satisfied', () => {
+    expect(evaluateTriggerRule(['a', 'b'], new Set(['a']), new Set(), new Set(['b']))).toBe(true);
+  });
+
+  it('defaults to all_success', () => {
+    expect(evaluateTriggerRule(['a'], new Set(['a']), new Set(), new Set())).toBe(true);
+    expect(evaluateTriggerRule(['a'], new Set(), new Set(), new Set())).toBe(false);
+  });
+
+  it('returns true for empty deps', () => {
+    expect(evaluateTriggerRule([], new Set(), new Set(), new Set())).toBe(true);
+  });
+});

apps/coder/src/services/arena-decisions.ts

@@ -9,7 +9,7 @@
  * A contestant's status lifecycle:
  *   queued → running → done | error
  */
-import type { BattleType, ContestantLane } from '@boocode/contracts/arena';
+import type { BattleType, ContestantLane, TokenBreakdown } from '@boocode/contracts/arena';
 
 // ─── Lane classification ──────────────────────────────────────────────────────
 
@@ -73,6 +73,7 @@ export function isBattleComplete(contestants: readonly { status: string }[]): bo
 export interface Benchmark {
   durationMs: number;
   tokensPerSec: number | null;
+  tokenBreakdown: TokenBreakdown | null;
 }
 
 /**
@@ -86,13 +87,14 @@ export function computeBenchmark(
   endedAt: Date,
   costTokens: number | null,
   lane: ContestantLane,
+  tokenBreakdown: TokenBreakdown | null = null,
 ): Benchmark {
   const durationMs = Math.max(0, endedAt.getTime() - startedAt.getTime());
   const tokensPerSec =
     lane === 'local' && costTokens !== null && durationMs > 0
       ? (costTokens / durationMs) * 1000
       : null;
-  return { durationMs, tokensPerSec };
+  return { durationMs, tokensPerSec, tokenBreakdown };
 }
 
 // ─── Slug / path helpers ──────────────────────────────────────────────────────

apps/coder/src/services/audit-session.ts

@@ -0,0 +1,747 @@
+import { mkdir, readFile, writeFile, readdir, rm, appendFile } from 'node:fs/promises';
+import { existsSync } from 'node:fs';
+import { join, resolve } from 'node:path';
+
+export const RUNS_REL = '.boo/runs';
+export const DAILY_REL = '.boo/runs/daily';
+export const GUIDELINES_REL = '.boo/guidelines';
+
+export interface SessionJson {
+  session_id: string;
+  task: string;
+  start_time: string;
+  end_time?: string;
+  status: 'in_progress' | 'completed';
+  expected_record_types: string[];
+}
+
+export interface AuditTrailEntry {
+  timestamp: string;
+  record_type: string;
+  action_type: string;
+  tool?: string;
+  files?: string[];
+  detail?: string;
+  input?: string;
+  output?: string;
+}
+
+export interface IndexEntry {
+  id: string;
+  task: string;
+  status: string;
+  record_count: number;
+  start_time: string;
+  max_anomaly_level?: string;
+}
+
+export interface IndexJson {
+  entries: IndexEntry[];
+}
+
+export interface StartSessionResult {
+  sessionId: string;
+  contextSummary: {
+    recentActivity: IndexEntry[];
+    userCorrections: UserCorrectionRecord[];
+    unfinishedSessions: SessionJson[];
+  };
+}
+
+export interface EndSessionResult {
+  sessionId: string;
+  integrity: IntegrityCheck[];
+  correctionCount: number;
+  summaryPath: string;
+}
+
+export interface IntegrityCheck {
+  check: string;
+  passed: boolean;
+  detail?: string;
+}
+
+export interface RecoverResult {
+  level: number;
+  sessionId?: string;
+  task?: string;
+  recentActivity: IndexEntry[];
+  lastTrailEntries: AuditTrailEntry[];
+  userCorrections: UserCorrectionRecord[];
+  conclusions: string[];
+  dailyAnomalies: string[];
+  dailyBacklog: string[];
+  fullTrail?: AuditTrailEntry[];
+  anomalies?: string[];
+}
+
+export interface DailyReport {
+  date: string;
+  sections: {
+    taskOverview: string;
+    operationStats: { label: string; count: number }[];
+    changes: { time: string; target: string; detail: string }[];
+    userFeedback: { feedback: string; resolution: string; persistedTo: string }[];
+    anomalyAlerts: string[];
+    backlogTracking: string[];
+    integritySummary: string;
+  };
+  path: string;
+}
+
+export interface UserCorrectionRecord {
+  record_type: 'conversation';
+  action_type: 'user_correction';
+  priority: 'critical_for_recovery';
+  timestamp: string;
+  original_claim: string;
+  correction: string;
+  principle_extracted: string;
+  persisted_to: string[];
+}
+
+function runsDir(basePath?: string): string {
+  return resolve(basePath ?? process.cwd(), RUNS_REL);
+}
+
+function dailyDir(basePath?: string): string {
+  return resolve(basePath ?? process.cwd(), DAILY_REL);
+}
+
+function sessionDir(sessionId: string, basePath?: string): string {
+  return join(runsDir(basePath), sessionId);
+}
+
+function currentSessionPath(basePath?: string): string {
+  return join(runsDir(basePath), '.current_session');
+}
+
+function indexJsonPath(basePath?: string): string {
+  return join(runsDir(basePath), 'index.json');
+}
+
+function auditBufferPath(basePath?: string): string {
+  return join(runsDir(basePath), 'audit_buffer.jsonl');
+}
+
+function auditPendingPath(basePath?: string): string {
+  return join(runsDir(basePath), 'audit_pending.jsonl');
+}
+
+function trailPath(sessionId: string, basePath?: string): string {
+  return join(sessionDir(sessionId, basePath), 'audit_trail.jsonl');
+}
+
+function sessionJsonPath(sessionId: string, basePath?: string): string {
+  return join(sessionDir(sessionId, basePath), 'session.json');
+}
+
+function summaryPath(sessionId: string, basePath?: string): string {
+  return join(sessionDir(sessionId, basePath), 'session_summary.md');
+}
+
+export function generateSessionId(): string {
+  const now = new Date();
+  const y = now.getFullYear();
+  const m = String(now.getMonth() + 1).padStart(2, '0');
+  const d = String(now.getDate()).padStart(2, '0');
+  const hh = String(now.getHours()).padStart(2, '0');
+  const mm = String(now.getMinutes()).padStart(2, '0');
+  return `adhoc_${y}${m}${d}_${hh}${mm}`;
+}
+
+function isoNow(): string {
+  return new Date().toISOString();
+}
+
+function isoDate(d?: Date): string {
+  const dt = d ?? new Date();
+  return `${dt.getFullYear()}${String(dt.getMonth() + 1).padStart(2, '0')}${String(dt.getDate()).padStart(2, '0')}`;
+}
+
+function isTodayIso(iso: string): boolean {
+  return iso.startsWith(new Date().toISOString().slice(0, 10));
+}
+
+function tryParseJson<T>(raw: string): T | null {
+  try {
+    return JSON.parse(raw) as T;
+  } catch {
+    return null;
+  }
+}
+
+async function ensureDir(p: string): Promise<void> {
+  if (!existsSync(p)) {
+    await mkdir(p, { recursive: true });
+  }
+}
+
+async function readLines(p: string): Promise<string[]> {
+  try {
+    const content = await readFile(p, 'utf-8');
+    return content.split('\n').filter(Boolean);
+  } catch {
+    return [];
+  }
+}
+
+async function readJsonFile<T>(p: string): Promise<T | null> {
+  try {
+    const raw = await readFile(p, 'utf-8');
+    return tryParseJson<T>(raw);
+  } catch {
+    return null;
+  }
+}
+
+function appendLine(p: string, line: string): Promise<void> {
+  return appendFile(p, line + '\n', 'utf-8');
+}
+
+async function clearFile(p: string): Promise<void> {
+  try {
+    await writeFile(p, '', 'utf-8');
+  } catch {
+    // File may not exist
+  }
+}
+
+export async function getCurrentSession(basePath?: string): Promise<string | null> {
+  try {
+    const raw = await readFile(currentSessionPath(basePath), 'utf-8');
+    return raw.trim();
+  } catch {
+    return null;
+  }
+}
+
+export async function getSessionJson(sessionId: string, basePath?: string): Promise<SessionJson | null> {
+  return readJsonFile<SessionJson>(sessionJsonPath(sessionId, basePath));
+}
+
+export async function getIndex(basePath?: string): Promise<IndexJson | null> {
+  return readJsonFile<IndexJson>(indexJsonPath(basePath));
+}
+
+async function writeIndex(entries: IndexEntry[], basePath?: string): Promise<void> {
+  await ensureDir(runsDir(basePath));
+  await writeFile(indexJsonPath(basePath), JSON.stringify({ entries }, null, 2), 'utf-8');
+}
+
+async function appendIndex(sessionId: string, task: string, basePath?: string): Promise<void> {
+  const existing = await getIndex(basePath);
+  const entry: IndexEntry = {
+    id: sessionId,
+    task,
+    status: 'in_progress',
+    record_count: 0,
+    start_time: isoNow(),
+  };
+  const entries = [entry, ...(existing?.entries ?? [])].slice(0, 100);
+  await writeIndex(entries, basePath);
+}
+
+async function updateIndexStatus(sessionId: string, status: string, basePath?: string): Promise<void> {
+  const idx = await getIndex(basePath);
+  if (!idx) return;
+  for (const e of idx.entries) {
+    if (e.id === sessionId) {
+      e.status = status;
+    }
+  }
+  await writeIndex(idx.entries, basePath);
+}
+
+export async function startSession(task: string, basePath?: string): Promise<StartSessionResult> {
+  const sessionId = generateSessionId();
+  const sDir = sessionDir(sessionId, basePath);
+  await ensureDir(sDir);
+
+  const session: SessionJson = {
+    session_id: sessionId,
+    task,
+    start_time: isoNow(),
+    status: 'in_progress',
+    expected_record_types: ['data', 'change', 'conversation'],
+  };
+
+  await writeFile(sessionJsonPath(sessionId, basePath), JSON.stringify(session, null, 2), 'utf-8');
+  await writeFile(currentSessionPath(basePath), sessionId, 'utf-8');
+  await appendIndex(sessionId, task, basePath);
+
+  // L0 context recovery
+  const idx = await getIndex(basePath);
+  const recentActivity = idx?.entries.slice(0, 5) ?? [];
+
+  // L2 user correction scan
+  const allCorrections = await scanAllTrailsForCorrections(basePath);
+
+  // Check for unfinished sessions
+  const unfinishedSessions = await findUnfinishedSessions(basePath);
+
+  return {
+    sessionId,
+    contextSummary: {
+      recentActivity,
+      userCorrections: allCorrections,
+      unfinishedSessions,
+    },
+  };
+}
+
+async function findUnfinishedSessions(basePath?: string): Promise<SessionJson[]> {
+  const rDir = runsDir(basePath);
+  if (!existsSync(rDir)) return [];
+
+  const entries = await readdir(rDir, { withFileTypes: true });
+  const unfinished: SessionJson[] = [];
+
+  for (const entry of entries) {
+    if (!entry.isDirectory()) continue;
+    const sess = await getSessionJson(entry.name, basePath);
+    if (sess && sess.status === 'in_progress') {
+      unfinished.push(sess);
+    }
+  }
+
+  return unfinished;
+}
+
+async function scanAllTrailsForCorrections(basePath?: string): Promise<UserCorrectionRecord[]> {
+  const rDir = runsDir(basePath);
+  if (!existsSync(rDir)) return [];
+
+  const entries = await readdir(rDir, { withFileTypes: true });
+  const corrections: UserCorrectionRecord[] = [];
+
+  for (const entry of entries) {
+    if (!entry.isDirectory()) continue;
+    const lines = await readLines(trailPath(entry.name, basePath));
+    for (const line of lines) {
+      const record = tryParseJson<UserCorrectionRecord>(line);
+      if (record?.action_type === 'user_correction') {
+        corrections.push(record);
+      }
+    }
+  }
+
+  // Also scan audit_pending.jsonl
+  const pendingLines = await readLines(auditPendingPath(basePath));
+  for (const line of pendingLines) {
+    const record = tryParseJson<UserCorrectionRecord>(line);
+    if (record?.action_type === 'user_correction') {
+      corrections.push(record);
+    }
+  }
+
+  return corrections;
+}
+
+export async function endSession(basePath?: string): Promise<EndSessionResult | null> {
+  const sessionId = await getCurrentSession(basePath);
+  if (!sessionId) return null;
+
+  const sDir = sessionDir(sessionId, basePath);
+  await ensureDir(sDir);
+
+  // Collect remaining buffer data
+  const bufferLines = await readLines(auditBufferPath(basePath));
+  const pendingLines = await readLines(auditPendingPath(basePath));
+  const allRemaining = [...bufferLines, ...pendingLines];
+
+  // Append to audit_trail.jsonl
+  const trail = trailPath(sessionId, basePath);
+  if (allRemaining.length > 0) {
+    await appendFile(trail, allRemaining.join('\n') + '\n', 'utf-8');
+  }
+
+  // Clear buffer files
+  await clearFile(auditBufferPath(basePath));
+  await clearFile(auditPendingPath(basePath));
+
+  // Read current trail for stats
+  const trailLines = await readLines(trail);
+
+  // Extract user_correction records
+  const corrections: UserCorrectionRecord[] = [];
+  for (const line of trailLines) {
+    const record = tryParseJson<UserCorrectionRecord>(line);
+    if (record?.action_type === 'user_correction') {
+      corrections.push(record);
+    }
+  }
+
+  // Integrity checks
+  const integrity: IntegrityCheck[] = [
+    {
+      check: 'Audit records exist',
+      passed: trailLines.length > 0,
+      detail: trailLines.length > 0 ? `${trailLines.length} records` : 'No audit records found',
+    },
+    {
+      check: 'File modifications tracked',
+      passed: trailLines.some((l) => {
+        const r = tryParseJson<AuditTrailEntry>(l);
+        return r && (r.tool === 'Write' || r.tool === 'Edit');
+      }),
+      detail: 'Checking for Write/Edit tool entries',
+    },
+    {
+      check: 'User corrections persisted',
+      passed: corrections.every((c) => (c.persisted_to?.length ?? 0) > 0),
+      detail: corrections.length > 0
+        ? `${corrections.length} corrections found, ${corrections.filter((c) => (c.persisted_to?.length ?? 0) > 0).length} persisted`
+        : 'No corrections to persist',
+    },
+  ];
+
+  // Generate session summary
+  const summaryContent = generateSessionSummary(sessionId, trailLines, corrections);
+  const summaryFile = summaryPath(sessionId, basePath);
+  await writeFile(summaryFile, summaryContent, 'utf-8');
+
+  // Update session.json
+  const session = await getSessionJson(sessionId, basePath);
+  if (session) {
+    session.status = 'completed';
+    session.end_time = isoNow();
+    await writeFile(sessionJsonPath(sessionId, basePath), JSON.stringify(session, null, 2), 'utf-8');
+    await updateIndexStatus(sessionId, 'completed', basePath);
+  }
+
+  // Update index.json record count
+  const idx = await getIndex(basePath);
+  if (idx) {
+    for (const e of idx.entries) {
+      if (e.id === sessionId) {
+        e.record_count = trailLines.length;
+        e.status = 'completed';
+      }
+    }
+    await writeIndex(idx.entries, basePath);
+  }
+
+  // Clear .current_session
+  try {
+    await rm(currentSessionPath(basePath));
+  } catch {
+    // Ok if already gone
+  }
+
+  return {
+    sessionId,
+    integrity,
+    correctionCount: corrections.length,
+    summaryPath: summaryFile,
+  };
+}
+
+function generateSessionSummary(
+  sessionId: string,
+  trailLines: string[],
+  corrections: UserCorrectionRecord[],
+): string {
+  const actions: string[] = [];
+  const outputs: string[] = [];
+
+  for (const line of trailLines) {
+    const record = tryParseJson<AuditTrailEntry>(line);
+    if (record) {
+      if (record.action_type) actions.push(record.action_type);
+      if (record.output) outputs.push(record.output);
+    }
+  }
+
+  return [
+    `# Session Summary | ${sessionId}`,
+    '',
+    `## Time: ${isoNow()}`,
+    `## Status: completed`,
+    '',
+    '## Completed work',
+    ...actions.map((a) => `- ${a}`),
+    '',
+    '## Key conclusions',
+    ...outputs.map((o) => `- ${o}`),
+    '',
+    '## User corrections',
+    ...(corrections.length > 0
+      ? corrections.map((c) => `- ${c.original_claim} → ${c.correction} (${c.principle_extracted})`)
+      : ['- None']),
+    '',
+  ].join('\n');
+}
+
+export async function recoverSession(
+  level: number,
+  specificSessionId?: string,
+  basePath?: string,
+): Promise<RecoverResult> {
+  const result: RecoverResult = { level, recentActivity: [], lastTrailEntries: [], userCorrections: [], conclusions: [], dailyAnomalies: [], dailyBacklog: [] };
+
+  // L0: index summary
+  const idx = await getIndex(basePath);
+  result.recentActivity = idx?.entries.slice(0, 5) ?? [];
+
+  if (level === 0) return result;
+
+  // L1: current session + last 3 trail entries
+  let activeSessionId = specificSessionId ?? await getCurrentSession(basePath);
+  if (activeSessionId) {
+    result.sessionId = activeSessionId;
+    const session = await getSessionJson(activeSessionId, basePath);
+    if (session) {
+      result.task = session.task;
+    }
+
+    const trailLines = await readLines(trailPath(activeSessionId, basePath));
+    result.lastTrailEntries = trailLines.slice(-3).map((l) => {
+      const r = tryParseJson<AuditTrailEntry>(l);
+      return r ?? { timestamp: '', record_type: '', action_type: '', input: l, output: l };
+    });
+  }
+
+  if (level === 1) return result;
+
+  // L2: user corrections + conclusions + daily anomalies
+  result.userCorrections = await scanAllTrailsForCorrections(basePath);
+
+  // Extract conclusions from trail entries
+  const allTrailLines = await readLines(trailPath(activeSessionId ?? '', basePath));
+  for (const line of allTrailLines) {
+    const record = tryParseJson<AuditTrailEntry>(line);
+    if (record?.output) {
+      result.conclusions.push(record.output);
+    }
+  }
+
+  // Read daily reports for anomalies + backlog
+  const dDir = dailyDir(basePath);
+  if (existsSync(dDir)) {
+    const dailyFiles = (await readdir(dDir)).filter((f) => f.endsWith('_daily.md')).sort().reverse();
+    if (dailyFiles.length > 0) {
+      const latest = await readFile(join(dDir, dailyFiles[0]!), 'utf-8');
+      const anomalies = latest.match(/## (?:四|4).*?[\s\S]*?(?=##|$)/);
+      if (anomalies) result.dailyAnomalies.push(anomalies[0]);
+      const backlog = latest.match(/## (?:六|6).*?[\s\S]*?(?=##|$)/);
+      if (backlog) result.dailyBacklog.push(backlog[0]);
+    }
+  }
+
+  if (level === 2) return result;
+
+  // L3: full trail + pending
+  if (level >= 3) {
+    if (activeSessionId) {
+      const fullLines = await readLines(trailPath(activeSessionId, basePath));
+      result.fullTrail = fullLines.map((l) => {
+        const r = tryParseJson<AuditTrailEntry>(l);
+        return r ?? { timestamp: '', record_type: '', action_type: '', input: l, output: l };
+      });
+    }
+  }
+
+  return result;
+}
+
+export async function generateDailyReport(
+  targetDate?: string,
+  review?: boolean,
+  basePath?: string,
+): Promise<DailyReport> {
+  const date = targetDate ?? isoDate();
+  const idx = await getIndex(basePath);
+  const rDir = runsDir(basePath);
+
+  const todayEntries = (idx?.entries ?? []).filter((e) => e.start_time.startsWith(date.slice(0, 4) + '-' + date.slice(4, 6) + '-' + date.slice(6, 8)));
+
+  let totalWriteEdit = 0;
+  let totalBash = 0;
+  let totalAuditBlocks = 0;
+  const changes: { time: string; target: string; detail: string }[] = [];
+  const feedback: { feedback: string; resolution: string; persistedTo: string }[] = [];
+  const anomalies: string[] = [];
+
+  for (const entry of todayEntries) {
+    const lines = await readLines(trailPath(entry.id, basePath));
+    for (const line of lines) {
+      const record = tryParseJson<AuditTrailEntry>(line);
+      if (!record) continue;
+      if (record.tool === 'Write' || record.tool === 'Edit') totalWriteEdit++;
+      if (record.tool === 'Bash') totalBash++;
+      if (record.action_type === 'audit_block') totalAuditBlocks++;
+      if (record.tool && (record.tool === 'Write' || record.tool === 'Edit') && record.files) {
+        changes.push({ time: record.timestamp, target: record.files.join(', '), detail: record.detail ?? '' });
+      }
+      if (record.action_type === 'user_correction') {
+        const uc = record as unknown as UserCorrectionRecord;
+        feedback.push({ feedback: uc.original_claim, resolution: uc.correction, persistedTo: (uc.persisted_to ?? []).join(', ') });
+      }
+    }
+  }
+
+  // Check for anomalies.json
+  if (existsSync(rDir)) {
+    const sessionDirs = await readdir(rDir, { withFileTypes: true });
+    for (const d of sessionDirs) {
+      if (!d.isDirectory()) continue;
+      const anomPath = join(rDir, d.name, 'anomalies.json');
+      if (existsSync(anomPath)) {
+        const anomContent = await readFile(anomPath, 'utf-8');
+        anomalies.push(`[${d.name}] ${anomContent.slice(0, 200)}`);
+      }
+    }
+  }
+
+  // Read previous day backlog
+  const prevDate = isoDate(new Date(Date.now() - 86400000));
+  let backlog: string[] = [];
+  const prevDailyPath = join(dailyDir(basePath), `${prevDate}_daily.md`);
+  if (existsSync(prevDailyPath)) {
+    const prevContent = await readFile(prevDailyPath, 'utf-8');
+    const m = prevContent.match(/## (?:六|6|明日待办)[\s\S]*?(?=##|$)/);
+    if (m) backlog = m[0].split('\n').filter((l) => l.trim().startsWith('-')).map((l) => l.replace(/^-\s*/, ''));
+  }
+
+  const reportPath = join(dailyDir(basePath), `${date}_daily.md`);
+  await ensureDir(dailyDir(basePath));
+
+  const sections = {
+    taskOverview: todayEntries.length > 0
+      ? todayEntries.map((e) => `| ${e.id} | ${e.task} | ${e.status} | ${e.record_count} |`).join('\n')
+      : 'No activity',
+    operationStats: [
+      { label: 'Write/Edit operations', count: totalWriteEdit },
+      { label: 'Bash executions', count: totalBash },
+      { label: 'Audit blocks', count: totalAuditBlocks },
+    ],
+    changes,
+    userFeedback: feedback,
+    anomalyAlerts: anomalies,
+    backlogTracking: backlog,
+    integritySummary: [
+      `| All sessions have audit records | ${todayEntries.every((e) => e.record_count > 0) ? '✅' : '⚠️'} |`,
+      `| Audit blocks persisted | ${totalAuditBlocks > 0 ? '✅' : '⚠️'} |`,
+      `| User corrections persisted | ${feedback.every((f) => f.persistedTo.length > 0) ? '✅' : '⚠️'} |`,
+    ].join('\n'),
+  };
+
+  const reportContent = generateDailyReportContent(date, sections);
+  await writeFile(reportPath, reportContent, 'utf-8');
+
+  // If review mode, also generate morning review
+  if (review) {
+    const reviewPath = join(dailyDir(basePath), `${date}_morning_review.md`);
+    const reviewContent = generateMorningReview(sections, date);
+    await writeFile(reviewPath, reviewContent, 'utf-8');
+  }
+
+  return { date, sections, path: reportPath };
+}
+
+function generateDailyReportContent(date: string, sections: DailyReport['sections']): string {
+  return [
+    `# Work Report | ${date}`,
+    '',
+    `> Auto-generated: ${isoNow()}`,
+    `> Data source: .boo/runs/index.json + session audit_trail`,
+    `> Coverage: ${date.slice(0, 4)}-${date.slice(4, 6)}-${date.slice(6, 8)} 00:00 — 23:59`,
+    '',
+    '---',
+    '',
+    '## I. Task Overview',
+    '',
+    '| Session ID | Task | Status | Records |',
+    '|-----------|------|--------|---------|',
+    sections.taskOverview,
+    '',
+    '---',
+    '',
+    '## II. Operation Stats',
+    '',
+    '| Metric | Count |',
+    '|--------|-------|',
+    ...sections.operationStats.map((s) => `| ${s.label} | ${s.count} |`),
+    '',
+    '---',
+    '',
+    '## III. Change Records',
+    '',
+    ...(sections.changes.length > 0
+      ? ['| Time | Target | Detail |', '|------|--------|--------|', ...sections.changes.map((c) => `| ${c.time} | ${c.target} | ${c.detail} |`)]
+      : ['No changes recorded today.']),
+    '',
+    '---',
+    '',
+    '## IV. User Feedback & Corrections',
+    '',
+    ...(sections.userFeedback.length > 0
+      ? ['| Feedback | Resolution | Persisted To |', '|---------|------------|--------------|', ...sections.userFeedback.map((f) => `| ${f.feedback} | ${f.resolution} | ${f.persistedTo} |`)]
+      : ['None.']),
+    '',
+    '---',
+    '',
+    '## V. Anomaly Alerts',
+    '',
+    ...(sections.anomalyAlerts.length > 0 ? sections.anomalyAlerts.map((a) => `- ${a}`) : ['None.']),
+    '',
+    '---',
+    '',
+    '## VI. Backlog Tracking',
+    '',
+    ...(sections.backlogTracking.length > 0 ? sections.backlogTracking.map((b) => `- ${b}`) : ['None.']),
+    '',
+    '---',
+    '',
+    '## VII. Integrity Summary',
+    '',
+    '| Check | Result |',
+    '|-------|--------|',
+    sections.integritySummary,
+    '',
+  ].join('\n');
+}
+
+function generateMorningReview(sections: DailyReport['sections'], date: string): string {
+  const anomalies = sections.anomalyAlerts;
+  const hasUnhandledAnomalies = anomalies.some((a) => !a.includes('resolved'));
+  const hasUnpersistedFeedback = sections.userFeedback.some((f) => !f.persistedTo);
+  const hasIncompleteBacklog = sections.backlogTracking.length > 0;
+
+  return [
+    `# Morning Self-Review | ${date}`,
+    '',
+    `> Generated: ${isoNow()}`,
+    '',
+    '## Self-Correction Check',
+    '',
+    `- Unresolved anomalies: ${hasUnhandledAnomalies ? '⚠️ Yes — needs attention' : '✅ None'}`,
+    `- Unpersisted user feedback: ${hasUnpersistedFeedback ? '⚠️ Needs documentation' : '✅ All persisted'}`,
+    `- Outstanding backlog: ${hasIncompleteBacklog ? '⚠️ Carry-over items' : '✅ Clean slate'}`,
+    '',
+    '## Today\'s Recommended Priorities',
+    '',
+    ...(sections.backlogTracking.length > 0
+      ? sections.backlogTracking.map((b) => `- [ ] ${b} (carry-over)`)
+      : []),
+    '- [ ] Review yesterday\'s user feedback and persist any remaining corrections',
+    '- [ ] Continue highest-priority task from session overview',
+    '',
+  ].join('\n');
+}
+
+export async function ensureBooDirs(basePath?: string): Promise<void> {
+  await ensureDir(runsDir(basePath));
+  await ensureDir(dailyDir(basePath));
+}
+
+export async function writeAuditBuffer(entry: AuditTrailEntry, basePath?: string): Promise<void> {
+  await ensureDir(runsDir(basePath));
+  await appendLine(auditBufferPath(basePath), JSON.stringify(entry));
+}
+
+export async function writeAuditPending(entry: AuditTrailEntry, basePath?: string): Promise<void> {
+  await ensureDir(runsDir(basePath));
+  await appendLine(auditPendingPath(basePath), JSON.stringify(entry));
+}

apps/coder/src/services/correction-service.ts

@@ -0,0 +1,186 @@
+import { readFile, writeFile, appendFile } from 'node:fs/promises';
+import { existsSync } from 'node:fs';
+import { join, resolve } from 'node:path';
+
+export interface UserCorrectionRecord {
+  id: string;
+  record_type: 'conversation';
+  action_type: 'user_correction';
+  priority: 'critical_for_recovery';
+  timestamp: string;
+  original_claim: string;
+  correction: string;
+  principle_extracted: string;
+  persisted_to: string[];
+}
+
+const CORRECTIONS_REL = '.boo/corrections/index.json';
+
+function correctionsDir(basePath?: string): string {
+  return resolve(basePath ?? process.cwd(), '.boo/corrections');
+}
+
+function correctionsPath(basePath?: string): string {
+  return resolve(basePath ?? process.cwd(), CORRECTIONS_REL);
+}
+
+function tryParseJson<T>(raw: string): T | null {
+  try {
+    return JSON.parse(raw) as T;
+  } catch {
+    return null;
+  }
+}
+
+export interface CorrectionsIndex {
+  corrections: UserCorrectionRecord[];
+}
+
+async function readCorrections(basePath?: string): Promise<CorrectionsIndex> {
+  try {
+    const raw = await readFile(correctionsPath(basePath), 'utf-8');
+    return tryParseJson<CorrectionsIndex>(raw) ?? { corrections: [] };
+  } catch {
+    return { corrections: [] };
+  }
+}
+
+async function writeCorrections(idx: CorrectionsIndex, basePath?: string): Promise<void> {
+  const dir = correctionsDir(basePath);
+  if (!existsSync(dir)) {
+    const { mkdir } = await import('node:fs/promises');
+    await mkdir(dir, { recursive: true });
+  }
+  await writeFile(correctionsPath(basePath), JSON.stringify(idx, null, 2), 'utf-8');
+}
+
+let idCounter = 0;
+
+function nextId(): string {
+  idCounter++;
+  return `uc_${Date.now()}_${idCounter}`;
+}
+
+function isoNow(): string {
+  return new Date().toISOString();
+}
+
+/**
+ * Record a user correction. Stores it in .boo/corrections/index.json
+ * and returns the record with the assigned id.
+ */
+export async function recordCorrection(
+  originalClaim: string,
+  correction: string,
+  principleExtracted: string,
+  persistedTo: string[] = [],
+  basePath?: string,
+): Promise<UserCorrectionRecord> {
+  const idx = await readCorrections(basePath);
+  const record: UserCorrectionRecord = {
+    id: nextId(),
+    record_type: 'conversation',
+    action_type: 'user_correction',
+    priority: 'critical_for_recovery',
+    timestamp: isoNow(),
+    original_claim: originalClaim,
+    correction,
+    principle_extracted: principleExtracted,
+    persisted_to: persistedTo,
+  };
+  idx.corrections.push(record);
+  await writeCorrections(idx, basePath);
+  return record;
+}
+
+/**
+ * Scan an audit_trail.jsonl file for user_correction records.
+ * Returns all matching records found in the file.
+ */
+export async function scanForCorrections(
+  auditPath: string,
+): Promise<UserCorrectionRecord[]> {
+  try {
+    const raw = await readFile(auditPath, 'utf-8');
+    const lines = raw.split('\n').filter(Boolean);
+    const corrections: UserCorrectionRecord[] = [];
+    for (const line of lines) {
+      const record = tryParseJson<Record<string, unknown>>(line);
+      if (record?.action_type === 'user_correction') {
+        corrections.push(record as unknown as UserCorrectionRecord);
+      }
+    }
+    return corrections;
+  } catch {
+    return [];
+  }
+}
+
+/**
+ * Check if a proposed action contradicts any known user correction.
+ * Returns an array of contradiction warnings — empty means no contradictions.
+ */
+export function checkContradiction(
+  action: string,
+  corrections: UserCorrectionRecord[],
+): { contradicts: boolean; warnings: { correction: UserCorrectionRecord; reason: string }[] } {
+  const warnings: { correction: UserCorrectionRecord; reason: string }[] = [];
+
+  for (const c of corrections) {
+    // Check if the action mentions the original claim's topic
+    const actionLower = action.toLowerCase();
+    const claimFragments = c.original_claim.toLowerCase().split(/\s+/).filter((w) => w.length > 4);
+
+    // If any significant word from the original claim appears in the proposed action,
+    // flag this as a potential contradiction
+    const matchingFragments = claimFragments.filter((f) => actionLower.includes(f));
+    if (matchingFragments.length >= 2) {
+      warnings.push({
+        correction: c,
+        reason: `Action "${action.slice(0, 60)}" may contradict prior correction: "${c.original_claim}" → "${c.correction}" (principle: ${c.principle_extracted})`,
+      });
+    }
+  }
+
+  return {
+    contradicts: warnings.length > 0,
+    warnings,
+  };
+}
+
+/**
+ * Add a file path to a correction's persisted_to array.
+ */
+export async function markPersisted(
+  correctionId: string,
+  filePath: string,
+  basePath?: string,
+): Promise<UserCorrectionRecord | null> {
+  const idx = await readCorrections(basePath);
+  const record = idx.corrections.find((c) => c.id === correctionId);
+  if (!record) return null;
+
+  if (!record.persisted_to.includes(filePath)) {
+    record.persisted_to.push(filePath);
+  }
+  await writeCorrections(idx, basePath);
+  return record;
+}
+
+/**
+ * Get all stored user corrections.
+ */
+export async function listCorrections(basePath?: string): Promise<UserCorrectionRecord[]> {
+  const idx = await readCorrections(basePath);
+  return idx.corrections;
+}
+
+/**
+ * Append a correction record to an audit_trail.jsonl file (inline storage).
+ */
+export async function appendCorrectionToTrail(
+  trailPath: string,
+  correction: UserCorrectionRecord,
+): Promise<void> {
+  await appendFile(trailPath, JSON.stringify(correction) + '\n', 'utf-8');
+}

apps/coder/src/services/dispatcher.ts

@@ -4,7 +4,7 @@ import type { Broker } from '@boocode/server/broker';
 import type { WsFrame } from '@boocode/contracts/ws-frames';
 import type { Config } from '../config.js';
 import { createWorktree, diffWorktree, cleanupWorktree, ensureSessionWorktree } from './worktrees.js';
-import { applyAll } from './pending_changes.js';
+import { asPermissionMode } from './tools/types.js';
 import { createCheckpoint } from './checkpoints.js';
 import { makeDcpStreamStripper } from './dcp-strip.js';
 import { dispatchViaAcp } from './acp-dispatch.js';
@@ -32,7 +32,13 @@ import {
 import { shouldFailOnMissingAgent } from './flow-runner-decisions.js';
 
 interface InferenceRunner {
-  enqueue: (sessionId: string, chatId: string, assistantId: string, user: string) => void;
+  enqueue: (
+    sessionId: string,
+    chatId: string,
+    assistantId: string,
+    user: string,
+    permissionMode?: 'plan' | 'ask' | 'bypass',
+  ) => void;
   cancel: (sessionId: string, chatId: string) => Promise<boolean>;
   hasActive: (chatId: string) => boolean;
 }
@@ -358,8 +364,9 @@ export function createDispatcher(deps: Deps): {
       `;
       const assistantId = assistantMsg!.id;
 
-      // Enqueue inference
+      // Enqueue inference — pass the native permission gate (plan/ask/bypass)
-      inference.enqueue(sessionId, chatId, assistantId, 'default');
+      // through to the write-tool context. Non-unified mode ids → undefined.
+      inference.enqueue(sessionId, chatId, assistantId, 'default', asPermissionMode(task.mode_id));
 
       // Wait for inference to complete (poll message status)
       const finalStatus = await waitForCompletion(assistantId);
@@ -392,22 +399,6 @@ export function createDispatcher(deps: Deps): {
           WHERE id = ${taskId}
         `;
         log.info({ taskId, costTokens }, 'dispatcher: task completed (native)');
-        // Bypass permission mode: auto-apply the staged edits to disk after the
-        // turn. Ask/Plan leave them in the pending-changes queue for review.
-        if (task.mode_id === 'bypass') {
-          try {
-            const [proj] = await sql<{ path: string }[]>`SELECT path FROM projects WHERE id = ${task.project_id}`;
-            if (proj?.path) {
-              const applied = await applyAll(sql, sessionId, proj.path);
-              log.info({ taskId, applied: applied.length }, 'dispatcher: native bypass auto-applied pending changes');
-            }
-          } catch (applyErr) {
-            log.warn(
-              { taskId, err: applyErr instanceof Error ? applyErr.message : String(applyErr) },
-              'dispatcher: native bypass auto-apply failed',
-            );
-          }
-        }
       } else {
         const [msg] = await sql<{ content: string | null }[]>`
           SELECT content FROM messages WHERE id = ${assistantId}

apps/coder/src/services/edit-guards-imports.ts

@@ -0,0 +1,47 @@
+// edit-guards-imports — detects dropped imports in edited files.
+// Ported from opencode-morph-fast-apply (MIT).
+
+export interface ImportCheckResult {
+  ok: boolean;
+  missingImports: string[];
+  reason?: string;
+}
+
+const IMPORT_PATTERNS = [
+  /^import\s+(?:\{[^}]*\}|\*\s+as\s+\w+|\w+)\s+from\s+['"][^'"]+['"]\s*;?$/m,
+  /^import\s+['"][^'"]+['"]\s*;?$/m,
+  /^export\s+.*\s+from\s+['"][^'"]+['"]\s*;?$/m,
+  /^require\s*\(\s*['"][^'"]+['"]\s*\)\s*;?$/m,
+  /^import\s+type\s+\{[^}]*\}\s+from\s+['"][^'"]+['"]\s*;?$/m,
+];
+
+function extractImportLines(content: string): string[] {
+  return content.split('\n').filter((line) =>
+    IMPORT_PATTERNS.some((p) => p.test(line.trim())),
+  );
+}
+
+export function checkDroppedImports(
+  original: string,
+  updated: string,
+  filePath: string,
+): ImportCheckResult {
+  const originalImports = extractImportLines(original);
+  const updatedImports = extractImportLines(updated);
+
+  if (originalImports.length === 0) {
+    return { ok: true, missingImports: [] };
+  }
+
+  const missing = originalImports.filter((imp) => !updatedImports.includes(imp));
+
+  if (missing.length > 0 && originalImports.length > 0) {
+    return {
+      ok: false,
+      missingImports: missing,
+      reason: `Edit would drop ${missing.length} import(s) from ${filePath}`,
+    };
+  }
+
+  return { ok: true, missingImports: [] };
+}

apps/coder/src/services/edit-guards.ts

@@ -0,0 +1,42 @@
+// v2.8 Morph safety guards — prevents catastrophic truncation, marker leakage,
+// and accidental import deletion during native edit_file application.
+// Ported from opencode-morph-fast-apply (MIT) with threshold values preserved.
+
+export interface GuardResult {
+  ok: boolean;
+  reason?: string;
+  charLoss?: number;
+  lineLoss?: number;
+}
+
+const TRUNCATION_CHAR_THRESHOLD = 0.6;
+const TRUNCATION_LINE_THRESHOLD = 0.5;
+
+export function validateEditResult(
+  original: string,
+  updated: string,
+  filePath: string,
+): GuardResult {
+  // Check for catastrophic content truncation
+  if (original.length > 0 && updated.length > 0) {
+    const charLoss = 1 - updated.length / original.length;
+    const originalLines = original.split('\n').length;
+    const updatedLines = updated.split('\n').length;
+    const lineLoss = 1 - updatedLines / originalLines;
+
+    if (charLoss > TRUNCATION_CHAR_THRESHOLD && lineLoss > TRUNCATION_LINE_THRESHOLD) {
+      return {
+        ok: false,
+        reason: `Edit would truncate ${Math.round(charLoss * 100)}% of characters and ${Math.round(lineLoss * 100)}% of lines`,
+        charLoss,
+        lineLoss,
+      };
+    }
+  }
+
+  return { ok: true };
+}
+
+export function formatGuardError(guard: GuardResult, filePath: string): string {
+  return `Edit guard rejected change to ${filePath}: ${guard.reason ?? 'unknown error'}`;
+}

apps/coder/src/services/flow-artifacts.ts

@@ -0,0 +1,23 @@
+import { mkdir, writeFile } from 'node:fs/promises';
+import { join } from 'node:path';
+import { existsSync } from 'node:fs';
+
+const ARTIFACTS_ROOT = 'data/flow-artifacts';
+
+export function getArtifactPath(flowRunId: string, stepId: string): string {
+  return join(ARTIFACTS_ROOT, flowRunId, `${stepId}.md`);
+}
+
+export async function writeFlowArtifact(
+  flowRunId: string,
+  stepId: string,
+  content: string,
+): Promise<string> {
+  const dir = join(ARTIFACTS_ROOT, flowRunId);
+  if (!existsSync(dir)) {
+    await mkdir(dir, { recursive: true });
+  }
+  const path = getArtifactPath(flowRunId, stepId);
+  await writeFile(path, content, 'utf8');
+  return path;
+}

apps/coder/src/services/flow-runner-decisions.ts

@@ -22,7 +22,7 @@
  * "Settled" = done ∪ skipped ∪ excluded. Only settled deps unblock a step;
  * an inFlight dep does NOT (the runner waits for its terminal callback).
  */
-import type { Flow, Step, StepContext } from '../conductor/types.js';
+import type { Flow, Step, StepContext, TriggerRule } from '../conductor/types.js';
 
 export interface SchedulerState {
   /** step ids that completed successfully (results available) */
@@ -62,7 +62,7 @@ export function readySteps(flow: Flow, state: SchedulerState): Step[] {
       !state.skipped.has(s.id) &&
       !state.inFlight.has(s.id) &&
       !state.excluded.has(s.id) &&
-      (s.deps ?? []).every((d) => isSatisfied(state, d)),
+      ((s.deps ?? []).length === 0 || evaluateTriggerRule(s.deps ?? [], state.done, state.skipped, state.excluded, s.trigger_rule)),
   );
 }
 
@@ -167,6 +167,32 @@ export function shouldFailOnMissingAgent(agent: string, modeId: string | null):
   return agent === 'qwen' && modeId === 'plan';
 }
 
+/**
+ * Evaluate a trigger rule against dependency results.
+ * - all_success: every dep must be done (not skipped/failed)
+ * - one_success: at least one dep must be done
+ * - all_done: every dep must be settled regardless of outcome
+ */
+export function evaluateTriggerRule(
+  deps: string[],
+  done: ReadonlySet<string>,
+  skipped: ReadonlySet<string>,
+  excluded: ReadonlySet<string>,
+  rule?: TriggerRule,
+): boolean {
+  if (deps.length === 0) return true;
+  const satisfied = new Set([...done, ...skipped, ...excluded]);
+
+  switch (rule ?? 'all_success') {
+    case 'all_success':
+      return deps.every((d) => done.has(d) || skipped.has(d) || excluded.has(d));
+    case 'one_success':
+      return deps.some((d) => done.has(d));
+    case 'all_done':
+      return deps.every((d) => satisfied.has(d));
+  }
+}
+
 /**
  * Reconcile every step of an in-flight run for startup resume. Returns one
  * decision per step. Pure — no IO.

apps/coder/src/services/flow-runner.ts

@@ -346,6 +346,20 @@ export function createFlowRunner(deps: Deps): FlowRunner {
         continue; // re-evaluate — code output can unblock the next wave
       }
 
+      // Approval gate steps: pause and wait for human decision.
+      const approvalReady = toRun.filter((s) => s.kind === 'approval');
+      if (approvalReady.length > 0) {
+        for (const s of approvalReady) {
+          await sql`
+            UPDATE flow_steps SET status = 'blocked', updated_at = clock_timestamp()
+            WHERE run_id = ${runId} AND step_id = ${s.id}
+          `;
+          await appendStepEvent(sql, runId, s.id, 'paused', { reason: 'awaiting approval' });
+          publishStep(runId, s.id, 'blocked');
+        }
+        return;
+      }
+
       // Only agent steps remain ready → dispatch the whole parallel wave, then wait.
       for (const s of toRun) {
         await dispatchAgentStep(runId, run.project_id, model, s, ctx);
@@ -378,7 +392,8 @@ export function createFlowRunner(deps: Deps): FlowRunner {
     // flow's step.run already bakes in the evidence/YAGNI contracts.
     const persona = step.agent ? await loadPersona(step.agent) : '';
     const taskPrompt = await step.run(ctx);
-    const fullPrompt = persona ? `${persona}\n\n---\n\n${taskPrompt}` : taskPrompt;
+    const resolvedPrompt = resolveVariables(taskPrompt, ctx.results);
+    const fullPrompt = persona ? `${persona}\n\n---\n\n${resolvedPrompt}` : resolvedPrompt;
 
     // READ-ONLY (D-4): agent='qwen', mode_id='plan' are hardcoded, never
     // user-overridable. The dispatcher's qwen+plan rule forces the PTY hard gate.
@@ -392,6 +407,7 @@ export function createFlowRunner(deps: Deps): FlowRunner {
       SET task_id = ${task!.id}, status = 'running', input = ${fullPrompt}, updated_at = clock_timestamp()
       WHERE run_id = ${runId} AND step_id = ${step.id}
     `;
+    await appendStepEvent(sql, runId, step.id, 'started', { taskId: task!.id });
   }
 
   /**
@@ -438,6 +454,7 @@ export function createFlowRunner(deps: Deps): FlowRunner {
         WHERE run_id = ${runId} AND step_id = ${stepId}
       `;
     }
+    await appendStepEvent(sql, runId, stepId, status, output ? { outputLength: output.length } : undefined);
   }
 
   // ─── run completion ─────────────────────────────────────────────────────────
@@ -483,6 +500,7 @@ export function createFlowRunner(deps: Deps): FlowRunner {
     if (updated.count === 0) return;
     const stepId = failedStepId ?? (flow ? lastAgentStepId(flow, input, model) : 'run');
     log.warn({ runId, error }, 'flow-runner: run failed');
+    await appendStepEvent(sql, runId, stepId, 'failed', { error });
     publishStep(runId, stepId, 'failed', { run_status: 'failed' });
   }
 
@@ -522,7 +540,7 @@ export function createFlowRunner(deps: Deps): FlowRunner {
   function publishStep(
     runId: string,
     stepId: string,
-    status: 'running' | 'completed' | 'failed' | 'skipped' | 'cancelled',
+    status: 'running' | 'completed' | 'failed' | 'skipped' | 'cancelled' | 'blocked',
     extra?: { run_status?: 'running' | 'completed' | 'failed' | 'cancelled'; report?: string },
   ): void {
     publishUser({
@@ -763,3 +781,40 @@ export function createFlowRunner(deps: Deps): FlowRunner {
 function errMsg(e: unknown): string {
   return e instanceof Error ? e.message : String(e);
 }
+
+// ─── Event log ───────────────────────────────────────────────────────────────
+
+async function appendStepEvent(
+  sql: Sql,
+  runId: string,
+  stepId: string,
+  event: string,
+  payload?: Record<string, unknown>,
+): Promise<void> {
+  await sql`
+    INSERT INTO flow_step_events (run_id, step_id, event, payload)
+    VALUES (${runId}, ${stepId}, ${event}, ${payload ? sql.json(payload as never) : null})
+  `;
+}
+
+// ─── Variable substitution ───────────────────────────────────────────────────
+
+const VAR_PATTERN = /\$(\w+)\.output(?:\.(\w+(?:\.\w+)*))?/g;
+
+export function resolveVariables(prompt: string, results: Record<string, string>): string {
+  return prompt.replace(VAR_PATTERN, (match, stepId, fieldPath) => {
+    const output = results[stepId];
+    if (!output) return match;
+    if (!fieldPath) return output;
+    try {
+      const lines = output.split('\n');
+      for (const line of lines) {
+        const parsed = line.match(new RegExp(`^${fieldPath}:\\s*(.+)$`, 'i'));
+        if (parsed) return parsed[1]!.trim();
+      }
+    } catch {
+      // fall through
+    }
+    return match;
+  });
+}

apps/coder/src/services/fuzzy-match.ts

@@ -21,7 +21,16 @@
 //                         punctuation to ASCII on both sides; the match is
 //                         mapped back to original offsets.
 //   4. levenshtein      — best line-window by normalized edit-distance
-//                         similarity; accepted only at >= SIMILARITY_THRESHOLD.
+//                         similarity; accepted only at >= SIMILARITY_THRESHOLD,
+//                         anchored on an exact first+last line for multi-line
+//                         needles, and REFUSED (ambiguous) when a second window
+//                         scores within AMBIGUITY_EPSILON of the best. Like the
+//                         exact/whitespace tiers, this tier fails CLOSED — it
+//                         never splices over a merely-plausible guess, because a
+//                         wrong-window splice corrupts the file (it leaves the
+//                         real target intact and duplicates it). This mirrors
+//                         opencode/cline/qwen, whose fuzzy tiers all keep the
+//                         unique-match requirement rather than picking a winner.
 //
 // Pure and dependency-free (Levenshtein is the standard iterative two-row DP),
 // reimplemented from the general technique — no vendored source.
@@ -31,8 +40,31 @@ export type MatchResult =
   | { kind: 'ambiguous'; count: number }
   | { kind: 'not_found' };
 
-/** Levenshtein similarity floor for the final fuzzy fallback (strategy 4). */
+/**
-export const SIMILARITY_THRESHOLD = 0.66;
+ * Levenshtein similarity floor for the final fuzzy fallback (strategy 4).
+ * 0.66 was far too low — at two-thirds similarity a structurally-wrong window
+ * (e.g. one of three near-identical form blocks) clears the bar and gets spliced
+ * over, leaving the real target intact and duplicated. Competent agents anchor
+ * far tighter (opencode's BlockAnchor needs an exact anchor; cline needs exact
+ * first+last lines). 0.85 keeps genuine quantized-model drift (a typo, an indent
+ * shift) while refusing a different block.
+ */
+export const SIMILARITY_THRESHOLD = 0.85;
+
+/**
+ * If a second candidate window scores within this of the best, the match is
+ * ambiguous and tier 4 refuses rather than guessing — the same fail-closed
+ * stance the exact and whitespace tiers take on multiple hits. Repetitive files
+ * (the duplicate-block corruption case) produce near-tied windows; this is what
+ * turns that into a clean "add more context" error instead of a wrong splice.
+ */
+export const AMBIGUITY_EPSILON = 0.05;
+
+/** Multi-line needles at or above this length must anchor on an exact (after
+ *  trim + unicode-fold) first AND last line before similarity is even scored —
+ *  the cline/opencode block-anchor rule. Below it, threshold + uniqueness alone
+ *  guard the match. */
+const ANCHOR_MIN_LINES = 3;
 
 export function locateMatch(content: string, needle: string): MatchResult {
   // Empty needle has no meaningful match.
@@ -252,20 +284,39 @@ function locateByLevenshtein(content: string, needle: string): MatchResult | nul
 
   const needleJoined = needleLines.map((l) => l.trim()).join('\n');
 
-  let best = -1;
+  // Block-anchor gate for multi-line needles: the first and last lines must match
-  let bestSpan: { start: number; end: number } | null = null;
+  // exactly (after trim + unicode-fold) or the window is not even scored. This
+  // stops a high interior-similarity from dragging a structurally-wrong window
+  // over the threshold — the failure that duplicates blocks in repetitive files.
+  const anchored = n >= ANCHOR_MIN_LINES;
+  const needleFirst = canonicalize(needleLines[0]!.trim());
+  const needleLast = canonicalize(needleLines[n - 1]!.trim());
+
+  const scored: Array<{ score: number; start: number; end: number }> = [];
   for (let i = 0; i + n <= contentLines.length; i++) {
     const window = contentLines.slice(i, i + n);
-    const windowJoined = window.map((l) => l.text.trim()).join('\n');
+    if (anchored) {
-    const score = similarity(windowJoined, needleJoined);
+      const winFirst = canonicalize(window[0]!.text.trim());
-    if (score > best) {
+      const winLast = canonicalize(window[n - 1]!.text.trim());
-      best = score;
+      if (winFirst !== needleFirst || winLast !== needleLast) continue;
-      bestSpan = { start: window[0]!.start, end: window[n - 1]!.end };
     }
+    const windowJoined = window.map((l) => l.text.trim()).join('\n');
+    scored.push({
+      score: similarity(windowJoined, needleJoined),
+      start: window[0]!.start,
+      end: window[n - 1]!.end,
+    });
   }
 
-  if (bestSpan && best >= SIMILARITY_THRESHOLD) {
+  if (scored.length === 0) return null;
-    return { kind: 'fuzzy', start: bestSpan.start, end: bestSpan.end };
+  scored.sort((a, b) => b.score - a.score);
-  }
+  const best = scored[0]!;
-  return null;
+  if (best.score < SIMILARITY_THRESHOLD) return null;
+
+  // Uniqueness guard: refuse when a second window is within epsilon of the best.
+  // Fail closed (ambiguous) rather than silently splicing one of several lookalikes.
+  const tied = scored.filter((s) => s.score >= best.score - AMBIGUITY_EPSILON);
+  if (tied.length > 1) return { kind: 'ambiguous', count: tied.length };
+
+  return { kind: 'fuzzy', start: best.start, end: best.end };
 }

apps/coder/src/services/guideline-service.ts

@@ -0,0 +1,560 @@
+import { readFile, writeFile, mkdir, readdir } from 'node:fs/promises';
+import { existsSync } from 'node:fs';
+import { join, resolve } from 'node:path';
+
+export type Criticality = 'low' | 'medium' | 'high';
+
+export interface GuidelineContent {
+  condition: string;
+  action: string | null;
+  description: string | null;
+}
+
+export interface Guideline {
+  id: string;
+  creationUtc: string;
+  content: GuidelineContent;
+  enabled: boolean;
+  tags: string[];
+  labels: string[];
+  metadata: Record<string, unknown>;
+  criticality: Criticality;
+  title: string | null;
+  priority: number;
+}
+
+export interface CreateGuidelineParams {
+  condition: string;
+  action?: string;
+  description?: string;
+  tags?: string[];
+  labels?: string[];
+  criticality?: Criticality;
+  title?: string;
+  priority?: number;
+}
+
+export interface UpdateGuidelineParams {
+  condition?: string;
+  action?: string | null;
+  description?: string | null;
+  enabled?: boolean;
+  tags?: string[];
+  labels?: string[];
+  metadata?: Record<string, unknown>;
+  criticality?: Criticality;
+  title?: string | null;
+  priority?: number;
+}
+
+export interface ListGuidelinesFilter {
+  tags?: string[];
+  labels?: string[];
+}
+
+interface GuidelineStoreData {
+  version: string;
+  guidelines: Guideline[];
+  migrationLog: string[];
+}
+
+const GUIDELINES_REL = '.boo/guidelines';
+const STORE_FILE = 'guidelines.json';
+const CURRENT_VERSION = 'v0.11.0';
+
+function storeDir(basePath?: string): string {
+  return resolve(basePath ?? process.cwd(), GUIDELINES_REL);
+}
+
+function storePath(basePath?: string): string {
+  return join(storeDir(basePath), STORE_FILE);
+}
+
+function tryParseJson<T>(raw: string): T | null {
+  try {
+    return JSON.parse(raw) as T;
+  } catch {
+    return null;
+  }
+}
+
+let idCounter = 0;
+
+function nextId(): string {
+  idCounter++;
+  return `gl_${Date.now()}_${idCounter}`;
+}
+
+function isoNow(): string {
+  return new Date().toISOString();
+}
+
+async function ensureStoreDir(basePath?: string): Promise<void> {
+  const dir = storeDir(basePath);
+  if (!existsSync(dir)) {
+    await mkdir(dir, { recursive: true });
+  }
+}
+
+const MIGRATIONS: { from: string; to: string; migrate: (data: GuidelineStoreData) => GuidelineStoreData }[] = [
+  {
+    from: 'v0.1.0',
+    to: 'v0.2.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.2.0',
+      guidelines: data.guidelines.map((g) => ({
+        ...g,
+        enabled: g.enabled ?? true,
+      })),
+      migrationLog: [...data.migrationLog, 'v0.1.0→v0.2.0: add enabled field'],
+    }),
+  },
+  {
+    from: 'v0.2.0',
+    to: 'v0.3.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.3.0',
+      migrationLog: [...data.migrationLog, 'v0.2.0→v0.3.0: remove guideline_set'],
+    }),
+  },
+  {
+    from: 'v0.3.0',
+    to: 'v0.4.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.4.0',
+      guidelines: data.guidelines.map((g) => ({
+        ...g,
+        content: {
+          ...g.content,
+          action: g.content.action ?? null,
+          description: g.content.description ?? null,
+        },
+        metadata: g.metadata ?? {},
+      })),
+      migrationLog: [...data.migrationLog, 'v0.3.0→v0.4.0: add optional action, description, metadata'],
+    }),
+  },
+  {
+    from: 'v0.4.0',
+    to: 'v0.5.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.5.0',
+      migrationLog: [...data.migrationLog, 'v0.4.0→v0.5.0: description as optional'],
+    }),
+  },
+  {
+    from: 'v0.5.0',
+    to: 'v0.6.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.6.0',
+      guidelines: data.guidelines.map((g) => ({
+        ...g,
+        criticality: g.criticality ?? 'medium',
+      })),
+      migrationLog: [...data.migrationLog, 'v0.5.0→v0.6.0: add criticality'],
+    }),
+  },
+  {
+    from: 'v0.6.0',
+    to: 'v0.7.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.7.0',
+      migrationLog: [...data.migrationLog, 'v0.6.0→v0.7.0: add composition_mode (optional)'],
+    }),
+  },
+  {
+    from: 'v0.7.0',
+    to: 'v0.8.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.8.0',
+      migrationLog: [...data.migrationLog, 'v0.7.0→v0.8.0: add track (default true)'],
+    }),
+  },
+  {
+    from: 'v0.8.0',
+    to: 'v0.9.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.9.0',
+      guidelines: data.guidelines.map((g) => ({
+        ...g,
+        labels: g.labels ?? [],
+      })),
+      migrationLog: [...data.migrationLog, 'v0.8.0→v0.9.0: add labels'],
+    }),
+  },
+  {
+    from: 'v0.9.0',
+    to: 'v0.10.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.10.0',
+      guidelines: data.guidelines.map((g) => ({
+        ...g,
+        priority: g.priority ?? 0,
+      })),
+      migrationLog: [...data.migrationLog, 'v0.9.0→v0.10.0: add priority'],
+    }),
+  },
+  {
+    from: 'v0.10.0',
+    to: 'v0.11.0',
+    migrate: (data) => ({
+      ...data,
+      version: 'v0.11.0',
+      guidelines: data.guidelines.map((g) => ({
+        ...g,
+        title: g.title ?? null,
+      })),
+      migrationLog: [...data.migrationLog, 'v0.10.0→v0.11.0: add title'],
+    }),
+  },
+];
+
+function applyMigrations(data: GuidelineStoreData): GuidelineStoreData {
+  let current = { ...data };
+  for (const migration of MIGRATIONS) {
+    if (current.version === migration.from) {
+      current = migration.migrate(current);
+    }
+  }
+  return current;
+}
+
+async function readStore(basePath?: string): Promise<GuidelineStoreData> {
+  try {
+    const raw = await readFile(storePath(basePath), 'utf-8');
+    const data = tryParseJson<GuidelineStoreData>(raw);
+    if (!data) return { version: CURRENT_VERSION, guidelines: [], migrationLog: [] };
+    if (data.version !== CURRENT_VERSION) {
+      return applyMigrations(data);
+    }
+    return data;
+  } catch {
+    return { version: CURRENT_VERSION, guidelines: [], migrationLog: [] };
+  }
+}
+
+async function writeStore(data: GuidelineStoreData, basePath?: string): Promise<void> {
+  await ensureStoreDir(basePath);
+  await writeFile(storePath(basePath), JSON.stringify(data, null, 2), 'utf-8');
+}
+
+export async function createGuideline(
+  params: CreateGuidelineParams,
+  basePath?: string,
+): Promise<Guideline> {
+  const data = await readStore(basePath);
+  const guideline: Guideline = {
+    id: nextId(),
+    creationUtc: isoNow(),
+    content: {
+      condition: params.condition,
+      action: params.action ?? null,
+      description: params.description ?? null,
+    },
+    enabled: true,
+    tags: params.tags ?? [],
+    labels: params.labels ?? [],
+    metadata: {},
+    criticality: params.criticality ?? 'medium',
+    title: params.title ?? null,
+    priority: params.priority ?? 0,
+  };
+  data.guidelines.push(guideline);
+  await writeStore(data, basePath);
+  return guideline;
+}
+
+export async function listGuidelines(
+  filter?: ListGuidelinesFilter,
+  basePath?: string,
+): Promise<Guideline[]> {
+  const data = await readStore(basePath);
+  let results = data.guidelines;
+
+  if (filter?.tags && filter.tags.length > 0) {
+    results = results.filter((g) => filter.tags!.some((tag) => g.tags.includes(tag)));
+  }
+
+  if (filter?.labels && filter.labels.length > 0) {
+    results = results.filter((g) => filter.labels!.every((label) => g.labels.includes(label)));
+  }
+
+  return results;
+}
+
+export async function readGuideline(
+  id: string,
+  basePath?: string,
+): Promise<Guideline | null> {
+  const data = await readStore(basePath);
+  return data.guidelines.find((g) => g.id === id) ?? null;
+}
+
+export async function updateGuideline(
+  id: string,
+  params: UpdateGuidelineParams,
+  basePath?: string,
+): Promise<Guideline | null> {
+  const data = await readStore(basePath);
+  const idx = data.guidelines.findIndex((g) => g.id === id);
+  if (idx === -1) return null;
+
+  const existing = data.guidelines[idx]!;
+
+  if (params.condition !== undefined) existing.content.condition = params.condition;
+  if (params.action !== undefined) existing.content.action = params.action;
+  if (params.description !== undefined) existing.content.description = params.description;
+  if (params.enabled !== undefined) existing.enabled = params.enabled;
+  if (params.tags !== undefined) existing.tags = params.tags;
+  if (params.labels !== undefined) existing.labels = params.labels;
+  if (params.metadata !== undefined) existing.metadata = params.metadata;
+  if (params.criticality !== undefined) existing.criticality = params.criticality;
+  if (params.title !== undefined) existing.title = params.title;
+  if (params.priority !== undefined) existing.priority = params.priority;
+
+  data.guidelines[idx] = existing;
+  await writeStore(data, basePath);
+  return existing;
+}
+
+export async function deleteGuideline(
+  id: string,
+  basePath?: string,
+): Promise<boolean> {
+  const data = await readStore(basePath);
+  const lenBefore = data.guidelines.length;
+  data.guidelines = data.guidelines.filter((g) => g.id !== id);
+  if (data.guidelines.length === lenBefore) return false;
+  await writeStore(data, basePath);
+  return true;
+}
+
+export async function findGuideline(
+  content: { condition: string; action?: string },
+  basePath?: string,
+): Promise<Guideline | null> {
+  const data = await readStore(basePath);
+  return data.guidelines.find((g) => {
+    const condMatch = g.content.condition === content.condition;
+    if (!condMatch) return false;
+    if (content.action !== undefined) {
+      return g.content.action === content.action;
+    }
+    return true;
+  }) ?? null;
+}
+
+// ─── Journey → Guideline projection (port of Parlant's JourneyGuidelineProjection) ───
+
+export interface JourneyNode {
+  id: string;
+  action: string;
+  description?: string;
+}
+
+export interface JourneyEdge {
+  sourceNodeId: string;
+  targetNodeId: string;
+  condition: string;
+}
+
+export interface Journey {
+  id: string;
+  name: string;
+  nodes: JourneyNode[];
+  edges: JourneyEdge[];
+}
+
+export interface JourneyProjectionResult {
+  guidelines: Guideline[];
+  followUps: Map<string, string[]>;
+}
+
+/**
+ * Project a Journey into an ordered list of Guidelines.
+ * DFS traversal from root nodes: each (edge, node) pair → one Guideline.
+ * Edge condition becomes guideline condition, node action becomes guideline action.
+ * BFS queue avoids infinite loops via visited set.
+ */
+export function projectJourneyToGuidelines(
+  journey: Journey,
+  baseTags?: string[],
+): JourneyProjectionResult {
+  const guidelines: Guideline[] = [];
+  const followUps = new Map<string, string[]>();
+  const visited = new Set<string>();
+  const nodeMap = new Map<string, JourneyNode>();
+
+  for (const node of journey.nodes) {
+    nodeMap.set(node.id, node);
+  }
+
+  // Build adjacency list
+  const adjacency = new Map<string, JourneyEdge[]>();
+  for (const edge of journey.edges) {
+    const list = adjacency.get(edge.sourceNodeId) ?? [];
+    list.push(edge);
+    adjacency.set(edge.sourceNodeId, list);
+  }
+
+  // Find root nodes (no incoming edges)
+  const hasIncoming = new Set<string>();
+  for (const edge of journey.edges) {
+    hasIncoming.add(edge.targetNodeId);
+  }
+  const roots = journey.nodes
+    .filter((n) => !hasIncoming.has(n.id))
+    .map((n) => n.id);
+
+  const queue: { nodeId: string; fromEdge?: JourneyEdge }[] = [];
+
+  // BFS from roots
+  for (const rootId of roots) {
+    if (!visited.has(rootId)) {
+      queue.push({ nodeId: rootId });
+    }
+  }
+
+  while (queue.length > 0) {
+    const { nodeId, fromEdge } = queue.shift()!;
+    if (visited.has(nodeId)) continue;
+    visited.add(nodeId);
+
+    const node = nodeMap.get(nodeId);
+    if (!node) continue;
+
+    // If we arrived via an edge, create a guideline
+    if (fromEdge) {
+      const guideline = createGuidelineFromJourneyEdge(
+        journey,
+        node,
+        fromEdge,
+        baseTags,
+      );
+      guidelines.push(guideline);
+
+      // Track follow-ups
+      const sourceId = findGuidelineForNode(fromEdge.sourceNodeId, journey.nodes);
+      if (sourceId) {
+        const existing = followUps.get(sourceId) ?? [];
+        existing.push(guideline.id);
+        followUps.set(sourceId, existing);
+      }
+    }
+
+    // Enqueue downstream nodes
+    const outgoingEdges = adjacency.get(nodeId) ?? [];
+    for (const edge of outgoingEdges) {
+      if (!visited.has(edge.targetNodeId)) {
+        queue.push({ nodeId: edge.targetNodeId, fromEdge: edge });
+      }
+    }
+  }
+
+  return { guidelines, followUps };
+}
+
+function findGuidelineForNode(nodeId: string, nodes: JourneyNode[]): string | null {
+  // Placeholder: in a full implementation, map nodeId → guideline id
+  // For now return null — downstream consumers handle missing follow-ups gracefully
+  return null;
+}
+
+function createGuidelineFromJourneyEdge(
+  journey: Journey,
+  targetNode: JourneyNode,
+  edge: JourneyEdge,
+  baseTags?: string[],
+): Guideline {
+  const now = isoNow();
+  return {
+    id: nextId(),
+    creationUtc: now,
+    content: {
+      condition: edge.condition,
+      action: targetNode.action,
+      description: targetNode.description ?? null,
+    },
+    enabled: true,
+    tags: baseTags ?? [journey.name],
+    labels: [],
+    metadata: {
+      journey_id: journey.id,
+      journey_node: targetNode.id,
+      source_edge_id: `${edge.sourceNodeId}→${edge.targetNodeId}`,
+    },
+    criticality: 'medium',
+    title: targetNode.description
+      ? `[${journey.name}] ${targetNode.description.slice(0, 60)}`
+      : null,
+    priority: 0,
+  };
+}
+
+// ─── Backtrack detection ───
+
+export interface BacktrackCheckInput {
+  journeyId: string;
+  currentNodeId: string;
+  previousNodeId: string;
+}
+
+export interface BacktrackCheckResult {
+  journeyId: string;
+  currentNodeId: string;
+  previousNodeId: string;
+  isBacktrack: boolean;
+  recommendation: string | null;
+}
+
+/**
+ * Check if moving from previousNodeId to currentNodeId is a backtrack
+ * (regression to an already-visited node not on a forward path).
+ */
+export function checkBacktrack(
+  input: BacktrackCheckInput,
+  journey: Journey,
+): BacktrackCheckResult {
+  const adjacency = new Map<string, string[]>();
+  for (const edge of journey.edges) {
+    const list = adjacency.get(edge.sourceNodeId) ?? [];
+    list.push(edge.targetNodeId);
+    adjacency.set(edge.sourceNodeId, list);
+  }
+
+  // Find forward reachable nodes from the current node
+  const forwardReachable = new Set<string>();
+  const bfsQueue = [input.currentNodeId];
+  while (bfsQueue.length > 0) {
+    const nid = bfsQueue.shift()!;
+    if (forwardReachable.has(nid)) continue;
+    forwardReachable.add(nid);
+    const next = adjacency.get(nid) ?? [];
+    for (const n of next) {
+      if (!forwardReachable.has(n)) bfsQueue.push(n);
+    }
+  }
+
+  const isBacktrack = input.previousNodeId !== input.currentNodeId
+    && !forwardReachable.has(input.previousNodeId)
+    && input.previousNodeId !== input.currentNodeId;
+
+  return {
+    journeyId: input.journeyId,
+    currentNodeId: input.currentNodeId,
+    previousNodeId: input.previousNodeId,
+    isBacktrack,
+    recommendation: isBacktrack
+      ? `Revisiting node "${input.previousNodeId}" after "${input.currentNodeId}" — this may indicate a regression. Consider whether the forward path from "${input.currentNodeId}" is the correct one.`
+      : null,
+  };
+}

apps/coder/src/services/lsp/client.ts

@@ -0,0 +1,75 @@
+import { createInterface } from 'node:readline';
+import type { Readable, Writable } from 'node:stream';
+
+interface RpcRequest {
+  jsonrpc: '2.0';
+  id: number;
+  method: string;
+  params?: unknown;
+}
+
+interface RpcResponse {
+  jsonrpc: '2.0';
+  id: number;
+  result?: unknown;
+  error?: { code: number; message: string };
+}
+
+export class LspClient {
+  private nextId = 1;
+  private pending = new Map<number, { resolve: (v: RpcResponse) => void; reject: (e: Error) => void }>();
+  private buffer = '';
+
+  constructor(
+    private stdin: Writable,
+    private stdout: Readable,
+  ) {
+    const rl = createInterface({ input: stdout, crlfDelay: Infinity });
+    rl.on('line', (line) => this.handleLine(line));
+  }
+
+  private handleLine(line: string): void {
+    this.buffer += line + '\n';
+    const match = this.buffer.match(/Content-Length: (\d+)\r?\n\r?\n/);
+    if (!match || !match[1]) return;
+    const len = parseInt(match[1], 10);
+    const headerEnd = match.index! + match[0].length;
+    const body = this.buffer.slice(headerEnd, headerEnd + len);
+    if (body.length < len) return;
+    this.buffer = this.buffer.slice(headerEnd + len);
+    try {
+      const msg: RpcResponse = JSON.parse(body);
+      const cb = this.pending.get(msg.id);
+      if (cb) {
+        this.pending.delete(msg.id);
+        cb.resolve(msg);
+      }
+    } catch {
+      // Malformed JSON, ignore
+    }
+  }
+
+  async request(method: string, params?: unknown): Promise<unknown> {
+    const id = this.nextId++;
+    const req: RpcRequest = { jsonrpc: '2.0', id, method, params };
+    const body = JSON.stringify(req);
+    const header = `Content-Length: ${Buffer.byteLength(body, 'utf8')}\r\n\r\n`;
+
+    return new Promise((resolve, reject) => {
+      this.pending.set(id, {
+        resolve: (resp) => {
+          if (resp.error) reject(new Error(resp.error.message));
+          else resolve(resp.result);
+        },
+        reject,
+      });
+      this.stdin.write(header + body);
+    });
+  }
+
+  async notify(method: string, params?: unknown): Promise<void> {
+    const body = JSON.stringify({ jsonrpc: '2.0', method, params });
+    const header = `Content-Length: ${Buffer.byteLength(body, 'utf8')}\r\n\r\n`;
+    this.stdin.write(header + body);
+  }
+}

apps/coder/src/services/lsp/config.ts

@@ -0,0 +1,19 @@
+export interface LspServerConfig {
+  command: string;
+  args: string[];
+  rootPatterns: string[];
+}
+
+const TS_CONFIG: LspServerConfig = {
+  command: 'typescript-language-server',
+  args: ['--stdio'],
+  rootPatterns: ['package.json', 'tsconfig.json'],
+};
+
+const SUPPORTED_EXTS = new Set(['ts', 'tsx', 'js', 'jsx', 'mjs', 'cjs']);
+
+export function getServerConfig(filePath: string): LspServerConfig | null {
+  const ext = filePath.split('.').pop()?.toLowerCase();
+  if (ext && SUPPORTED_EXTS.has(ext)) return TS_CONFIG;
+  return null;
+}

apps/coder/src/services/lsp/operations.ts

@@ -0,0 +1,86 @@
+import type { LspClient } from './client.js';
+import type { Diagnostic, Location } from './types.js';
+
+function fileUri(filePath: string): string {
+  return `file://${filePath.startsWith('/') ? '' : '/'}${filePath}`;
+}
+
+export async function openDocument(
+  client: LspClient,
+  filePath: string,
+  content: string,
+  version: number = 1,
+): Promise<void> {
+  const uri = fileUri(filePath);
+  await client.notify('textDocument/didOpen', {
+    textDocument: { uri, languageId: 'typescript', version, text: content },
+  });
+}
+
+export async function closeDocument(client: LspClient, filePath: string): Promise<void> {
+  await client.notify('textDocument/didClose', {
+    textDocument: { uri: fileUri(filePath) },
+  });
+}
+
+export async function getDiagnostics(
+  client: LspClient,
+  filePath: string,
+  content: string,
+): Promise<Diagnostic[]> {
+  const uri = fileUri(filePath);
+  await openDocument(client, filePath, content);
+  const result: any = await client.request('textDocument/diagnostic', {
+    textDocument: { uri },
+  });
+  await closeDocument(client, filePath);
+  const diagnostics: Diagnostic[] = [];
+  if (result?.diagnostics) {
+    for (const d of result.diagnostics) {
+      diagnostics.push({
+        range: d.range,
+        severity: d.severity ?? 1,
+        message: d.message,
+        source: d.source,
+      });
+    }
+  }
+  return diagnostics;
+}
+
+export async function gotoDefinition(
+  client: LspClient,
+  filePath: string,
+  content: string,
+  line: number,
+  character: number,
+): Promise<Location | null> {
+  const uri = fileUri(filePath);
+  await openDocument(client, filePath, content);
+  const result: any = await client.request('textDocument/definition', {
+    textDocument: { uri },
+    position: { line, character },
+  });
+  await closeDocument(client, filePath);
+  if (!result) return null;
+  const loc = Array.isArray(result) ? result[0] : result;
+  return loc ? { uri: loc.uri, range: loc.range } : null;
+}
+
+export async function findReferences(
+  client: LspClient,
+  filePath: string,
+  content: string,
+  line: number,
+  character: number,
+): Promise<Location[]> {
+  const uri = fileUri(filePath);
+  await openDocument(client, filePath, content);
+  const result: any = await client.request('textDocument/references', {
+    textDocument: { uri },
+    position: { line, character },
+    context: { includeDeclaration: true },
+  });
+  await closeDocument(client, filePath);
+  return (result ?? []).map((loc: any) => ({ uri: loc.uri, range: loc.range }));
+}

apps/coder/src/services/lsp/server-manager.ts

@@ -0,0 +1,119 @@
+import { spawn, type ChildProcess } from 'node:child_process';
+import { join } from 'node:path';
+import { existsSync } from 'node:fs';
+import { LspClient } from './client.js';
+import { getServerConfig } from './config.js';
+
+const IDLE_TIMEOUT_MS = 5 * 60 * 1000;
+const SWEEP_INTERVAL_MS = 30_000;
+
+interface LspInstance {
+  client: LspClient;
+  proc: ChildProcess;
+  lastUsed: number;
+  timer: ReturnType<typeof setTimeout>;
+}
+
+export class LspServerManager {
+  private instances = new Map<string, LspInstance>();
+  private sweepTimer: ReturnType<typeof setInterval> | null = null;
+
+  constructor() {
+    this.startSweeper();
+  }
+
+  private startSweeper(): void {
+    this.sweepTimer = setInterval(() => this.sweep(), SWEEP_INTERVAL_MS);
+    this.sweepTimer.unref?.();
+  }
+
+  private findProjectRoot(filePath: string): string | null {
+    let dir = filePath;
+    const config = getServerConfig(filePath);
+    if (!config) return null;
+    while (true) {
+      for (const pattern of config.rootPatterns) {
+        if (existsSync(join(dir, pattern))) return dir;
+      }
+      const parent = join(dir, '..');
+      if (parent === dir) return dir;
+      dir = parent;
+    }
+  }
+
+  async getClient(filePath: string): Promise<LspClient | null> {
+    const config = getServerConfig(filePath);
+    if (!config) return null;
+    const projectRoot = this.findProjectRoot(filePath);
+    if (!projectRoot) return null;
+
+    const existing = this.instances.get(projectRoot);
+    if (existing) {
+      existing.lastUsed = Date.now();
+      clearTimeout(existing.timer);
+      existing.timer = setTimeout(() => this.kill(projectRoot), IDLE_TIMEOUT_MS);
+      existing.timer.unref?.();
+      return existing.client;
+    }
+
+    return this.spawn(projectRoot, config.command, config.args);
+  }
+
+  private async spawn(projectRoot: string, command: string, args: string[]): Promise<LspClient> {
+    const proc = spawn(command, args, { stdio: ['pipe', 'pipe', 'pipe'], cwd: projectRoot });
+    const client = new LspClient(proc.stdin!, proc.stdout!);
+
+    await client.request('initialize', {
+      processId: process.pid,
+      rootUri: `file://${projectRoot}`,
+      capabilities: {
+        textDocument: {
+          diagnostic: { dynamicRegistration: false },
+          definition: { dynamicRegistration: false },
+          references: { dynamicRegistration: false },
+        },
+      },
+    });
+    await client.notify('initialized', {});
+
+    const timer = setTimeout(() => this.kill(projectRoot), IDLE_TIMEOUT_MS);
+    timer.unref?.();
+
+    this.instances.set(projectRoot, { client, proc, lastUsed: Date.now(), timer });
+    proc.on('exit', () => this.instances.delete(projectRoot));
+
+    return client;
+  }
+
+  private kill(projectRoot: string): void {
+    const inst = this.instances.get(projectRoot);
+    if (!inst) return;
+    this.instances.delete(projectRoot);
+    inst.proc.kill('SIGTERM');
+    setTimeout(() => {
+      if (inst.proc.exitCode === null) inst.proc.kill('SIGKILL');
+    }, 5000);
+  }
+
+  private sweep(): void {
+    const now = Date.now();
+    for (const [root, inst] of this.instances) {
+      if (now - inst.lastUsed > IDLE_TIMEOUT_MS) {
+        this.kill(root);
+      }
+    }
+  }
+
+  shutdown(): void {
+    if (this.sweepTimer) clearInterval(this.sweepTimer);
+    for (const root of [...this.instances.keys()]) {
+      this.kill(root);
+    }
+  }
+
+  getActiveCount(): number {
+    return this.instances.size;
+  }
+}
+
+export const lspManager = new LspServerManager();

apps/coder/src/services/lsp/types.ts

@@ -0,0 +1,28 @@
+export interface Position {
+  line: number;
+  character: number;
+}
+
+export interface Range {
+  start: Position;
+  end: Position;
+}
+
+export interface Location {
+  uri: string;
+  range: Range;
+}
+
+export interface Diagnostic {
+  range: Range;
+  severity: number;
+  message: string;
+  source?: string;
+}
+
+export interface TextDocumentItem {
+  uri: string;
+  languageId: string;
+  version: number;
+  text: string;
+}

apps/coder/src/services/pending_changes.ts

@@ -1,9 +1,120 @@
-import { readFile, writeFile, unlink, mkdir } from 'node:fs/promises';
+import { readFile, writeFile, unlink, mkdir, rename, realpath } from 'node:fs/promises';
-import { dirname } from 'node:path';
+import { dirname, join, basename } from 'node:path';
+import { randomBytes } from 'node:crypto';
 import type { Sql } from '../db.js';
 import { resolveWritePath } from './write_guard.js';
 import { locateMatch } from './fuzzy-match.js';
 
+/**
+ * Write a file atomically: stage to a sibling temp file, then rename over the
+ * target. rename(2) on the same filesystem is atomic, so a crash mid-write can
+ * never leave a half-written (truncated/corrupt) source file — readers see
+ * either the old content or the complete new content. The temp lives in the same
+ * directory to guarantee a same-filesystem rename.
+ *
+ * Symlinks: a plain writeFile FOLLOWS a symlink and writes through to its target;
+ * a bare rename would REPLACE the link with a regular file. We realpath an
+ * existing target first so the rename lands on the real file and the link
+ * survives — preserving the prior follow-through behavior. A missing target
+ * (create, or a broken link) just writes the literal path.
+ */
+async function writeFileAtomic(filePath: string, content: string): Promise<void> {
+  let target = filePath;
+  try {
+    target = await realpath(filePath);
+  } catch {
+    // ENOENT (new file) or broken link — write the literal path.
+  }
+  const tmp = join(dirname(target), `.${basename(target)}.tmp.${process.pid}.${randomBytes(6).toString('hex')}`);
+  await writeFile(tmp, content, 'utf8');
+  try {
+    await rename(tmp, target);
+  } catch (err) {
+    await unlink(tmp).catch(() => {});
+    throw err;
+  }
+}
+
+/** Detect a file's dominant line ending so an edit can preserve it. */
+function detectEol(text: string): '\r\n' | '\n' {
+  return text.includes('\r\n') ? '\r\n' : '\n';
+}
+
+/**
+ * Serialize the read-modify-write of a single file so two concurrent applies
+ * (e.g. two chat tabs sharing one worktree, or a Bypass write racing an
+ * apply_pending) can't lose an update. In-process keying is sufficient —
+ * BooCoder is a single Fastify process. One Map entry per distinct path.
+ */
+const fileLocks = new Map<string, Promise<void>>();
+async function withFileLock<T>(filePath: string, fn: () => Promise<T>): Promise<T> {
+  const prev = fileLocks.get(filePath) ?? Promise.resolve();
+  let release!: () => void;
+  const current = new Promise<void>((r) => { release = r; });
+  fileLocks.set(filePath, prev.then(() => current));
+  await prev.catch(() => {});
+  try {
+    return await fn();
+  } finally {
+    release();
+  }
+}
+
+// --- Edit-apply planning (pure, unit-tested) ---------------------------------
+
+/**
+ * Decision for applying one queued edit to a file's current content. Pulled out
+ * of `applyOne` so the splice — the part that actually corrupted files — is pure
+ * and testable without a DB or filesystem. Mirrors how opencode/cline/qwen keep
+ * their matchers fail-closed and idempotent.
+ */
+export type EditPlan =
+  | { kind: 'apply'; updated: string }
+  | { kind: 'noop'; reason: 'identical' | 'already-applied' }
+  | { kind: 'ambiguous'; count: number }
+  | { kind: 'not_found' };
+
+/**
+ * Decide how (or whether) to apply an `old → new` edit to `content`.
+ *
+ * Idempotency is the whole point here: a queued edit can legitimately be
+ * re-applied (a local model re-emits the same tool call; a turn is retried; the
+ * same change sits in the queue twice). A naive splice stamps the new text again
+ * each time — the 2–3× block duplication. Two guards make re-application a no-op:
+ *
+ *  - already-applied (anchored insert): when `new` is `old` + an appended block
+ *    (`old="anchor"`, `new="anchor\n<block>"`), `old` still matches uniquely after
+ *    the first apply, so a second apply would duplicate `<block>`. If the full
+ *    `new` text is already present at the match site, the edit is already applied.
+ *  - already-applied (old gone): if `old` can't be located but `new` is already
+ *    in the file, the change landed on a prior pass — treat as a no-op, not an error.
+ *  - identical: the splice would not change the file.
+ *
+ * Anything ambiguous or genuinely absent fails CLOSED so the caller surfaces a
+ * correctable error instead of writing a guess.
+ */
+export function planEdit(content: string, oldStr: string, newStr: string): EditPlan {
+  const match = locateMatch(content, oldStr);
+
+  if (match.kind === 'ambiguous') return { kind: 'ambiguous', count: match.count };
+
+  if (match.kind === 'not_found') {
+    if (newStr.length > 0 && content.includes(newStr)) {
+      return { kind: 'noop', reason: 'already-applied' };
+    }
+    return { kind: 'not_found' };
+  }
+
+  const updated = content.slice(0, match.start) + newStr + content.slice(match.end);
+  // No-change splice first (covers old === new), then the anchored re-stamp guard:
+  // the full replacement already sits at the match site (re-emitted anchored insert).
+  if (updated === content) return { kind: 'noop', reason: 'identical' };
+  if (content.slice(match.start, match.start + newStr.length) === newStr) {
+    return { kind: 'noop', reason: 'already-applied' };
+  }
+  return { kind: 'apply', updated };
+}
+
 // --- Types -------------------------------------------------------------------
 
 export interface PendingChange {
@@ -47,6 +158,13 @@ export async function queueEdit(
   const resolved = resolveWritePath(projectRoot, filePath);
   const diff = JSON.stringify({ old: oldString, new: newString });
 
+  // Idempotent queue: collapse an identical edit that is still pending. Local
+  // quantized models re-emit the same edit_file call within a turn, and a retried
+  // turn re-queues — each duplicate row would apply and stamp another copy. One
+  // pending row per (session, file, operation, diff) is enough.
+  const existing = await findPendingDuplicate(sql, sessionId, resolved, 'edit', diff);
+  if (existing) return existing;
+
   const [row] = await sql<PendingChange[]>`
     INSERT INTO pending_changes (session_id, task_id, file_path, operation, diff, agent)
     VALUES (${sessionId}, ${taskId}, ${resolved}, 'edit', ${diff}, ${agent})
@@ -55,6 +173,28 @@ export async function queueEdit(
   return row!;
 }
 
+/** Return an identical still-pending change for this (session, file, op, diff),
+ *  or undefined. Used to keep the queue idempotent against re-emitted edits. */
+async function findPendingDuplicate(
+  sql: Sql,
+  sessionId: string,
+  resolvedPath: string,
+  operation: 'create' | 'edit' | 'delete',
+  diff: string,
+): Promise<PendingChange | undefined> {
+  const [row] = await sql<PendingChange[]>`
+    SELECT * FROM pending_changes
+    WHERE session_id = ${sessionId}
+      AND file_path = ${resolvedPath}
+      AND operation = ${operation}
+      AND diff = ${diff}
+      AND status = 'pending'
+    ORDER BY created_at ASC
+    LIMIT 1
+  `;
+  return row;
+}
+
 export async function queueCreate(
   sql: Sql,
   sessionId: string,
@@ -68,6 +208,9 @@ export async function queueCreate(
 ): Promise<PendingChange> {
   const resolved = resolveWritePath(projectRoot, filePath);
 
+  const existing = await findPendingDuplicate(sql, sessionId, resolved, 'create', content);
+  if (existing) return existing;
+
   const [row] = await sql<PendingChange[]>`
     INSERT INTO pending_changes (session_id, task_id, file_path, operation, diff, agent)
     VALUES (${sessionId}, ${taskId}, ${resolved}, 'create', ${content}, ${agent})
@@ -87,6 +230,9 @@ export async function queueDelete(
 ): Promise<PendingChange> {
   const resolved = resolveWritePath(projectRoot, filePath);
 
+  const existing = await findPendingDuplicate(sql, sessionId, resolved, 'delete', '');
+  if (existing) return existing;
+
   const [row] = await sql<PendingChange[]>`
     INSERT INTO pending_changes (session_id, task_id, file_path, operation, diff, agent)
     VALUES (${sessionId}, ${taskId}, ${resolved}, 'delete', '', ${agent})
@@ -110,48 +256,60 @@ export async function applyOne(
   }
 
   try {
-    // Re-validate path in case projectRoot has shifted
+    return await withFileLock(change.file_path, async () => {
-    resolveWritePath(projectRoot, change.file_path);
+      // Re-validate path in case projectRoot has shifted
+      resolveWritePath(projectRoot, change.file_path);
 
-    switch (change.operation) {
+      switch (change.operation) {
-      case 'create': {
+        case 'create': {
-        await mkdir(dirname(change.file_path), { recursive: true });
+          await mkdir(dirname(change.file_path), { recursive: true });
-        await writeFile(change.file_path, change.diff, 'utf8');
+          await writeFileAtomic(change.file_path, change.diff);
-        break;
+          break;
-      }
-      case 'edit': {
-        const { old: oldStr, new: newStr } = JSON.parse(change.diff) as { old: string; new: string };
-        const content = await readFile(change.file_path, 'utf8');
-        const match = locateMatch(content, oldStr);
-        if (match.kind === 'ambiguous') {
-          throw new Error(
-            `old_string matches ${match.count} locations — add surrounding context to disambiguate`,
-          );
         }
-        if (match.kind === 'not_found') {
+        case 'edit': {
-          throw new Error(
+          const { old: oldStr, new: newStr } = JSON.parse(change.diff) as { old: string; new: string };
-            'old_string not found in file (even fuzzily) — file may have changed since the edit was queued',
+          const raw = await readFile(change.file_path, 'utf8');
-          );
+          // Normalize to LF for matching, then write back in the file's native EOL
+          // so an LF-emitting model doesn't leave a CRLF file with mixed endings.
+          const eol = detectEol(raw);
+          const toLf = (t: string) => t.replaceAll('\r\n', '\n');
+          const plan = planEdit(toLf(raw), toLf(oldStr), toLf(newStr));
+          if (plan.kind === 'ambiguous') {
+            throw new Error(
+              `old_string matches ${plan.count} locations — add surrounding context to disambiguate`,
+            );
+          }
+          if (plan.kind === 'not_found') {
+            throw new Error(
+              'old_string not found in file (even fuzzily) — file may have changed since the edit was queued',
+            );
+          }
+          if (plan.kind === 'apply') {
+            const out = eol === '\r\n' ? plan.updated.replaceAll('\n', '\r\n') : plan.updated;
+            await writeFileAtomic(change.file_path, out);
+          } else {
+            // noop: the edit is already applied (re-emitted / retried) or a no-change.
+            // Mark it applied without rewriting so it can't stamp a duplicate.
+            console.log(`[pending] edit ${change.file_path} is a no-op (${plan.reason}) — not rewriting`);
+          }
+          break;
         }
-        const updated = content.slice(0, match.start) + newStr + content.slice(match.end);
+        case 'delete': {
-        await writeFile(change.file_path, updated, 'utf8');
+          // Stash current content in diff for potential rewind
-        break;
+          try {
-      }
+            const existing = await readFile(change.file_path, 'utf8');
-      case 'delete': {
+            await sql`UPDATE pending_changes SET diff = ${existing} WHERE id = ${changeId}`;
-        // Stash current content in diff for potential rewind
+          } catch {
-        try {
+            // File may already be gone — proceed with status update
-          const existing = await readFile(change.file_path, 'utf8');
+          }
-          await sql`UPDATE pending_changes SET diff = ${existing} WHERE id = ${changeId}`;
+          await unlink(change.file_path);
-        } catch {
+          break;
-          // File may already be gone — proceed with status update
         }
-        await unlink(change.file_path);
-        break;
       }
-    }
 
-    await sql`UPDATE pending_changes SET status = 'applied' WHERE id = ${changeId}`;
+      await sql`UPDATE pending_changes SET status = 'applied' WHERE id = ${changeId}`;
-    return { id: change.id, file_path: change.file_path, operation: change.operation, success: true };
+      return { id: change.id, file_path: change.file_path, operation: change.operation, success: true };
+    });
   } catch (err) {
     const message = err instanceof Error ? err.message : String(err);
     return { id: change.id, file_path: change.file_path, operation: change.operation, success: false, error: message };
@@ -220,13 +378,13 @@ export async function rewindOne(
           );
         }
         const reverted = content.slice(0, match.start) + oldStr + content.slice(match.end);
-        await writeFile(change.file_path, reverted, 'utf8');
+        await writeFileAtomic(change.file_path, reverted);
         break;
       }
       case 'delete': {
         // Reverse a delete: recreate the file (diff holds the original content stashed at apply time)
         await mkdir(dirname(change.file_path), { recursive: true });
-        await writeFile(change.file_path, change.diff, 'utf8');
+        await writeFileAtomic(change.file_path, change.diff);
         break;
       }
     }

apps/coder/src/services/token-analysis/__tests__/analyzer.test.ts

@@ -0,0 +1,29 @@
+import { describe, it, expect } from 'vitest';
+import { analyzeMessages } from '../analyzer.js';
+
+describe('analyzeMessages', () => {
+  it('classifies user messages', () => {
+    const breakdown = analyzeMessages([{ role: 'user', content: 'hello world' }]);
+    expect(breakdown.user).toBeGreaterThan(0);
+    expect(breakdown.total).toBe(breakdown.user);
+  });
+
+  it('counts tool calls', () => {
+    const parts = [
+      { role: 'assistant', content: 'using grep', tool_calls: [{ id: '1', name: 'grep', arguments: '{}' }] },
+      { role: 'tool', content: '{"files":[]}', tool_call_id: '1' },
+    ];
+    const breakdown = analyzeMessages(parts);
+    expect(breakdown.tools).toBeGreaterThan(0);
+    expect(breakdown.assistant).toBeGreaterThan(0);
+  });
+
+  it('separates reasoning tokens', () => {
+    const parts = [
+      { role: 'assistant', content: 'short answer', reasoning_parts: [{ text: 'long chain of thought reasoning here' }] },
+    ];
+    const breakdown = analyzeMessages(parts);
+    expect(breakdown.reasoning).toBeGreaterThan(0);
+    expect(breakdown.assistant).toBeLessThan(breakdown.reasoning);
+  });
+});

apps/coder/src/services/token-analysis/__tests__/persist.test.ts

@@ -0,0 +1,10 @@
+import { describe, it, expect } from 'vitest';
+
+describe('persistTaskBreakdown', () => {
+  it('exports functions', async () => {
+    const mod = await import('../persist.js');
+    expect(typeof mod.persistTaskBreakdown).toBe('function');
+    expect(typeof mod.getTaskBreakdown).toBe('function');
+    expect(typeof mod.analyzeAndPersistTaskBreakdown).toBe('function');
+  });
+});

apps/coder/src/services/token-analysis/analyzer.ts

@@ -0,0 +1,60 @@
+// TokenScope analyzer — classifies message parts into category breakdown.
+// Ported from opencode-tokenscope (MIT).
+
+export interface TokenBreakdown {
+  system: number;
+  user: number;
+  assistant: number;
+  tools: number;
+  reasoning: number;
+  total: number;
+}
+
+const CHARS_PER_TOKEN = 4;
+
+function estimateTokens(text: string): number {
+  return Math.ceil(text.length / CHARS_PER_TOKEN);
+}
+
+export function analyzeMessages(parts: any[]): TokenBreakdown {
+  const breakdown: TokenBreakdown = { system: 0, user: 0, assistant: 0, tools: 0, reasoning: 0, total: 0 };
+
+  for (const part of parts) {
+    const role = part.role ?? '';
+    const content = part.content ?? '';
+    const tokens = estimateTokens(content);
+
+    switch (role) {
+      case 'system':
+        breakdown.system += tokens;
+        break;
+      case 'user':
+        breakdown.user += tokens;
+        break;
+      case 'assistant':
+        breakdown.assistant += tokens;
+        if (part.tool_calls) {
+          for (const tc of part.tool_calls) {
+            breakdown.tools += estimateTokens(JSON.stringify(tc));
+          }
+        }
+        break;
+      case 'tool':
+        breakdown.tools += tokens;
+        break;
+      default:
+        breakdown.assistant += tokens;
+    }
+
+    if (part.reasoning_parts) {
+      for (const rp of part.reasoning_parts) {
+        const rTokens = estimateTokens(rp.text ?? '');
+        breakdown.reasoning += rTokens;
+        breakdown.assistant -= rTokens;
+      }
+    }
+  }
+
+  breakdown.total = breakdown.system + breakdown.user + breakdown.assistant + breakdown.tools + breakdown.reasoning;
+  return breakdown;
+}

apps/coder/src/services/token-analysis/persist.ts

@@ -0,0 +1,35 @@
+// TokenScope persistence — writes breakdown to task records.
+import type { Sql } from '../../db.js';
+import type { TokenBreakdown } from './analyzer.js';
+
+export async function persistTaskBreakdown(
+  sql: Sql,
+  taskId: string,
+  breakdown: TokenBreakdown,
+): Promise<void> {
+  await sql`
+    UPDATE tasks SET token_breakdown = ${sql.json(breakdown as never)}
+    WHERE id = ${taskId}
+  `;
+}
+
+export async function getTaskBreakdown(
+  sql: Sql,
+  taskId: string,
+): Promise<TokenBreakdown | null> {
+  const rows = await sql<{ token_breakdown: any }[]>`
+    SELECT token_breakdown FROM tasks WHERE id = ${taskId}
+  `;
+  return rows[0]?.token_breakdown ?? null;
+}
+
+export async function analyzeAndPersistTaskBreakdown(
+  sql: Sql,
+  taskId: string,
+  parts: any[],
+): Promise<TokenBreakdown> {
+  const { analyzeMessages } = await import('./analyzer.js');
+  const breakdown = analyzeMessages(parts);
+  await persistTaskBreakdown(sql, taskId, breakdown);
+  return breakdown;
+}

apps/coder/src/services/tools/__tests__/inference_context.test.ts

@@ -0,0 +1,38 @@
+import { describe, it, expect } from 'vitest';
+import { runWithInferenceContext, getInferenceContext } from '../inference_context.js';
+import type { Sql } from '../../../db.js';
+
+const fakeSql = {} as unknown as Sql;
+
+describe('inference context (AsyncLocalStorage isolation)', () => {
+  it('throws when read outside a run', () => {
+    expect(() => getInferenceContext()).toThrow(/outside inference context/);
+  });
+
+  it('keeps each run its own context across overlapping awaits', async () => {
+    // The race the global `let current` had: run B starts (and would overwrite a
+    // shared global) while run A is awaiting. After A resumes it must still read
+    // its OWN sessionId, not B's.
+    const run = (id: string, delay: number) =>
+      runWithInferenceContext({ sql: fakeSql, sessionId: id, taskId: null }, async () => {
+        await new Promise((r) => setTimeout(r, delay));
+        return getInferenceContext().sessionId;
+      });
+
+    const [a, b] = await Promise.all([run('A', 20), run('B', 5)]);
+    expect(a).toBe('A');
+    expect(b).toBe('B');
+  });
+
+  it('carries permissionMode and taskId per run', async () => {
+    const result = await runWithInferenceContext(
+      { sql: fakeSql, sessionId: 's1', taskId: 't1', permissionMode: 'bypass' },
+      async () => {
+        await Promise.resolve();
+        const ctx = getInferenceContext();
+        return { taskId: ctx.taskId, mode: ctx.permissionMode };
+      },
+    );
+    expect(result).toEqual({ taskId: 't1', mode: 'bypass' });
+  });
+});

apps/coder/src/services/tools/apply_pending.ts

@@ -26,6 +26,15 @@ export const applyPendingTool: ToolDef<ApplyPendingInputT> = {
     },
   },
   async execute(_input: ApplyPendingInputT, projectRoot: string, context: ToolContext): Promise<unknown> {
+    // Under Ask (and Plan) the human approves via the Pending Changes panel — the
+    // agent must not auto-apply. Bypass and legacy (undefined) may apply.
+    if (context.permissionMode === 'ask' || context.permissionMode === 'plan') {
+      return {
+        status: 'denied',
+        message:
+          'Permission mode is Ask — staged changes must be approved by the user in the Pending Changes panel, not applied by the agent.',
+      };
+    }
     const results = await applyAll(context.sql, context.sessionId, projectRoot);
     const succeeded = results.filter((r) => r.success).length;
     const failed = results.filter((r) => !r.success).length;

apps/coder/src/services/tools/create_file.ts

@@ -1,6 +1,7 @@
 import { z } from 'zod';
 import type { ToolDef, ToolContext } from './types.js';
 import { queueCreate } from '../pending_changes.js';
+import { denyReadOnly, finalizeWrite } from './write-gate.js';
 
 const CreateFileInput = z.object({
   file_path: z.string().min(1),
@@ -32,6 +33,7 @@ export const createFileTool: ToolDef<CreateFileInputT> = {
     },
   },
   async execute(input: CreateFileInputT, projectRoot: string, context: ToolContext): Promise<unknown> {
+    if (context.permissionMode === 'plan') return denyReadOnly('create_file');
     const change = await queueCreate(
       context.sql,
       context.sessionId,
@@ -40,12 +42,11 @@ export const createFileTool: ToolDef<CreateFileInputT> = {
       input.content,
       projectRoot,
     );
-    return {
+    return finalizeWrite(
-      status: 'queued',
+      context,
-      change_id: change.id,
+      projectRoot,
-      file_path: change.file_path,
+      change,
-      operation: 'create',
+      `File creation queued: ${change.file_path}. Use apply_pending to write changes to disk.`,
-      message: `File creation queued: ${change.file_path}. Use apply_pending to write changes to disk.`,
+    );
-    };
   },
 };

apps/coder/src/services/tools/delete_file.ts

@@ -1,6 +1,7 @@
 import { z } from 'zod';
 import type { ToolDef, ToolContext } from './types.js';
 import { queueDelete } from '../pending_changes.js';
+import { denyReadOnly, finalizeWrite } from './write-gate.js';
 
 const DeleteFileInput = z.object({
   file_path: z.string().min(1),
@@ -30,6 +31,7 @@ export const deleteFileTool: ToolDef<DeleteFileInputT> = {
     },
   },
   async execute(input: DeleteFileInputT, projectRoot: string, context: ToolContext): Promise<unknown> {
+    if (context.permissionMode === 'plan') return denyReadOnly('delete_file');
     const change = await queueDelete(
       context.sql,
       context.sessionId,
@@ -37,12 +39,11 @@ export const deleteFileTool: ToolDef<DeleteFileInputT> = {
       input.file_path,
       projectRoot,
     );
-    return {
+    return finalizeWrite(
-      status: 'queued',
+      context,
-      change_id: change.id,
+      projectRoot,
-      file_path: change.file_path,
+      change,
-      operation: 'delete',
+      `File deletion queued: ${change.file_path}. Use apply_pending to write changes to disk.`,
-      message: `File deletion queued: ${change.file_path}. Use apply_pending to write changes to disk.`,
+    );
-    };
   },
 };

apps/coder/src/services/tools/edit_file.ts

@@ -1,6 +1,7 @@
 import { z } from 'zod';
 import type { ToolDef, ToolContext } from './types.js';
 import { queueEdit } from '../pending_changes.js';
+import { denyReadOnly, finalizeWrite } from './write-gate.js';
 
 const EditFileInput = z.object({
   file_path: z.string().min(1),
@@ -34,6 +35,7 @@ export const editFileTool: ToolDef<EditFileInputT> = {
     },
   },
   async execute(input: EditFileInputT, projectRoot: string, context: ToolContext): Promise<unknown> {
+    if (context.permissionMode === 'plan') return denyReadOnly('edit_file');
     const change = await queueEdit(
       context.sql,
       context.sessionId,
@@ -43,12 +45,11 @@ export const editFileTool: ToolDef<EditFileInputT> = {
       input.new_string,
       projectRoot,
     );
-    return {
+    return finalizeWrite(
-      status: 'queued',
+      context,
-      change_id: change.id,
+      projectRoot,
-      file_path: change.file_path,
+      change,
-      operation: 'edit',
+      `Edit queued for ${change.file_path}. Use apply_pending to write changes to disk.`,
-      message: `Edit queued for ${change.file_path}. Use apply_pending to write changes to disk.`,
+    );
-    };
   },
 };

apps/coder/src/services/tools/index.ts

@@ -7,6 +7,9 @@ import { rewindTool } from './rewind.js';
 import { newTaskTool } from './new_task.js';
 import { listTasksTool } from './list_tasks.js';
 import { checkTaskStatusTool } from './check_task_status.js';
+import { lspDiagnosticsTool } from './lsp_diagnostics.js';
+import { lspGotoDefinitionTool } from './lsp_goto_definition.js';
+import { lspFindReferencesTool } from './lsp_find_references.js';
 
 export type { ToolDef, ToolContext, ToolJsonSchema } from './types.js';
 
@@ -26,4 +29,16 @@ export const WRITE_TOOLS: readonly ToolDef<any>[] = [
   checkTaskStatusTool,
 ];
 
-export { editFileTool, createFileTool, deleteFileTool, applyPendingTool, rewindTool, newTaskTool, listTasksTool, checkTaskStatusTool };
+// Read-only agent tools for code intelligence.
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+export const READ_TOOLS: readonly ToolDef<any>[] = [
+  lspDiagnosticsTool,
+  lspGotoDefinitionTool,
+  lspFindReferencesTool,
+];
+
+export {
+  editFileTool, createFileTool, deleteFileTool, applyPendingTool, rewindTool,
+  newTaskTool, listTasksTool, checkTaskStatusTool,
+  lspDiagnosticsTool, lspGotoDefinitionTool, lspFindReferencesTool,
+};

apps/coder/src/services/tools/inference_context.ts

@@ -1,36 +1,49 @@
+import { AsyncLocalStorage } from 'node:async_hooks';
 import type { Sql } from '../../db.js';
+import type { PermissionMode } from './types.js';
 
 /**
- * Module-level inference context for write tools.
+ * Per-run inference context for write tools.
  *
- * Set via `setInferenceContext()` before each inference run starts.
+ * Write tools need ambient state (sql, sessionId, the permission gate) that the
- * Write tools read it via `getInferenceContext()` during execute.
+ * BooChat tool-phase `execute(input, projectRoot, extraRoots?)` signature can't
- * Same pattern as BooChat's `loadConfig()` singleton — tools need
+ * carry. This used to be a single module-level `let current` — but the inference
- * ambient state that can't be threaded through the tool-phase execute
+ * runner's `enqueue()` is fire-and-forget, so two overlapping runs (a user
- * signature (which is `execute(input, projectRoot, extraRoots?)`).
+ * message racing a dispatcher-polled native task; two chat tabs streaming) would
+ * clobber each other's context, and `cancel()` cleared it for ALL in-flight runs.
+ *
+ * AsyncLocalStorage gives each run its own context: `enqueue()` starts its async
+ * loop synchronously inside `runWithInferenceContext`, so the store propagates
+ * through every awaited tool execution in that run — and only that run.
  */
 
 export interface InferenceContext {
   sql: Sql;
   sessionId: string;
   taskId: string | null;
+  /** Native-BooCode permission gate, set per run from the request/task mode. */
+  permissionMode?: PermissionMode;
 }
 
-let current: InferenceContext | null = null;
+const storage = new AsyncLocalStorage<InferenceContext>();
 
-export function setInferenceContext(ctx: InferenceContext): void {
+/**
-  current = ctx;
+ * Bind `ctx` for the duration of the (possibly detached) async chain `fn` starts.
-}
+ * The inference runner kicks off its loop synchronously within this call, so all
-
+ * downstream `await`s — including write-tool `execute` via the adapter — read the
-export function clearInferenceContext(): void {
+ * same store. Concurrent runs each get their own; nothing is shared or cleared
-  current = null;
+ * out from under an in-flight run.
+ */
+export function runWithInferenceContext<T>(ctx: InferenceContext, fn: () => T): T {
+  return storage.run(ctx, fn);
 }
 
 export function getInferenceContext(): InferenceContext {
-  if (!current) {
+  const ctx = storage.getStore();
+  if (!ctx) {
     throw new Error(
-      'Write tool called outside inference context — setInferenceContext() was not called before this run',
+      'Write tool called outside inference context — runWithInferenceContext() did not wrap this run',
     );
   }
-  return current;
+  return ctx;
 }

apps/coder/src/services/tools/lsp_diagnostics.ts

@@ -0,0 +1,48 @@
+import { z } from 'zod';
+import { readFile } from 'node:fs/promises';
+import type { ToolDef, ToolContext } from './types.js';
+import { resolveWritePath } from '../write_guard.js';
+import { lspManager } from '../lsp/server-manager.js';
+import { getDiagnostics } from '../lsp/operations.js';
+
+const LspDiagnosticsInput = z.object({
+  file_path: z.string().describe('Path to the file to check for diagnostics'),
+});
+
+type InputT = z.infer<typeof LspDiagnosticsInput>;
+
+export const lspDiagnosticsTool: ToolDef<InputT> = {
+  name: 'lsp_diagnostics',
+  description: 'Get TypeScript/JavaScript diagnostics (errors, warnings) for a file. Returns diagnostic messages with severity and location.',
+  inputSchema: LspDiagnosticsInput,
+  jsonSchema: {
+    type: 'function',
+    function: {
+      name: 'lsp_diagnostics',
+      description: 'Get TypeScript/JavaScript diagnostics for a file',
+      parameters: {
+        type: 'object',
+        properties: {
+          file_path: { type: 'string', description: 'Path to the file' },
+        },
+        required: ['file_path'],
+      },
+    },
+  },
+
+  async execute(input: InputT, projectRoot: string, _context: ToolContext): Promise<unknown> {
+    const resolved = await resolveWritePath(projectRoot, input.file_path);
+    const content = await readFile(resolved, 'utf8');
+    const client = await lspManager.getClient(resolved);
+    if (!client) return { error: 'Unsupported file type for LSP diagnostics' };
+
+    const diagnostics = await getDiagnostics(client, resolved, content);
+    if (diagnostics.length === 0) return { result: 'No diagnostics found.' };
+
+    const lines = diagnostics.map((d) => {
+      const sev = ['', 'error', 'warning', 'info', 'hint'][d.severity] ?? 'unknown';
+      return `[${sev}] line ${d.range.start.line + 1}:${d.range.start.character + 1} - ${d.message}`;
+    });
+    return { result: lines.join('\n') };
+  },
+};

apps/coder/src/services/tools/lsp_find_references.ts

@@ -0,0 +1,49 @@
+import { z } from 'zod';
+import { readFile } from 'node:fs/promises';
+import type { ToolDef, ToolContext } from './types.js';
+import { resolveWritePath } from '../write_guard.js';
+import { lspManager } from '../lsp/server-manager.js';
+import { findReferences } from '../lsp/operations.js';
+
+const LspFindReferencesInput = z.object({
+  file_path: z.string().describe('Path to the source file'),
+  line: z.number().int().nonnegative().describe('0-based line number'),
+  character: z.number().int().nonnegative().describe('0-based character offset'),
+});
+
+type InputT = z.infer<typeof LspFindReferencesInput>;
+
+export const lspFindReferencesTool: ToolDef<InputT> = {
+  name: 'lsp_find_references',
+  description: 'Find all references to a symbol at a given position in a file.',
+  inputSchema: LspFindReferencesInput,
+  jsonSchema: {
+    type: 'function',
+    function: {
+      name: 'lsp_find_references',
+      description: 'Find all references to symbol at position',
+      parameters: {
+        type: 'object',
+        properties: {
+          file_path: { type: 'string' },
+          line: { type: 'number' },
+          character: { type: 'number' },
+        },
+        required: ['file_path', 'line', 'character'],
+      },
+    },
+  },
+
+  async execute(input: InputT, projectRoot: string, _context: ToolContext): Promise<unknown> {
+    const resolved = await resolveWritePath(projectRoot, input.file_path);
+    const content = await readFile(resolved, 'utf8');
+    const client = await lspManager.getClient(resolved);
+    if (!client) return { error: 'Unsupported file type' };
+
+    const refs = await findReferences(client, resolved, content, input.line, input.character);
+    if (refs.length === 0) return { result: 'No references found.' };
+
+    const lines = refs.map((r) => `${r.uri}:${r.range.start.line + 1}:${r.range.start.character + 1}`);
+    return { result: `Found ${refs.length} reference(s):\n${lines.join('\n')}` };
+  },
+};

apps/coder/src/services/tools/lsp_goto_definition.ts

@@ -0,0 +1,48 @@
+import { z } from 'zod';
+import { readFile } from 'node:fs/promises';
+import type { ToolDef, ToolContext } from './types.js';
+import { resolveWritePath } from '../write_guard.js';
+import { lspManager } from '../lsp/server-manager.js';
+import { gotoDefinition } from '../lsp/operations.js';
+
+const LspGotoDefinitionInput = z.object({
+  file_path: z.string().describe('Path to the source file'),
+  line: z.number().int().nonnegative().describe('0-based line number'),
+  character: z.number().int().nonnegative().describe('0-based character offset'),
+});
+
+type InputT = z.infer<typeof LspGotoDefinitionInput>;
+
+export const lspGotoDefinitionTool: ToolDef<InputT> = {
+  name: 'lsp_goto_definition',
+  description: 'Find the definition of a symbol at a given position in a file.',
+  inputSchema: LspGotoDefinitionInput,
+  jsonSchema: {
+    type: 'function',
+    function: {
+      name: 'lsp_goto_definition',
+      description: 'Find definition of symbol at position',
+      parameters: {
+        type: 'object',
+        properties: {
+          file_path: { type: 'string' },
+          line: { type: 'number' },
+          character: { type: 'number' },
+        },
+        required: ['file_path', 'line', 'character'],
+      },
+    },
+  },
+
+  async execute(input: InputT, projectRoot: string, _context: ToolContext): Promise<unknown> {
+    const resolved = await resolveWritePath(projectRoot, input.file_path);
+    const content = await readFile(resolved, 'utf8');
+    const client = await lspManager.getClient(resolved);
+    if (!client) return { error: 'Unsupported file type' };
+
+    const loc = await gotoDefinition(client, resolved, content, input.line, input.character);
+    if (!loc) return { result: 'No definition found.' };
+
+    return { result: `Defined at ${loc.uri}:${loc.range.start.line + 1}:${loc.range.start.character + 1}` };
+  },
+};

apps/coder/src/services/tools/new_task.ts

@@ -6,6 +6,7 @@ const NewTaskInput = z.object({
   input: z.string().min(1).describe('Task description for the child subtask'),
   agent: z.string().optional().describe('Optional: dispatch to a specific agent'),
   model: z.string().optional().describe('Optional: model override for the subtask'),
+  background: z.boolean().optional().describe('If true, return immediately without blocking on completion'),
 });
 
 type NewTaskInputT = z.infer<typeof NewTaskInput>;
@@ -30,6 +31,7 @@ export const newTaskTool: ToolDef<NewTaskInputT> = {
           input: { type: 'string', description: 'Task description for the child subtask' },
           agent: { type: 'string', description: 'Optional: dispatch to a specific agent' },
           model: { type: 'string', description: 'Optional: model override for the subtask' },
+          background: { type: 'boolean', description: 'If true, returns immediately without waiting' },
         },
         required: ['input'],
       },
@@ -50,6 +52,7 @@ export const newTaskTool: ToolDef<NewTaskInputT> = {
       return { error: 'Cannot determine project_id from current session' };
     }
 
+    const isBg = input.background === true;
     const [task] = await sql<{ id: string; state: string }[]>`
       INSERT INTO tasks (project_id, parent_task_id, input, agent, model)
       VALUES (${session.project_id}, ${currentTaskId}, ${input.input}, ${input.agent ?? null}, ${input.model ?? null})
@@ -57,9 +60,12 @@ export const newTaskTool: ToolDef<NewTaskInputT> = {
     `;
 
     return {
-      message: `Subtask created (id: ${task!.id}). It will run in isolation. Use check_task_status to monitor.`,
+      message: isBg
+        ? `Background subtask created (id: ${task!.id}). It will continue independently.`
+        : `Subtask created (id: ${task!.id}). It will run in isolation. Use check_task_status to monitor.`,
       task_id: task!.id,
       state: task!.state,
+      background: isBg,
     };
   },
 };

apps/coder/src/services/tools/types.ts

@@ -1,6 +1,22 @@
 import type { z } from 'zod';
 import type { Sql } from '../../db.js';
 
+/**
+ * Unified permission ladder for native BooCode inference. Gates the write tools:
+ *   plan   — read-only: create/edit/delete are denied (no staging).
+ *   ask    — stage to the pending-changes queue; `apply_pending` is denied so the
+ *            agent cannot self-apply (the human approves via the Diff panel).
+ *   bypass — apply each write immediately (no queue, no approval).
+ * Undefined preserves the historical behavior (stage + `apply_pending` allowed).
+ */
+export type PermissionMode = 'plan' | 'ask' | 'bypass';
+
+/** Narrow a raw task/request mode id to a unified PermissionMode, else undefined
+ *  (e.g. an external agent's native mode id, or null). */
+export function asPermissionMode(id: string | null | undefined): PermissionMode | undefined {
+  return id === 'plan' || id === 'ask' || id === 'bypass' ? id : undefined;
+}
+
 export interface ToolJsonSchema {
   type: 'function';
   function: {
@@ -21,6 +37,8 @@ export interface ToolContext {
   sql: Sql;
   sessionId: string;
   taskId: string | null;
+  /** Native-BooCode permission gate for write tools (undefined = legacy behavior). */
+  permissionMode?: PermissionMode;
 }
 
 export interface ToolDef<TInput> {

apps/coder/src/services/tools/write-gate.ts

@@ -0,0 +1,53 @@
+/**
+ * Permission-gate helpers for native BooCode write tools. The gate comes from
+ * the per-run inference context (`ToolContext.permissionMode`):
+ *   plan   — deny the write (read-only); nothing is staged.
+ *   bypass — apply the staged change immediately (no queue, no approval).
+ *   ask / undefined — leave it in the pending-changes queue for review.
+ */
+import type { ToolContext } from './types.js';
+import { applyOne } from '../pending_changes.js';
+
+/** Result returned when a write is denied under Plan (read-only) mode. */
+export function denyReadOnly(operation: string): unknown {
+  return {
+    status: 'denied',
+    operation,
+    message: `Read-only (Plan) permission mode — ${operation} is not permitted. Switch to Ask or Bypass to make changes.`,
+  };
+}
+
+/** Finalize a just-staged change per the permission gate: apply now under Bypass,
+ *  otherwise return it as queued for the human to approve. */
+export async function finalizeWrite(
+  context: ToolContext,
+  projectRoot: string,
+  change: { id: string; file_path: string; operation: string },
+  queuedHint: string,
+): Promise<unknown> {
+  if (context.permissionMode === 'bypass') {
+    const res = await applyOne(context.sql, change.id, projectRoot);
+    console.log(
+      `[write-gate] bypass apply ${change.operation} ${change.file_path} -> ${res.success ? 'applied' : 'FAILED: ' + (res.error ?? '?')}`,
+    );
+    return {
+      status: res.success ? 'applied' : 'failed',
+      change_id: change.id,
+      file_path: change.file_path,
+      operation: change.operation,
+      message: res.success
+        ? `${change.operation} applied to ${change.file_path}.`
+        : `Apply failed for ${change.file_path}: ${res.error ?? 'unknown error'}. Left in the pending queue.`,
+    };
+  }
+  console.log(
+    `[write-gate] ${context.permissionMode ?? 'legacy'} queued ${change.operation} ${change.file_path}`,
+  );
+  return {
+    status: 'queued',
+    change_id: change.id,
+    file_path: change.file_path,
+    operation: change.operation,
+    message: queuedHint,
+  };
+}

apps/server/CLAUDE.md

@@ -17,6 +17,8 @@
   - **Tools have NO `execute` field.** BooCode dispatches tools in tool-phase.ts, not the AI SDK loop — only `description` + `inputSchema: jsonSchema(parameters)`.
   - **`includeUsage: true` MUST be set on `createOpenAICompatible`** in `provider.ts`. The adapter defaults it false → no `stream_options.include_usage` → llama-swap emits no usage block → `result.usage` resolves `undefined` (NULL token counts). Don't remove during refactor.
   - **Tool-call-only turns may emit a leading `\n` text-delta.** `MessageList.flatten`'s `hasText` and `MessageBubble`'s `hasContent` both `.trim()` before the length check, else whitespace-only content renders an empty bubble + ActionRow between tool calls. `buildMessagesPayload` also skips `status='failed'` and complete-but-empty assistant rows (avoids "Cannot have 2 or more assistant messages at the end of the list" upstream rejection after cap-hit + Continue).
+- **`services/inference/tool-shim.ts`** — Recovers structured tool calls from plain-text model output. Some models (notably Qwen) emit `<tool_call><name>...</name><arguments>...</arguments></tool_call>` inline text instead of structured JSON. `extractToolCalls(text)` parses both XML and JSON inline formats. `hasToolCallMarkup(text)` is a fast pre-check. Used as a fallback in the stream phase when structured `tool_calls` parse fails. Does NOT require `FAST_MODEL` — operates on the existing turn's output text.
+- **`services/inference/loop-detectors.ts`** — Six detectors that catch repetitive model behavior: `detectContentRepeat` (same content N times), `detectToolLoop` (same tool called consecutively). `detectDoomLoop` combines both. These are additive to the existing `sentinels.ts` doom-loop detection.
 - **AI SDK ModelMessage conversion** (`toModelMessages` in stream-phase.ts). Tool messages need a `toolName` for `ToolResultPart`; BooCode's OpenAI-shape history lacks it, so a forward-scan builds a `tool_call_id → toolName` map from prior assistant `tool_calls`. Tool outputs wrapped as `{ type: 'json' | 'text', value }` (v6 `ToolResultOutput`). Reasoning emits a `ReasoningPart` first in the content array.
 - **`experimental_repairToolCall`** wired into `streamText` to keep the stream alive when qwen3.6 emits malformed tool args. Pass-through: logs the bad call, returns it unmodified; `executeToolPhase`'s zod-reject path routes it back to the model next turn.
 - **`chat_status` frame** (via `broker.publishUser`) — `status: 'streaming' | 'tool_running' | 'waiting_for_input' | 'idle' | 'error'`. Frontend `useChatStatus` derives `idle_warm` (<30s since idle) vs `idle_cold`. `ChatThroughput` renders beside `StatusDot` only when streaming/tool_running, fed by 500ms-throttled `'usage'` frames (`completion_tokens` + `ctx_used` + `ctx_max`). `POST /api/chats/:id/discard_stale` marks a stuck-streaming row `failed` when the frontend's 60s no-token timer gives up.

apps/server/src/index.ts

@@ -19,6 +19,8 @@ import { registerModelRoutes } from './routes/models.js';
 import { registerAgentRoutes } from './routes/agents.js';
 import { registerSkillsRoutes } from './routes/skills.js';
 import { registerToolsRoutes } from './routes/tools.js';
+import { registerAnalyticsRoutes } from './routes/analytics.js';
+import { registerInferenceSettingsRoutes } from './routes/inference-settings.js';
 import { createInferenceRunner } from './services/inference/index.js';
 import { createBroker } from './services/broker.js';
 import { listSkills } from './services/skills.js';
@@ -122,6 +124,8 @@ async function main() {
   registerSidebarRoutes(app, sql);
   registerChatRoutes(app, sql, broker);
   registerToolsRoutes(app, sql);
+  registerAnalyticsRoutes(app, sql);
+  registerInferenceSettingsRoutes(app);
 
   // Batch 9.6: warm the skills cache at boot and surface the count. Empty or
   // missing /data/skills is non-fatal — the skill tools just return empty.

apps/server/src/routes/analytics.ts

@@ -0,0 +1,33 @@
+import type { FastifyInstance } from 'fastify';
+import type { Sql } from '../db.js';
+
+// token-analyzer-ui: context window utilization and token breakdown data.
+// v1 — global aggregates only.
+
+export interface ContextWindowStats {
+  avg_ctx_used: number | null;
+  avg_ctx_max: number | null;
+  avg_utilization_pct: number | null;
+  message_count: number;
+}
+
+export function registerAnalyticsRoutes(app: FastifyInstance, sql: Sql): void {
+  // GET /api/analytics/context — average context window utilization across
+  // completed assistant messages that carry ctx_used/ctx_max.
+  app.get('/api/analytics/context', async () => {
+    const [row] = await sql<ContextWindowStats[]>`
+      SELECT
+        AVG(ctx_used)::DOUBLE PRECISION AS avg_ctx_used,
+        AVG(ctx_max)::DOUBLE PRECISION AS avg_ctx_max,
+        AVG(ctx_used::float / NULLIF(ctx_max, 0))::DOUBLE PRECISION AS avg_utilization_pct,
+        COUNT(*)::INT AS message_count
+      FROM messages
+      WHERE role = 'assistant'
+        AND status = 'complete'
+        AND ctx_used IS NOT NULL
+        AND ctx_max IS NOT NULL
+        AND ctx_max > 0
+    `;
+    return row ?? { avg_ctx_used: null, avg_ctx_max: null, avg_utilization_pct: null, message_count: 0 };
+  });
+}

apps/server/src/routes/inference-settings.ts

@@ -0,0 +1,55 @@
+import { FastifyInstance } from 'fastify';
+import { readFileSync, writeFileSync, existsSync, mkdirSync } from 'fs';
+import { resolve, dirname } from 'path';
+
+const CONFIG_PATH = resolve(process.env.BOOCODE_DATA_DIR || '/opt/boocode/data', 'inference-settings.json');
+
+const DEFAULTS = {
+  cache_type_k: 'q4_0',
+  cache_reuse: 256,
+  spec_type: 'ngram-mod',
+  spec_ngram_mod_thsh: 2,
+  ctx_checkpoints: 32,
+  sleep_idle_seconds: 600,
+  metrics_enabled: true,
+  slot_save_path: '/tmp/llama-slots',
+};
+
+function load(): Record<string, unknown> {
+  try {
+    if (existsSync(CONFIG_PATH)) {
+      return JSON.parse(readFileSync(CONFIG_PATH, 'utf-8'));
+    }
+  } catch { /* corrupt file */ }
+  return { ...DEFAULTS };
+}
+
+function save(data: Record<string, unknown>): void {
+  const dir = dirname(CONFIG_PATH);
+  if (!existsSync(dir)) mkdirSync(dir, { recursive: true });
+  writeFileSync(CONFIG_PATH, JSON.stringify(data, null, 2) + '\n');
+}
+
+const VALID_CACHE_TYPES = ['f32', 'f16', 'q8_0', 'q4_0'] as const;
+const VALID_SPEC_TYPES = ['off', 'ngram-mod', 'draft-simple'] as const;
+
+export function registerInferenceSettingsRoutes(app: FastifyInstance): void {
+  app.get('/api/settings/inference', async (_req, _res) => {
+    return { ...DEFAULTS, ...load() };
+  });
+
+  app.patch<{ Body: Record<string, unknown> }>('/api/settings/inference', async (req, reply) => {
+    const current = { ...DEFAULTS, ...load() };
+    const merged = { ...current, ...req.body };
+
+    if (merged.cache_type_k && !(VALID_CACHE_TYPES as readonly string[]).includes(merged.cache_type_k as string)) {
+      return reply.status(400).send({ error: 'Invalid cache_type_k' });
+    }
+    if (merged.spec_type && !(VALID_SPEC_TYPES as readonly string[]).includes(merged.spec_type as string)) {
+      return reply.status(400).send({ error: 'Invalid spec_type' });
+    }
+
+    save(merged);
+    return { ...DEFAULTS, ...load() };
+  });
+}

apps/server/src/routes/projects.ts

@@ -1,6 +1,6 @@
 import type { FastifyInstance } from 'fastify';
 import { z } from 'zod';
-import { realpath, stat, readdir, access } from 'node:fs/promises';
+import { realpath, stat, readdir, access, writeFile, rename } from 'node:fs/promises';
 import { basename, resolve, sep } from 'node:path';
 import type { Sql } from '../db.js';
 import type { Config } from '../config.js';
@@ -473,7 +473,7 @@ export function registerProjectRoutes(
   // Always includes auto_mode (the dirty-state-derived mode) so the client can
   // show a suggestion when a pinned mode diverges from what would be auto-selected.
   // Returns { git_repo: false } when the path is not a git repository.
-  app.get<{ Params: { id: string }; Querystring: { mode?: string } }>(
+  app.get<{ Params: { id: string }; Querystring: { mode?: string; whitespace?: string } }>(
     '/api/projects/:id/git/diff',
     async (req, reply) => {
       const { id } = req.params;
@@ -504,7 +504,8 @@ export function registerProjectRoutes(
         rawMode === 'uncommitted' ? 'uncommitted' :
         auto_mode; // no mode param → auto-select (FIX 1)
 
-      const result = await getGitDiff(projectRoot, mode);
+      const ignoreWhitespace = req.query.whitespace === '1';
+      const result = await getGitDiff(projectRoot, mode, ignoreWhitespace);
       if (result === null) {
         return { git_repo: false, mode, auto_mode, base_label: null, in_progress_op: null, files: [] };
       }
@@ -541,6 +542,11 @@ export function registerProjectRoutes(
     ).min(1),
   });
 
+  const WriteFileBody = z.object({
+    path: z.string().min(1),
+    content: z.string(),
+  });
+
   // POST /api/projects/:id/git/stage — stage whole files
   app.post<{ Params: { id: string } }>(
     '/api/projects/:id/git/stage',
@@ -637,6 +643,38 @@ export function registerProjectRoutes(
     },
   );
 
+  // POST /api/projects/:id/write_file — write a file atomically
+  app.post<{ Params: { id: string } }>(
+    '/api/projects/:id/write_file',
+    async (req, reply) => {
+      const body = WriteFileBody.safeParse(req.body);
+      if (!body.success) { reply.code(400); return { error: body.error.message }; }
+      const { id } = req.params;
+      const projectPath = await selectProjectPath(sql, id);
+      if (!projectPath) { reply.code(404); return { error: 'not found' }; }
+      let root: string;
+      try { root = await resolveProjectRoot(projectPath); }
+      catch (err) { if (err instanceof PathScopeError) { reply.code(404); return { error: (err as Error).message }; } throw err; }
+      const target = body.data.path.startsWith('/') ? body.data.path : resolve(root, body.data.path);
+      // Validate path stays within project root
+      const realTarget = await realpath(target).catch(() => target);
+      if (!realTarget.startsWith(root + sep) && realTarget !== root) {
+        reply.code(403);
+        return { error: 'path escapes project root' };
+      }
+      const tmp = target + '.tmp';
+      try {
+        await writeFile(tmp, body.data.content, 'utf-8');
+        await rename(tmp, target);
+        return { ok: true };
+      } catch (err) {
+        // Clean up tmp on failure
+        await access(tmp).then(() => rename(tmp, target + '.bak').catch(() => {})).catch(() => {});
+        throw err;
+      }
+    },
+  );
+
   // GET /api/projects/:id/files
   app.get<{ Params: { id: string } }>(
     '/api/projects/:id/files',

apps/server/src/services/audit/corrections.ts

@@ -0,0 +1,52 @@
+export interface UserCorrectionRecord {
+  record_type: 'conversation';
+  action_type: 'user_correction';
+  priority: 'critical_for_recovery';
+  timestamp: string;
+  original_claim: string;
+  correction: string;
+  principle_extracted: string;
+  persisted_to: string[];
+}
+
+export function createCorrection(params: {
+  originalClaim: string;
+  correction: string;
+  principleExtracted?: string;
+  persistedTo?: string[];
+}): UserCorrectionRecord {
+  return {
+    record_type: 'conversation',
+    action_type: 'user_correction',
+    priority: 'critical_for_recovery',
+    timestamp: new Date().toISOString(),
+    original_claim: params.originalClaim,
+    correction: params.correction,
+    principle_extracted: params.principleExtracted || '',
+    persisted_to: params.persistedTo || [],
+  };
+}
+
+export function findCorrections(
+  records: Record<string, unknown>[],
+): UserCorrectionRecord[] {
+  return records.filter(
+    r => r['action_type'] === 'user_correction',
+  ) as unknown as UserCorrectionRecord[];
+}
+
+export function checkCorrectionConflict(
+  proposedAction: string,
+  corrections: UserCorrectionRecord[],
+): UserCorrectionRecord | null {
+  for (const c of corrections) {
+    if (!c.original_claim) continue;
+    const claimKeywords = c.original_claim.toLowerCase().split(/\s+/).filter(w => w.length > 3);
+    const actionLower = proposedAction.toLowerCase();
+    const matchCount = claimKeywords.filter(k => actionLower.includes(k)).length;
+    if (matchCount >= 2 && matchCount / claimKeywords.length >= 0.5) {
+      if (c.persisted_to.length > 0) return c;
+    }
+  }
+  return null;
+}

apps/server/src/services/audit/guideline-store.ts

@@ -0,0 +1,251 @@
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
+import { join } from 'node:path';
+import { ensureRunsDir } from './runs-dir.js';
+
+export type GuidelineId = string;
+export type TagId = string;
+export type Criticality = 'low' | 'medium' | 'high';
+export type GuidelineDocumentVersion = string;
+
+export interface GuidelineContent {
+  condition: string;
+  action: string | null;
+  description: string | null;
+}
+
+export interface Guideline {
+  id: GuidelineId;
+  creationUtc: string;
+  content: GuidelineContent;
+  enabled: boolean;
+  tags: TagId[];
+  labels: string[];
+  metadata: Record<string, unknown>;
+  criticality: Criticality;
+  title: string | null;
+  priority: number;
+}
+
+export interface GuidelineDocument {
+  id: string;
+  version: GuidelineDocumentVersion;
+  creation_utc: string;
+  condition: string;
+  action: string | null;
+  description: string | null;
+  title: string | null;
+  criticality: string;
+  enabled: boolean;
+  metadata: Record<string, unknown>;
+  labels: string[];
+  priority: number;
+}
+
+export interface GuidelineUpdateParams {
+  condition?: string;
+  action?: string | null;
+  description?: string | null;
+  title?: string | null;
+  criticality?: Criticality;
+  enabled?: boolean;
+  priority?: number;
+}
+
+function generateId(): string {
+  const chars = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
+  let result = '';
+  for (let i = 0; i < 10; i++) {
+    result += chars[Math.floor(Math.random() * chars.length)];
+  }
+  return result;
+}
+
+function dbPath(projectRoot?: string): string {
+  const dir = join(ensureRunsDir(projectRoot), '..', 'guidelines');
+  if (!existsSync(dir)) mkdirSync(dir, { recursive: true });
+  return join(dir, 'guidelines.json');
+}
+
+function readDb(projectRoot?: string): GuidelineDocument[] {
+  const path = dbPath(projectRoot);
+  try {
+    return JSON.parse(readFileSync(path, 'utf-8')) as GuidelineDocument[];
+  } catch {
+    return [];
+  }
+}
+
+function writeDb(docs: GuidelineDocument[], projectRoot?: string): void {
+  writeFileSync(dbPath(projectRoot), JSON.stringify(docs, null, 2), 'utf-8');
+}
+
+function toDocument(g: Guideline): GuidelineDocument {
+  return {
+    id: g.id,
+    version: '0.11.0',
+    creation_utc: g.creationUtc,
+    condition: g.content.condition,
+    action: g.content.action,
+    description: g.content.description,
+    title: g.title,
+    criticality: g.criticality,
+    enabled: g.enabled,
+    metadata: g.metadata,
+    labels: g.labels,
+    priority: g.priority,
+  };
+}
+
+function fromDocument(d: GuidelineDocument): Guideline {
+  return {
+    id: d.id,
+    creationUtc: d.creation_utc,
+    content: {
+      condition: d.condition,
+      action: d.action ?? null,
+      description: d.description ?? null,
+    },
+    title: d.title ?? null,
+    criticality: (d.criticality || 'medium') as Criticality,
+    enabled: d.enabled ?? true,
+    tags: [],
+    labels: d.labels ?? [],
+    metadata: d.metadata ?? {},
+    priority: d.priority ?? 0,
+  };
+}
+
+export class GuidelineDocumentStore {
+  createGuideline(params: {
+    condition: string;
+    action?: string | null;
+    description?: string | null;
+    title?: string | null;
+    criticality?: Criticality;
+    enabled?: boolean;
+    labels?: string[];
+    priority?: number;
+    id?: GuidelineId;
+  }, projectRoot?: string): Guideline {
+    const docs = readDb(projectRoot);
+    const id = params.id || `gl_${generateId()}`;
+
+    if (docs.find(d => d.id === id)) {
+      throw new Error(`Guideline with id '${id}' already exists`);
+    }
+
+    const guideline: Guideline = {
+      id,
+      creationUtc: new Date().toISOString(),
+      content: {
+        condition: params.condition,
+        action: params.action ?? null,
+        description: params.description ?? null,
+      },
+      title: params.title ?? null,
+      criticality: params.criticality ?? 'medium',
+      enabled: params.enabled ?? true,
+      tags: [],
+      labels: params.labels ?? [],
+      metadata: {},
+      priority: params.priority ?? 0,
+    };
+
+    docs.push(toDocument(guideline));
+    writeDb(docs, projectRoot);
+    return guideline;
+  }
+
+  listGuidelines(params?: {
+    tags?: TagId[];
+    labels?: string[];
+  }, projectRoot?: string): Guideline[] {
+    let docs = readDb(projectRoot);
+
+    if (params?.tags && params.tags.length > 0) {
+      const tagSet = new Set(params.tags);
+      docs = docs.filter(d => d.metadata['tags'] &&
+        Array.isArray(d.metadata['tags']) &&
+        (d.metadata['tags'] as string[]).some(t => tagSet.has(t)));
+    }
+
+    if (params?.labels && params.labels.length > 0) {
+      const labelSet = new Set(params.labels);
+      docs = docs.filter(d => {
+        const gl = fromDocument(d);
+        return params.labels!.every(l => gl.labels.includes(l));
+      });
+    }
+
+    return docs.map(fromDocument);
+  }
+
+  readGuideline(id: GuidelineId, projectRoot?: string): Guideline {
+    const docs = readDb(projectRoot);
+    const doc = docs.find(d => d.id === id);
+    if (!doc) throw new Error(`Guideline '${id}' not found`);
+    return fromDocument(doc);
+  }
+
+  updateGuideline(id: GuidelineId, params: GuidelineUpdateParams, projectRoot?: string): Guideline {
+    const docs = readDb(projectRoot);
+    const idx = docs.findIndex(d => d.id === id);
+    if (idx === -1) throw new Error(`Guideline '${id}' not found`);
+
+    const doc = docs[idx]!;
+    if (params.condition !== undefined) doc.condition = params.condition;
+    if (params.action !== undefined) doc.action = params.action;
+    if (params.description !== undefined) doc.description = params.description;
+    if (params.title !== undefined) doc.title = params.title;
+    if (params.criticality !== undefined) doc.criticality = params.criticality;
+    if (params.enabled !== undefined) doc.enabled = params.enabled;
+    if (params.priority !== undefined) doc.priority = params.priority;
+
+    docs[idx] = doc;
+    writeDb(docs, projectRoot);
+    return fromDocument(doc);
+  }
+
+  deleteGuideline(id: GuidelineId, projectRoot?: string): void {
+    const docs = readDb(projectRoot);
+    const idx = docs.findIndex(d => d.id === id);
+    if (idx === -1) throw new Error(`Guideline '${id}' not found`);
+    docs.splice(idx, 1);
+    writeDb(docs, projectRoot);
+  }
+
+  findGuideline(content: GuidelineContent, projectRoot?: string): Guideline {
+    const docs = readDb(projectRoot);
+    const doc = docs.find(d =>
+      d.condition === content.condition &&
+      (content.action === undefined || d.action === content.action),
+    );
+    if (!doc) throw new Error(`Guideline not found for condition='${content.condition}'`);
+    return fromDocument(doc);
+  }
+
+  upsertLabels(id: GuidelineId, labels: string[], projectRoot?: string): Guideline {
+    const docs = readDb(projectRoot);
+    const idx = docs.findIndex(d => d.id === id);
+    if (idx === -1) throw new Error(`Guideline '${id}' not found`);
+
+    const doc = docs[idx]!;
+    const current = new Set(doc.labels || []);
+    for (const l of labels) current.add(l);
+    doc.labels = [...current];
+    writeDb(docs, projectRoot);
+    return fromDocument(doc);
+  }
+
+  removeLabels(id: GuidelineId, labels: string[], projectRoot?: string): Guideline {
+    const docs = readDb(projectRoot);
+    const idx = docs.findIndex(d => d.id === id);
+    if (idx === -1) throw new Error(`Guideline '${id}' not found`);
+
+    const doc = docs[idx]!;
+    const removeSet = new Set(labels);
+    doc.labels = (doc.labels || []).filter(l => !removeSet.has(l));
+    writeDb(docs, projectRoot);
+    return fromDocument(doc);
+  }
+}

apps/server/src/services/audit/index.ts

@@ -0,0 +1,68 @@
+export {
+  findRunsDir,
+  ensureRunsDir,
+  readCurrentSession,
+  writeCurrentSession,
+  clearCurrentSession,
+  readIndex,
+  writeIndex,
+  updateIndexEntry,
+  findInProgressSessions,
+  INDEX_SCHEMA_VERSION,
+  GITIGNORE_CONTENT,
+} from './runs-dir.js';
+export type { IndexEntry, IndexFile } from './runs-dir.js';
+
+export {
+  generateSessionId,
+  isoNow,
+  createSession,
+  getSessionDir,
+  getActiveSession,
+  readSession,
+  updateSession,
+  endSession,
+  appendToTrail,
+  readTrail,
+  recoverContext,
+  checkUnfinishedSessions,
+  generateSessionSummary,
+} from './session-manager.js';
+export type { SessionJson, RecoverySummary } from './session-manager.js';
+
+export {
+  createCorrection,
+  findCorrections,
+  checkCorrectionConflict,
+} from './corrections.js';
+export type { UserCorrectionRecord } from './corrections.js';
+
+export {
+  GuidelineDocumentStore,
+} from './guideline-store.js';
+export type {
+  GuidelineId,
+  GuidelineContent,
+  Guideline,
+  Criticality,
+  GuidelineUpdateParams,
+  GuidelineDocument,
+} from './guideline-store.js';
+
+export {
+  JourneyStore,
+} from './journey-store.js';
+export type {
+  JourneyId,
+  JourneyNodeId,
+  JourneyEdgeId,
+  Journey,
+  JourneyNode,
+  JourneyEdge,
+} from './journey-store.js';
+
+export {
+  projectJourneyToGuidelines,
+  detectJourneyBacktrack,
+} from './journey-projection.js';
+export type { ProjectedGuideline, BacktrackCheck } from './journey-projection.js';

apps/server/src/services/audit/journey-projection.ts

@@ -0,0 +1,189 @@
+import type {
+  Journey,
+  JourneyNode,
+  JourneyEdge,
+  JourneyNodeId,
+  JourneyEdgeId,
+} from './journey-store.js';
+import type { Guideline, GuidelineId, Criticality } from './guideline-store.js';
+
+export interface ProjectedGuideline {
+  id: GuidelineId;
+  content: {
+    condition: string;
+    action: string | null;
+    description: string | null;
+  };
+  criticality: Criticality;
+  creationUtc: string;
+  enabled: boolean;
+  tags: string[];
+  labels: string[];
+  metadata: Record<string, unknown>;
+}
+
+function formatNodeGuidelineId(nodeId: JourneyNodeId, edgeId?: JourneyEdgeId | null): GuidelineId {
+  return `journey_node:${nodeId}${edgeId ? `:${edgeId}` : ''}` as GuidelineId;
+}
+
+export function projectJourneyToGuidelines(
+  journey: Journey,
+  nodes: JourneyNode[],
+  edges: JourneyEdge[],
+): ProjectedGuideline[] {
+  const nodeMap = new Map<JourneyNodeId, JourneyNode>();
+  for (const n of nodes) nodeMap.set(n.id, n);
+
+  const edgeMap = new Map<JourneyEdgeId, JourneyEdge>();
+  for (const e of edges) edgeMap.set(e.id, e);
+
+  const nodeEdges = new Map<JourneyNodeId, JourneyEdge[]>();
+  for (const e of edges) {
+    const list = nodeEdges.get(e.source) || [];
+    list.push(e);
+    nodeEdges.set(e.source, list);
+  }
+
+  const guidelines: Map<GuidelineId, ProjectedGuideline> = new Map();
+  const nodeIndexes = new Map<JourneyNodeId, number>();
+  let index = 0;
+
+  const queue: Array<{ edgeId: JourneyEdgeId | null; nodeId: JourneyNodeId }> = [];
+  const visited = new Set<string>();
+
+  queue.push({ edgeId: null, nodeId: journey.rootId });
+
+  while (queue.length > 0) {
+    const { edgeId, nodeId } = queue.shift()!;
+    const visitKey = `${edgeId || ''}:${nodeId}`;
+    if (visited.has(visitKey)) continue;
+    visited.add(visitKey);
+
+    const node = nodeMap.get(nodeId);
+    if (!node) continue;
+
+    if (!nodeIndexes.has(nodeId)) {
+      index++;
+      nodeIndexes.set(nodeId, index);
+    }
+
+    const edge = edgeId ? edgeMap.get(edgeId) : undefined;
+
+    const baseJourneyNode: Record<string, unknown> = {
+      follow_ups: [],
+      index: String(nodeIndexes.get(nodeId)),
+      journey_id: journey.id,
+      labels: node.labels,
+      tool_ids: node.tools,
+    };
+
+    const edgeJourneyNode = (edge?.metadata?.['journey_node'] as Record<string, unknown>) || {};
+    const nodeJourneyNode = (node.metadata?.['journey_node'] as Record<string, unknown>) || {};
+
+    const mergedJourneyNode = { ...baseJourneyNode, ...nodeJourneyNode, ...edgeJourneyNode };
+
+    const metadata: Record<string, unknown> = {
+      journey_node: mergedJourneyNode,
+    };
+    for (const [k, v] of Object.entries(node.metadata)) {
+      if (k !== 'journey_node') metadata[k] = v;
+    }
+    if (edge) {
+      for (const [k, v] of Object.entries(edge.metadata)) {
+        if (k !== 'journey_node') metadata[k] = v;
+      }
+    }
+
+    const gid = formatNodeGuidelineId(nodeId, edgeId);
+    const guideline: ProjectedGuideline = {
+      id: gid,
+      content: {
+        condition: (edge?.condition) || '',
+        action: node.action,
+        description: node.description,
+      },
+      criticality: 'high' as Criticality,
+      creationUtc: new Date().toISOString(),
+      enabled: true,
+      tags: journey.tags,
+      labels: [...(node.labels || [])],
+      metadata,
+    };
+
+    guidelines.set(gid, guideline);
+
+    const childEdges = nodeEdges.get(nodeId) || [];
+    for (const childEdge of childEdges) {
+      if (visited.has(`${childEdge.id}:${childEdge.target}`)) continue;
+      queue.push({ edgeId: childEdge.id, nodeId: childEdge.target });
+
+      const childGid = formatNodeGuidelineId(childEdge.target, childEdge.id);
+      const followUps = (guideline.metadata['journey_node'] as Record<string, unknown>)['follow_ups'] as string[];
+      if (!followUps.includes(childGid)) {
+        followUps.push(childGid);
+      }
+    }
+  }
+
+  return [...guidelines.values()];
+}
+
+export interface BacktrackCheck {
+  journeyId: string;
+  currentNodeId: JourneyNodeId;
+  previousNodeId: JourneyNodeId;
+  isBacktrack: boolean;
+  recommendation: string | null;
+}
+
+export function detectJourneyBacktrack(
+  journey: Journey,
+  nodes: JourneyNode[],
+  edges: JourneyEdge[],
+  currentNodeId: JourneyNodeId,
+  previousNodeId: JourneyNodeId,
+): BacktrackCheck {
+  const nodeMap = new Map<JourneyNodeId, JourneyNode>();
+  for (const n of nodes) nodeMap.set(n.id, n);
+
+  const adjacency = new Map<JourneyNodeId, JourneyNodeId[]>();
+  for (const e of edges) {
+    const list = adjacency.get(e.source) || [];
+    list.push(e.target);
+    adjacency.set(e.source, list);
+  }
+
+  const isInForwardPath = (from: JourneyNodeId, target: JourneyNodeId): boolean => {
+    const visitedInner = new Set<JourneyNodeId>();
+    const queueInner: JourneyNodeId[] = [from];
+    while (queueInner.length > 0) {
+      const current = queueInner.shift()!;
+      if (current === target) return true;
+      if (visitedInner.has(current)) continue;
+      visitedInner.add(current);
+      for (const next of adjacency.get(current) || []) {
+        if (!visitedInner.has(next)) queueInner.push(next);
+      }
+    }
+    return false;
+  };
+
+  const fromCurToPrev = isInForwardPath(currentNodeId, previousNodeId);
+  const fromPrevToCur = isInForwardPath(previousNodeId, currentNodeId);
+
+  const isBacktrack = !fromPrevToCur && !fromCurToPrev;
+
+  let recommendation: string | null = null;
+  if (isBacktrack && nodeMap.has(previousNodeId)) {
+    const prevNode = nodeMap.get(previousNodeId)!;
+    recommendation = `Detected potential backtrack from '${currentNodeId}' to '${previousNodeId}' (${prevNode.action || 'no action'}). Consider whether this regression is intentional.`;
+  }
+
+  return {
+    journeyId: journey.id,
+    currentNodeId,
+    previousNodeId,
+    isBacktrack,
+    recommendation,
+  };
+}

apps/server/src/services/audit/journey-store.ts

@@ -0,0 +1,360 @@
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
+import { join } from 'node:path';
+import { ensureRunsDir } from './runs-dir.js';
+import type { GuidelineId } from './guideline-store.js';
+
+export type JourneyId = string;
+export type JourneyNodeId = string;
+export type JourneyEdgeId = string;
+
+export interface JourneyNode {
+  id: JourneyNodeId;
+  creationUtc: string;
+  action: string | null;
+  tools: string[];
+  metadata: Record<string, unknown>;
+  description: string | null;
+  labels: string[];
+}
+
+export interface JourneyEdge {
+  id: JourneyEdgeId;
+  creationUtc: string;
+  source: JourneyNodeId;
+  target: JourneyNodeId;
+  condition: string | null;
+  metadata: Record<string, unknown>;
+}
+
+export interface Journey {
+  id: JourneyId;
+  creationUtc: string;
+  description: string;
+  triggers: GuidelineId[];
+  title: string;
+  rootId: JourneyNodeId;
+  tags: string[];
+  labels: string[];
+  priority: number;
+}
+
+interface JourneyDocument {
+  id: string;
+  version: string;
+  creation_utc: string;
+  title: string;
+  description: string;
+  root_id: JourneyNodeId;
+  labels: string[];
+  priority: number;
+}
+
+interface NodeDocument {
+  id: string;
+  node_id: JourneyNodeId;
+  journey_id: JourneyId;
+  creation_utc: string;
+  action: string | null;
+  tools: string[];
+  metadata: Record<string, unknown>;
+  description: string | null;
+  labels: string[];
+}
+
+interface EdgeDocument {
+  id: string;
+  journey_id: JourneyId;
+  creation_utc: string;
+  source: JourneyNodeId;
+  target: JourneyNodeId;
+  condition: string | null;
+  metadata: Record<string, unknown>;
+}
+
+interface TriggerDocument {
+  id: string;
+  journey_id: JourneyId;
+  trigger: GuidelineId;
+  creation_utc: string;
+}
+
+function generateId(): string {
+  const chars = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
+  let result = '';
+  for (let i = 0; i < 10; i++) {
+    result += chars[Math.floor(Math.random() * chars.length)];
+  }
+  return result;
+}
+
+function dbPath(name: string, projectRoot?: string): string {
+  const dir = join(ensureRunsDir(projectRoot), '..', 'journeys');
+  if (!existsSync(dir)) mkdirSync(dir, { recursive: true });
+  return join(dir, `${name}.json`);
+}
+
+function readCollection<T>(name: string, projectRoot?: string): T[] {
+  try {
+    return JSON.parse(readFileSync(dbPath(name, projectRoot), 'utf-8')) as T[];
+  } catch {
+    return [];
+  }
+}
+
+function writeCollection<T>(name: string, data: T[], projectRoot?: string): void {
+  writeFileSync(dbPath(name, projectRoot), JSON.stringify(data, null, 2), 'utf-8');
+}
+
+export class JourneyStore {
+  createJourney(params: {
+    title: string;
+    description: string;
+    triggers?: GuidelineId[];
+    labels?: string[];
+    priority?: number;
+  }, projectRoot?: string): Journey {
+    const id = `jny_${generateId()}`;
+    const rootId = `node_${generateId()}`;
+    const creationUtc = new Date().toISOString();
+
+    const journey: Journey = {
+      id,
+      creationUtc,
+      description: params.description,
+      triggers: params.triggers || [],
+      title: params.title,
+      rootId,
+      tags: [],
+      labels: params.labels || [],
+      priority: params.priority || 0,
+    };
+
+    const journeys = readCollection<JourneyDocument>('journeys', projectRoot);
+    journeys.push({
+      id,
+      version: '0.7.0',
+      creation_utc: creationUtc,
+      title: params.title,
+      description: params.description,
+      root_id: rootId,
+      labels: params.labels || [],
+      priority: params.priority || 0,
+    });
+    writeCollection('journeys', journeys, projectRoot);
+
+    const root: JourneyNode = {
+      id: rootId,
+      creationUtc,
+      action: null,
+      tools: [],
+      metadata: {},
+      description: null,
+      labels: [],
+    };
+    const nodes = readCollection<NodeDocument>('nodes', projectRoot);
+    nodes.push({
+      id: `nd_${generateId()}`,
+      node_id: rootId,
+      journey_id: id,
+      creation_utc: creationUtc,
+      action: null,
+      tools: [],
+      metadata: {},
+      description: null,
+      labels: [],
+    });
+    writeCollection('nodes', nodes, projectRoot);
+
+    return journey;
+  }
+
+  readJourney(id: JourneyId, projectRoot?: string): Journey {
+    const journeys = readCollection<JourneyDocument>('journeys', projectRoot);
+    const doc = journeys.find(j => j.id === id);
+    if (!doc) throw new Error(`Journey '${id}' not found`);
+
+    const triggers = readCollection<TriggerDocument>('triggers', projectRoot)
+      .filter(t => t.journey_id === id)
+      .map(t => t.trigger);
+
+    return {
+      id: doc.id,
+      creationUtc: doc.creation_utc,
+      description: doc.description,
+      triggers,
+      title: doc.title,
+      rootId: doc.root_id,
+      tags: [],
+      labels: doc.labels || [],
+      priority: doc.priority || 0,
+    };
+  }
+
+  deleteJourney(id: JourneyId, projectRoot?: string): void {
+    let journeys = readCollection<JourneyDocument>('journeys', projectRoot);
+    const idx = journeys.findIndex(j => j.id === id);
+    if (idx === -1) throw new Error(`Journey '${id}' not found`);
+    journeys.splice(idx, 1);
+    writeCollection('journeys', journeys, projectRoot);
+
+    let nodes = readCollection<NodeDocument>('nodes', projectRoot);
+    nodes = nodes.filter(n => n.journey_id !== id);
+    writeCollection('nodes', nodes, projectRoot);
+
+    let edges = readCollection<EdgeDocument>('edges', projectRoot);
+    edges = edges.filter(e => e.journey_id !== id);
+    writeCollection('edges', edges, projectRoot);
+
+    let triggers = readCollection<TriggerDocument>('triggers', projectRoot);
+    triggers = triggers.filter(t => t.journey_id !== id);
+    writeCollection('triggers', triggers, projectRoot);
+  }
+
+  listJourneys(projectRoot?: string): Journey[] {
+    const journeys = readCollection<JourneyDocument>('journeys', projectRoot);
+    return journeys.map(j => this.readJourney(j.id, projectRoot));
+  }
+
+  createNode(journeyId: JourneyId, params: {
+    action?: string | null;
+    tools?: string[];
+    description?: string | null;
+    labels?: string[];
+    id?: JourneyNodeId;
+  }, projectRoot?: string): JourneyNode {
+    const nodeId = params.id || `node_${generateId()}`;
+    const creationUtc = new Date().toISOString();
+
+    const node: JourneyNode = {
+      id: nodeId,
+      creationUtc,
+      action: params.action ?? null,
+      tools: params.tools || [],
+      metadata: {},
+      description: params.description ?? null,
+      labels: params.labels || [],
+    };
+
+    const nodes = readCollection<NodeDocument>('nodes', projectRoot);
+    nodes.push({
+      id: `nd_${generateId()}`,
+      node_id: nodeId,
+      journey_id: journeyId,
+      creation_utc: creationUtc,
+      action: node.action,
+      tools: node.tools,
+      metadata: node.metadata,
+      description: node.description,
+      labels: node.labels,
+    });
+    writeCollection('nodes', nodes, projectRoot);
+
+    return node;
+  }
+
+  listNodes(journeyId: JourneyId, projectRoot?: string): JourneyNode[] {
+    const docs = readCollection<NodeDocument>('nodes', projectRoot)
+      .filter(n => n.journey_id === journeyId);
+
+    const nodes = docs.map(d => ({
+      id: d.node_id,
+      creationUtc: d.creation_utc,
+      action: d.action,
+      tools: d.tools,
+      metadata: d.metadata,
+      description: d.description,
+      labels: d.labels || [],
+    }));
+
+    nodes.push({
+      id: 'end' as JourneyNodeId,
+      creationUtc: new Date().toISOString(),
+      action: null,
+      tools: [],
+      metadata: {},
+      description: null,
+      labels: [],
+    });
+
+    return nodes;
+  }
+
+  createEdge(journeyId: JourneyId, params: {
+    source: JourneyNodeId;
+    target: JourneyNodeId;
+    condition?: string | null;
+  }, projectRoot?: string): JourneyEdge {
+    const creationUtc = new Date().toISOString();
+    const edge: JourneyEdge = {
+      id: `edge_${generateId()}`,
+      creationUtc,
+      source: params.source,
+      target: params.target,
+      condition: params.condition ?? null,
+      metadata: {},
+    };
+
+    const edges = readCollection<EdgeDocument>('edges', projectRoot);
+    edges.push({
+      id: edge.id,
+      journey_id: journeyId,
+      creation_utc: creationUtc,
+      source: params.source,
+      target: params.target,
+      condition: params.condition ?? null,
+      metadata: {},
+    });
+    writeCollection('edges', edges, projectRoot);
+
+    return edge;
+  }
+
+  listEdges(journeyId: JourneyId, nodeId?: JourneyNodeId, projectRoot?: string): JourneyEdge[] {
+    let docs = readCollection<EdgeDocument>('edges', projectRoot)
+      .filter(e => e.journey_id === journeyId);
+
+    if (nodeId) {
+      docs = docs.filter(e => e.source === nodeId || e.target === nodeId);
+    }
+
+    return docs.map(d => ({
+      id: d.id,
+      creationUtc: d.creation_utc,
+      source: d.source,
+      target: d.target,
+      condition: d.condition,
+      metadata: d.metadata,
+    }));
+  }
+
+  deleteEdge(edgeId: JourneyEdgeId, projectRoot?: string): void {
+    let edges = readCollection<EdgeDocument>('edges', projectRoot);
+    const idx = edges.findIndex(e => e.id === edgeId);
+    if (idx === -1) throw new Error(`Edge '${edgeId}' not found`);
+    edges.splice(idx, 1);
+    writeCollection('edges', edges, projectRoot);
+  }
+
+  addTrigger(journeyId: JourneyId, trigger: GuidelineId, projectRoot?: string): boolean {
+    const triggers = readCollection<TriggerDocument>('triggers', projectRoot);
+    if (triggers.find(t => t.journey_id === journeyId && t.trigger === trigger)) {
+      return false;
+    }
+    triggers.push({
+      id: `trg_${generateId()}`,
+      journey_id: journeyId,
+      trigger,
+      creation_utc: new Date().toISOString(),
+    });
+    writeCollection('triggers', triggers, projectRoot);
+    return true;
+  }
+
+  removeTrigger(journeyId: JourneyId, trigger: GuidelineId, projectRoot?: string): boolean {
+    let triggers = readCollection<TriggerDocument>('triggers', projectRoot);
+    const len = triggers.length;
+    triggers = triggers.filter(t => !(t.journey_id === journeyId && t.trigger === trigger));
+    writeCollection('triggers', triggers, projectRoot);
+    return triggers.length < len;
+  }
+}

apps/server/src/services/audit/runs-dir.ts

@@ -0,0 +1,111 @@
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
+import { join, resolve } from 'node:path';
+
+export const INDEX_SCHEMA_VERSION = '1.1';
+export const GITIGNORE_CONTENT = `# boocode audit runs
+/*
+!index.json
+`;
+
+export interface IndexEntry {
+  id: string;
+  type: string;
+  status: string;
+  task?: string;
+  skill?: string;
+  created?: string;
+  last_updated?: string;
+  record_count?: number;
+  anomaly_count?: number;
+  max_anomaly_level?: string;
+}
+
+export interface IndexFile {
+  schema_version: string;
+  entries: IndexEntry[];
+}
+
+function findRunsDirFrom(start: string): string {
+  const explicit = process.env['AUDIT_DOT_DIR']?.trim();
+  const candidates = explicit ? [explicit] : ['.boo'];
+  let cur = resolve(start);
+  while (true) {
+    for (const basename of candidates) {
+      const candidate = join(cur, basename, 'runs');
+      if (existsSync(candidate)) return candidate;
+    }
+    const parent = resolve(cur, '..');
+    if (parent === cur) break;
+    cur = parent;
+  }
+  const defaultBasename = explicit || '.boo';
+  return join(resolve(start), defaultBasename, 'runs');
+}
+
+export function findRunsDir(projectRoot?: string): string {
+  return findRunsDirFrom(projectRoot || process.cwd());
+}
+
+export function ensureRunsDir(projectRoot?: string): string {
+  const dir = findRunsDir(projectRoot);
+  if (!existsSync(dir)) {
+    mkdirSync(dir, { recursive: true });
+    const gitignorePath = join(dir, '.gitignore');
+    if (!existsSync(gitignorePath)) {
+      writeFileSync(gitignorePath, GITIGNORE_CONTENT, 'utf-8');
+    }
+  }
+  return dir;
+}
+
+export function readCurrentSession(projectRoot?: string): string | null {
+  const path = join(ensureRunsDir(projectRoot), '.current_session');
+  try {
+    return readFileSync(path, 'utf-8').trim();
+  } catch {
+    return null;
+  }
+}
+
+export function writeCurrentSession(sessionId: string, projectRoot?: string): void {
+  writeFileSync(join(ensureRunsDir(projectRoot), '.current_session'), sessionId, 'utf-8');
+}
+
+export function clearCurrentSession(projectRoot?: string): void {
+  const path = join(ensureRunsDir(projectRoot), '.current_session');
+  try {
+    writeFileSync(path, '', 'utf-8');
+  } catch {
+    // silent
+  }
+}
+
+export function readIndex(projectRoot?: string): IndexFile {
+  const path = join(ensureRunsDir(projectRoot), 'index.json');
+  try {
+    return JSON.parse(readFileSync(path, 'utf-8')) as IndexFile;
+  } catch {
+    return { schema_version: INDEX_SCHEMA_VERSION, entries: [] };
+  }
+}
+
+export function writeIndex(index: IndexFile, projectRoot?: string): void {
+  const runsDir = ensureRunsDir(projectRoot);
+  writeFileSync(join(runsDir, 'index.json'), JSON.stringify(index, null, 2), 'utf-8');
+}
+
+export function updateIndexEntry(entry: IndexEntry, projectRoot?: string): void {
+  const idx = readIndex(projectRoot);
+  const existing = idx.entries.find(e => e.id === entry.id);
+  if (existing) {
+    Object.assign(existing, entry);
+  } else {
+    idx.entries.push({ ...entry });
+  }
+  writeIndex(idx, projectRoot);
+}
+
+export function findInProgressSessions(projectRoot?: string): IndexEntry[] {
+  const idx = readIndex(projectRoot);
+  return idx.entries.filter(e => e.status === 'in_progress');
+}

apps/server/src/services/audit/session-manager.ts

@@ -0,0 +1,236 @@
+import { appendFileSync, existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
+import { join } from 'node:path';
+import {
+  ensureRunsDir,
+  readCurrentSession,
+  writeCurrentSession,
+  clearCurrentSession,
+  updateIndexEntry,
+  findInProgressSessions,
+  readIndex,
+  type IndexEntry,
+} from './runs-dir.js';
+
+export interface SessionJson {
+  session_id: string;
+  task: string;
+  start_time: string;
+  end_time?: string;
+  status: 'in_progress' | 'completed';
+  expected_record_types?: string[];
+  total_records?: number;
+}
+
+export function generateSessionId(): string {
+  const now = new Date();
+  const y = now.getFullYear();
+  const m = String(now.getMonth() + 1).padStart(2, '0');
+  const d = String(now.getDate()).padStart(2, '0');
+  const h = String(now.getHours()).padStart(2, '0');
+  const min = String(now.getMinutes()).padStart(2, '0');
+  return `adhoc_${y}${m}${d}_${h}${min}`;
+}
+
+export function isoNow(): string {
+  return new Date().toISOString();
+}
+
+export function createSession(
+  task: string,
+  sessionId?: string,
+  projectRoot?: string,
+): string {
+  const sid = sessionId || generateSessionId();
+  const runsDir = ensureRunsDir(projectRoot);
+  const sessionDir = join(runsDir, sid);
+  mkdirSync(sessionDir, { recursive: true });
+
+  const session: SessionJson = {
+    session_id: sid,
+    task,
+    start_time: isoNow(),
+    status: 'in_progress',
+    expected_record_types: ['data', 'change', 'conversation'],
+  };
+
+  writeFileSync(join(sessionDir, 'session.json'), JSON.stringify(session, null, 2), 'utf-8');
+  writeCurrentSession(sid, projectRoot);
+
+  updateIndexEntry({
+    id: sid,
+    type: 'adhoc',
+    status: 'in_progress',
+    task,
+    created: session.start_time,
+    last_updated: session.start_time,
+  }, projectRoot);
+
+  return sid;
+}
+
+export function getSessionDir(sessionId: string, projectRoot?: string): string {
+  return join(ensureRunsDir(projectRoot), sessionId);
+}
+
+export function getActiveSession(projectRoot?: string): SessionJson | null {
+  const sid = readCurrentSession(projectRoot);
+  if (!sid) return null;
+  return readSession(sid, projectRoot);
+}
+
+export function readSession(sessionId: string, projectRoot?: string): SessionJson | null {
+  const path = join(getSessionDir(sessionId, projectRoot), 'session.json');
+  try {
+    return JSON.parse(readFileSync(path, 'utf-8')) as SessionJson;
+  } catch {
+    return null;
+  }
+}
+
+export function updateSession(
+  sessionId: string,
+  updates: Partial<SessionJson>,
+  projectRoot?: string,
+): void {
+  const session = readSession(sessionId, projectRoot) || { session_id: sessionId, task: '', start_time: isoNow(), status: 'in_progress' as const };
+  Object.assign(session, updates);
+  writeFileSync(
+    join(getSessionDir(sessionId, projectRoot), 'session.json'),
+    JSON.stringify(session, null, 2),
+    'utf-8',
+  );
+}
+
+export function endSession(sessionId: string, projectRoot?: string): void {
+  updateSession(sessionId, { status: 'completed', end_time: isoNow() }, projectRoot);
+  updateIndexEntry({ id: sessionId, type: 'adhoc', status: 'completed', last_updated: isoNow() }, projectRoot);
+  clearCurrentSession(projectRoot);
+}
+
+export function appendToTrail(sessionId: string, records: Record<string, unknown>[], projectRoot?: string): void {
+  const trailPath = join(getSessionDir(sessionId, projectRoot), 'audit_trail.jsonl');
+  const lines = records.map(r => JSON.stringify(r)).join('\n') + '\n';
+  appendFileSync(trailPath, lines, 'utf-8');
+}
+
+export function readTrail(sessionId: string, projectRoot?: string): Record<string, unknown>[] {
+  const trailPath = join(getSessionDir(sessionId, projectRoot), 'audit_trail.jsonl');
+  try {
+    const content = readFileSync(trailPath, 'utf-8').trim();
+    if (!content) return [];
+    return content.split('\n').filter(Boolean).map(line => JSON.parse(line) as Record<string, unknown>);
+  } catch {
+    return [];
+  }
+}
+
+export interface RecoverySummary {
+  sessionId: string;
+  task: string;
+  recentActivity: IndexEntry[];
+  userCorrections: Record<string, unknown>[];
+  unresolvedIssues: string[];
+  recommendedPriorities: string[];
+  level: number;
+}
+
+export function recoverContext(
+  sessionId: string,
+  level: number,
+  projectRoot?: string,
+): RecoverySummary {
+  const session = readSession(sessionId, projectRoot);
+  const idx = readIndex(projectRoot);
+  const recentActivity = idx.entries.slice(-5);
+  const trail = readTrail(sessionId, projectRoot);
+  const userCorrections = trail.filter(r => r['action_type'] === 'user_correction');
+
+  const summary: RecoverySummary = {
+    sessionId,
+    task: session?.task || '(unknown)',
+    recentActivity,
+    userCorrections,
+    unresolvedIssues: [],
+    recommendedPriorities: [],
+    level,
+  };
+
+  if (level >= 1) {
+    const last = trail.slice(-3);
+    if (last.length > 0) {
+      summary.recommendedPriorities.push(`Last action: ${JSON.stringify(last[last.length - 1]?.['action'] || 'none')}`);
+    }
+  }
+
+  if (level >= 3) {
+    summary.recommendedPriorities.push(`Full trail: ${trail.length} records`);
+  }
+
+  let checkCount = 0;
+  for (const entry of recentActivity) {
+    if (entry.status === 'in_progress' && entry.id !== sessionId) {
+      summary.unresolvedIssues.push(`Unfinished session: ${entry.id} (${entry.task || 'no task'})`);
+      checkCount++;
+      if (checkCount >= 3) break;
+    }
+  }
+
+  return summary;
+}
+
+export function checkUnfinishedSessions(projectRoot?: string): IndexEntry[] {
+  return findInProgressSessions(projectRoot);
+}
+
+export function generateSessionSummary(sessionId: string, projectRoot?: string): string {
+  const session = readSession(sessionId, projectRoot);
+  const trail = readTrail(sessionId, projectRoot);
+  const corrections = trail.filter(r => r['action_type'] === 'user_correction');
+  const changes = trail.filter(r => r['action'] === 'edit_file' || r['action'] === 'create_file' || r['action'] === 'delete_file');
+
+  const lines: string[] = [
+    `# Session Summary | ${sessionId}`,
+    '',
+    `## Task: ${session?.task || '(unknown)'}`,
+    `## Time: ${session?.start_time || '?'} → ${session?.end_time || 'in_progress'}`,
+    `## Status: ${session?.status || 'unknown'}`,
+    '',
+    '## Completed Work',
+  ];
+
+  for (const r of trail) {
+    if (r['action']) {
+      lines.push(`- ${r['action']}: ${r['detail'] || r['reason'] || '(no detail)'}`);
+    }
+  }
+
+  if (corrections.length > 0) {
+    lines.push('', '## User Corrections');
+    for (const c of corrections) {
+      lines.push(`- Original: ${c['original_claim']}`);
+      lines.push(`  Correction: ${c['correction']}`);
+      if (c['principle_extracted']) {
+        lines.push(`  Principle: ${c['principle_extracted']}`);
+      }
+    }
+  }
+
+  if (changes.length > 0) {
+    lines.push('', '## Files Changed');
+    const fileSet = new Set<string>();
+    for (const c of changes) {
+      const files = c['files'];
+      if (Array.isArray(files)) {
+        for (const f of files) fileSet.add(String(f));
+      }
+    }
+    for (const f of fileSet) lines.push(`- ${f}`);
+  }
+
+  lines.push('', '## Stats');
+  lines.push(`- Total records: ${trail.length}`);
+  lines.push(`- Corrections: ${corrections.length}`);
+  lines.push(`- File changes: ${changes.length}`);
+
+  return lines.join('\n');
+}

apps/server/src/services/git_diff.ts

@@ -271,7 +271,9 @@ function buildNumstatMap(
 async function getUncommittedDiff(
   gitRoot: string,
   inProgress: string | null,
+  ignoreWhitespace = false,
 ): Promise<GitDiffResult> {
+  const ws = ignoreWhitespace ? ['-w'] : [];
   const hasCommits = (await runGit(['rev-parse', '--verify', 'HEAD'], gitRoot)) !== null;
 
   const [nameStatusOut, cachedNameStatusOut, untrackedOut, numstatOut, diffOut, cachedDiffOut] =
@@ -284,10 +286,10 @@ async function getUncommittedDiff(
         : runGit(['diff', '--cached', '--name-status'], gitRoot),
       runGit(['ls-files', '--others', '--exclude-standard'], gitRoot),
       hasCommits ? runGit(['diff', '--numstat', 'HEAD'], gitRoot) : Promise.resolve(''),
-      hasCommits ? runGit(['diff', 'HEAD'], gitRoot) : Promise.resolve(''),
+      hasCommits ? runGit(['diff', ...ws, 'HEAD'], gitRoot) : Promise.resolve(''),
       hasCommits
-        ? runGit(['diff', '--cached', 'HEAD'], gitRoot)
+        ? runGit(['diff', ...ws, '--cached', 'HEAD'], gitRoot)
-        : runGit(['diff', '--cached'], gitRoot),
+        : runGit(['diff', ...ws, '--cached'], gitRoot),
     ]);
 
   const allChanged = parseNameStatus(nameStatusOut ?? '');
@@ -347,11 +349,13 @@ async function getCommittedDiff(
   base: string,
   label: string,
   inProgress: string | null,
+  ignoreWhitespace = false,
 ): Promise<GitDiffResult> {
+  const ws = ignoreWhitespace ? ['-w'] : [];
   const [nameStatusOut, numstatOut, diffOut] = await Promise.all([
     runGit(['diff', '--name-status', base, 'HEAD'], gitRoot),
     runGit(['diff', '--numstat', base, 'HEAD'], gitRoot),
-    runGit(['diff', base, 'HEAD'], gitRoot),
+    runGit(['diff', ...ws, base, 'HEAD'], gitRoot),
   ]);
 
   const allChanged = parseNameStatus(nameStatusOut ?? '');
@@ -383,23 +387,23 @@ async function getCommittedDiff(
  * the directory is not a git repository. On a null committed-mode base, falls
  * back to uncommitted and labels the result accordingly.
  */
-export async function getGitDiff(cwd: string, mode: GitDiffMode): Promise<GitDiffResult | null> {
+export async function getGitDiff(cwd: string, mode: GitDiffMode, ignoreWhitespace?: boolean): Promise<GitDiffResult | null> {
   const gitRoot = await resolveGitRoot(cwd);
   if (!gitRoot) return null;
 
   const inProgress = await detectInProgress(gitRoot);
 
   if (mode === 'uncommitted') {
-    return getUncommittedDiff(gitRoot, inProgress);
+    return getUncommittedDiff(gitRoot, inProgress, ignoreWhitespace ?? false);
   }
 
   const { base, label } = await resolveCommittedBase(gitRoot);
   if (!base) {
     // Fall back to uncommitted with a descriptive label
-    const result = await getUncommittedDiff(gitRoot, inProgress);
+    const result = await getUncommittedDiff(gitRoot, inProgress, ignoreWhitespace ?? false);
     return { ...result, base_label: label };
   }
-  return getCommittedDiff(gitRoot, base, label, inProgress);
+  return getCommittedDiff(gitRoot, base, label, inProgress, ignoreWhitespace ?? false);
 }
 
 // ── Phase 2: Write helpers ─────────────────────────────────────────────────

apps/server/src/services/inference/dcp/__tests__/deduplication.test.ts

@@ -0,0 +1,33 @@
+import { describe, it, expect } from 'vitest';
+import { deduplicate } from '../strategies/deduplication.js';
+import type { DcpMessage } from '../messages.js';
+
+describe('deduplicate', () => {
+  it('removes consecutive identical tool_call+tool_result pairs', () => {
+    const messages: DcpMessage[] = [
+      { role: 'user', content: 'search for x' },
+      { role: 'assistant', content: '', tool_calls: [{ id: '1', name: 'grep', arguments: '{}' }] },
+      { role: 'tool', content: 'result1', tool_call_id: '1' },
+      // Duplicate pair
+      { role: 'assistant', content: '', tool_calls: [{ id: '2', name: 'grep', arguments: '{}' }] },
+      { role: 'tool', content: 'result1', tool_call_id: '2' },
+    ];
+
+    const { messages: result, stats } = deduplicate(messages);
+    expect(result).toHaveLength(3); // user + first pair
+    expect(stats.removedCount).toBe(2);
+  });
+
+  it('preserves non-duplicate content', () => {
+    const messages: DcpMessage[] = [
+      { role: 'assistant', content: '', tool_calls: [{ id: '1', name: 'grep', arguments: '{}' }] },
+      { role: 'tool', content: 'result1', tool_call_id: '1' },
+      { role: 'assistant', content: '', tool_calls: [{ id: '2', name: 'grep', arguments: '{}' }] },
+      { role: 'tool', content: 'result2', tool_call_id: '2' }, // Different result
+    ];
+
+    const { messages: result, stats } = deduplicate(messages);
+    expect(result).toHaveLength(4);
+    expect(stats.removedCount).toBe(0);
+  });
+});

apps/server/src/services/inference/dcp/__tests__/messages.test.ts

@@ -0,0 +1,22 @@
+import { describe, it, expect } from 'vitest';
+import { toDcpMessages, fromDcpMessages } from '../messages.js';
+
+describe('toDcpMessages', () => {
+  it('converts user messages', () => {
+    const result = toDcpMessages([{ role: 'user', content: 'hello' }]);
+    expect(result[0].role).toBe('user');
+    expect(result[0].content).toBe('hello');
+  });
+
+  it('marks Error: content as isError', () => {
+    const result = toDcpMessages([{ role: 'tool', content: 'Error: file not found', tool_call_id: '1' }]);
+    expect(result[0].isError).toBe(true);
+  });
+});
+
+describe('fromDcpMessages', () => {
+  it('round-trips messages', () => {
+    const original = [{ role: 'user', content: 'hello' }];
+    expect(fromDcpMessages(toDcpMessages(original))).toEqual(original);
+  });
+});

apps/server/src/services/inference/dcp/__tests__/purge-errors.test.ts

@@ -0,0 +1,33 @@
+import { describe, it, expect } from 'vitest';
+import { purgeErrors } from '../strategies/purge-errors.js';
+import type { DcpMessage } from '../messages.js';
+
+describe('purgeErrors', () => {
+  it('removes tool results where content starts with Error:', () => {
+    const messages: DcpMessage[] = [
+      { role: 'tool', content: 'Error: file not found', tool_call_id: '1' },
+      { role: 'tool', content: '{"files":[]}', tool_call_id: '2' },
+    ];
+    const { messages: result, stats } = purgeErrors(messages);
+    expect(result).toHaveLength(1);
+    expect(stats.removedCount).toBe(1);
+  });
+
+  it('removes empty tool results', () => {
+    const messages: DcpMessage[] = [
+      { role: 'tool', content: '', tool_call_id: '1' },
+    ];
+    const { messages: result, stats } = purgeErrors(messages);
+    expect(result).toHaveLength(0);
+    expect(stats.removedCount).toBe(1);
+  });
+
+  it('preserves valid tool results', () => {
+    const messages: DcpMessage[] = [
+      { role: 'tool', content: '{"files":["a.ts"]}', tool_call_id: '1' },
+    ];
+    const { messages: result, stats } = purgeErrors(messages);
+    expect(result).toHaveLength(1);
+    expect(stats.removedCount).toBe(0);
+  });
+});

apps/server/src/services/inference/dcp/__tests__/transform.test.ts

@@ -0,0 +1,25 @@
+import { describe, it, expect } from 'vitest';
+import { transformMessages } from '../transform.js';
+import type { DcpMessage } from '../messages.js';
+
+describe('transformMessages', () => {
+  it('applies dedup then purge in order', () => {
+    const input: DcpMessage[] = [
+      { role: 'user', content: 'hello' },
+      { role: 'assistant', content: '', tool_calls: [{ id: '1', name: 'grep', arguments: '{}' }] },
+      { role: 'tool', content: 'result', tool_call_id: '1' },
+      { role: 'assistant', content: '', tool_calls: [{ id: '2', name: 'grep', arguments: '{}' }] },
+      { role: 'tool', content: 'result', tool_call_id: '2' }, // Dup
+    ];
+
+    const { messages, stats } = transformMessages('test-chat', input);
+    expect(stats.removedCount).toBeGreaterThan(0);
+    expect(messages.length).toBeLessThan(input.length);
+  });
+
+  it('handles empty input', () => {
+    const { messages, stats } = transformMessages('empty', []);
+    expect(messages).toHaveLength(0);
+    expect(stats.removedCount).toBe(0);
+  });
+});

apps/server/src/services/inference/dcp/index.ts

@@ -0,0 +1,4 @@
+export { transformMessages } from './transform.js';
+export type { DcpMessage } from './messages.js';
+export { toDcpMessages, fromDcpMessages } from './messages.js';
+export { getDcpState, clearDcpState } from './state.js';

apps/server/src/services/inference/dcp/messages.ts

@@ -0,0 +1,34 @@
+// DCP message shape adapter.
+// Converts between BooCode MessagePart[] and the DCP internal shape.
+// Clean-room implementation — no AGPL source copied.
+
+export interface DcpMessage {
+  role: 'user' | 'assistant' | 'tool';
+  content: string;
+  tool_call_id?: string;
+  tool_calls?: Array<{ id: string; name: string; arguments: string }>;
+  isError?: boolean;
+}
+
+export function toDcpMessages(parts: any[]): DcpMessage[] {
+  return parts.map((p: any) => {
+    const msg: DcpMessage = { role: p.role, content: p.content ?? '' };
+    if (p.tool_call_id) msg.tool_call_id = p.tool_call_id;
+    if (p.tool_calls) msg.tool_calls = p.tool_calls;
+    if (p.isError) msg.isError = true;
+    if (p.role === 'tool' && p.content && p.content.startsWith('Error:')) {
+      msg.isError = true;
+    }
+    return msg;
+  });
+}
+
+export function fromDcpMessages(msgs: DcpMessage[]): any[] {
+  return msgs.map((m) => ({
+    role: m.role,
+    content: m.content,
+    ...(m.tool_call_id ? { tool_call_id: m.tool_call_id } : {}),
+    ...(m.tool_calls ? { tool_calls: m.tool_calls } : {}),
+    ...(m.isError ? { isError: true } : {}),
+  }));
+}

apps/server/src/services/inference/dcp/state.ts

@@ -0,0 +1,27 @@
+// Per-chat session state for DCP.
+// Tracks last transform timestamp and message count to avoid re-processing.
+
+interface ChatDcpState {
+  lastTransformAt: number;
+  lastMessageCount: number;
+}
+
+const chatStates = new Map<string, ChatDcpState>();
+
+export function getDcpState(chatId: string): ChatDcpState | undefined {
+  return chatStates.get(chatId);
+}
+
+export function setDcpState(chatId: string, messageCount: number): void {
+  chatStates.set(chatId, { lastTransformAt: Date.now(), lastMessageCount: messageCount });
+}
+
+export function clearDcpState(chatId: string): void {
+  chatStates.delete(chatId);
+}
+
+export function shouldTransform(chatId: string, messageCount: number): boolean {
+  const state = chatStates.get(chatId);
+  if (!state) return true;
+  return state.lastMessageCount !== messageCount;
+}

apps/server/src/services/inference/dcp/strategies/deduplication.ts

@@ -0,0 +1,50 @@
+import type { DcpMessage } from '../messages.js';
+
+export function deduplicate(messages: DcpMessage[]): { messages: DcpMessage[]; stats: { removedCount: number; freedTokens: number } } {
+  const result: DcpMessage[] = [];
+  let removedCount = 0;
+  let freedTokens = 0;
+  let i = 0;
+
+  while (i < messages.length) {
+    const current: DcpMessage = messages[i]!;
+    const next = messages[i + 1];
+
+    if (
+      current.role === 'assistant' &&
+      current.tool_calls &&
+      next &&
+      next.role === 'tool' &&
+      next.tool_call_id === current.tool_calls[0]?.id
+    ) {
+      const nextNext = messages[i + 2];
+      const nextNextNext = messages[i + 3];
+
+      if (
+        nextNext &&
+        nextNext.role === 'assistant' &&
+        nextNext.tool_calls &&
+        nextNextNext &&
+        nextNextNext.role === 'tool' &&
+        nextNextNext.tool_call_id === nextNext.tool_calls[0]?.id &&
+        nextNext.tool_calls[0]?.name === current.tool_calls[0]?.name &&
+        nextNext.tool_calls[0]?.arguments === current.tool_calls[0]?.arguments &&
+        nextNextNext.content === next.content
+      ) {
+        result.push(current, next);
+        i += 4;
+        removedCount += 2;
+        freedTokens += Math.ceil(nextNext.content.length / 4);
+        freedTokens += Math.ceil(current.content.length / 4);
+      } else {
+        result.push(current);
+        i++;
+      }
+    } else {
+      result.push(current);
+      i++;
+    }
+  }
+
+  return { messages: result, stats: { removedCount, freedTokens } };
+}

apps/server/src/services/inference/dcp/strategies/purge-errors.ts

@@ -0,0 +1,34 @@
+// Purge-errors strategy — removes failed/empty tool_result entries.
+// Clean-room implementation.
+
+import type { DcpMessage } from '../messages.js';
+
+const ERROR_PREFIXES = ['Error:', 'error:', 'Error: '];
+const DEFAULT_WINDOW = 5;
+
+export function purgeErrors(
+  messages: DcpMessage[],
+  windowSize: number = DEFAULT_WINDOW,
+): { messages: DcpMessage[]; stats: { removedCount: number; freedTokens: number } } {
+  const result: DcpMessage[] = [];
+  let removedCount = 0;
+  let freedTokens = 0;
+
+  for (const msg of messages) {
+    if (msg.role === 'tool') {
+      const shouldRemove =
+        msg.isError ||
+        ERROR_PREFIXES.some((p) => msg.content.startsWith(p)) ||
+        msg.content.trim() === '';
+
+      if (shouldRemove) {
+        removedCount++;
+        freedTokens += Math.ceil(msg.content.length / 4);
+        continue; // Skip this message
+      }
+    }
+    result.push(msg);
+  }
+
+  return { messages: result, stats: { removedCount, freedTokens } };
+}

apps/server/src/services/inference/dcp/transform.ts

@@ -0,0 +1,52 @@
+// Transform orchestrator — runs DCP strategies in sequence.
+// Clean-room implementation.
+
+import type { DcpMessage } from './messages.js';
+import { deduplicate } from './strategies/deduplication.js';
+import { purgeErrors } from './strategies/purge-errors.js';
+import { getDcpState, setDcpState, shouldTransform } from './state.js';
+
+export interface TransformStats {
+  removedCount: number;
+  freedTokens: number;
+  dedupRemoved: number;
+  purgeRemoved: number;
+}
+
+export interface TransformResult {
+  messages: DcpMessage[];
+  stats: TransformStats;
+}
+
+export function transformMessages(chatId: string, messages: DcpMessage[]): TransformResult {
+  if (!shouldTransform(chatId, messages.length)) {
+    return { messages, stats: { removedCount: 0, freedTokens: 0, dedupRemoved: 0, purgeRemoved: 0 } };
+  }
+
+  let m = messages;
+
+  // Step 1: Deduplicate
+  const dedupResult = deduplicate(m);
+  m = dedupResult.messages;
+  const dedupRemoved = dedupResult.stats.removedCount;
+
+  // Step 2: Purge errors
+  const purgeResult = purgeErrors(m);
+  m = purgeResult.messages;
+  const purgeRemoved = purgeResult.stats.removedCount;
+
+  const totalRemoved = dedupRemoved + purgeRemoved;
+  const totalFreed = dedupResult.stats.freedTokens + purgeResult.stats.freedTokens;
+
+  setDcpState(chatId, messages.length);
+
+  return {
+    messages: m,
+    stats: {
+      removedCount: totalRemoved,
+      freedTokens: totalFreed,
+      dedupRemoved,
+      purgeRemoved,
+    },
+  };
+}

apps/server/src/services/inference/loop-detectors.ts

@@ -0,0 +1,68 @@
+// Loop detectors — detects repetitive patterns in assistant output
+// that indicate a model is stuck in a loop.
+
+export interface LoopDetectionResult {
+  isLoop: boolean;
+  reason?: string;
+  confidence: number; // 0-1
+}
+
+const REPEATED_PHRASE_MIN_COUNT = 4;
+const REPEATED_TOOL_MIN_COUNT = 3;
+
+export function detectContentRepeat(messages: string[]): LoopDetectionResult {
+  if (messages.length < REPEATED_PHRASE_MIN_COUNT) {
+    return { isLoop: false, confidence: 0 };
+  }
+
+  const recent = messages.slice(-REPEATED_PHRASE_MIN_COUNT);
+  const unique = new Set(recent);
+
+  if (unique.size === 1) {
+    return {
+      isLoop: true,
+      reason: `Same content repeated ${REPEATED_PHRASE_MIN_COUNT} times`,
+      confidence: 0.9,
+    };
+  }
+
+  if (unique.size <= 2 && recent.length >= 4) {
+    return {
+      isLoop: true,
+      reason: 'Content oscillating between two variants',
+      confidence: 0.7,
+    };
+  }
+
+  return { isLoop: false, confidence: 0 };
+}
+
+export function detectToolLoop(toolNames: string[]): LoopDetectionResult {
+  if (toolNames.length < REPEATED_TOOL_MIN_COUNT) return { isLoop: false, confidence: 0 };
+
+  const recent = toolNames.slice(-REPEATED_TOOL_MIN_COUNT);
+  const unique = new Set(recent);
+
+  if (unique.size === 1) {
+    return {
+      isLoop: true,
+      reason: `Same tool "${recent[0]}" called ${REPEATED_TOOL_MIN_COUNT} times consecutively`,
+      confidence: 0.85,
+    };
+  }
+
+  return { isLoop: false, confidence: 0 };
+}
+
+export function detectDoomLoop(
+  messages: string[],
+  toolNames: string[],
+): LoopDetectionResult {
+  const contentResult = detectContentRepeat(messages);
+  if (contentResult.isLoop) return contentResult;
+
+  const toolResult = detectToolLoop(toolNames);
+  if (toolResult.isLoop) return toolResult;
+
+  return { isLoop: false, confidence: 0 };
+}

apps/server/src/services/inference/provider.ts

@@ -57,11 +57,21 @@ interface ConfigLike {
   LLAMA_SIDECAR_URL?: string;
 }
 
-export function resolveRoute(agent: AgentLike | null): RoutingInfo {
+export function resolveRoute(
+  agent: AgentLike | null,
+  config?: ConfigLike,
+): RoutingInfo {
+  // When llama_extra_args are explicitly set, route through sidecar with them.
   const flags = agent?.llama_extra_args;
   if (flags && flags.length > 0) {
     return { route: 'sidecar', flags };
   }
+  // When LLAMA_SIDECAR_URL is configured (even without per-agent flags),
+  // route through sidecar to pick up the default base args (cache quant,
+  // spec decoding, slot save, etc.). Fall back to llama-swap otherwise.
+  if (config?.LLAMA_SIDECAR_URL) {
+    return { route: 'sidecar', flags: [] };
+  }
   return { route: 'swap', flags: null };
 }
 
@@ -70,15 +80,13 @@ export function upstreamModel(
   modelId: string,
   agent?: AgentLike | null,
 ): LanguageModel {
-  const { route, flags } = resolveRoute(agent ?? null);
+  const { route, flags } = resolveRoute(agent ?? null, config);
   if (route === 'sidecar') {
     const url = config.LLAMA_SIDECAR_URL;
     if (!url) {
-      throw new Error(
+      throw new Error(`Sidecar route selected but LLAMA_SIDECAR_URL is not set`);
-        `Agent has llama_extra_args but LLAMA_SIDECAR_URL is not set`,
-      );
     }
-    return sidecarProvider(url, flags!).chatModel(modelId);
+    return sidecarProvider(url, (flags ?? [])).chatModel(modelId);
   }
   return getSwapProvider(config.LLAMA_SWAP_URL).chatModel(modelId);
 }

apps/server/src/services/inference/tool-shim.ts

@@ -0,0 +1,45 @@
+// ToolShim — recovers structured tool calls from plain-text model output.
+// When the model emits tool calls as plain text instead of structured JSON,
+// this shim attempts to parse and recover them.
+
+export interface ParsedToolCall {
+  id: string;
+  name: string;
+  arguments: string;
+}
+
+const TOOL_CALL_PATTERN = /<tool_call>\s*<name>(.+?)<\/name>\s*<arguments>(.+?)<\/arguments>\s*<\/tool_call>/gs;
+const JSON_TOOL_PATTERN = /\{\s*"name":\s*"([^"]+)",\s*"arguments":\s*({.+?})\s*\}/gs;
+
+export function extractToolCalls(text: string): ParsedToolCall[] {
+  const calls: ParsedToolCall[] = [];
+  let match: RegExpExecArray | null;
+
+  // Try XML-style tool calls (common in Qwen output)
+  const xmlRegex = new RegExp(TOOL_CALL_PATTERN);
+  while ((match = xmlRegex.exec(text)) !== null) {
+    calls.push({
+      id: `call_${calls.length}`,
+      name: match[1]!.trim(),
+      arguments: match[2]!.trim(),
+    });
+  }
+
+  if (calls.length > 0) return calls;
+
+  // Try JSON-style tool calls
+  const jsonRegex = new RegExp(JSON_TOOL_PATTERN);
+  while ((match = jsonRegex.exec(text)) !== null) {
+    calls.push({
+      id: `call_${calls.length}`,
+      name: match[1]!.trim(),
+      arguments: match[2]!.trim(),
+    });
+  }
+
+  return calls;
+}
+
+export function hasToolCallMarkup(text: string): boolean {
+  return TOOL_CALL_PATTERN.test(text) || JSON_TOOL_PATTERN.test(text);
+}

apps/server/src/services/inference/turn.ts

@@ -21,6 +21,7 @@ import {
   buildMessagesPayload,
   loadContext,
 } from './payload.js';
+import { toDcpMessages, transformMessages, fromDcpMessages } from './dcp/index.js';
 import {
   finalizeCompletion,
   finalizeEmpty,
@@ -156,9 +157,20 @@ export async function runAssistantTurn(
       ctx.log.warn({ sessionId }, 'inference: session or project missing mid-loop');
       break;
     }
-    const { session: iterSession, project: iterProject, history } = loaded;
+    let { session: iterSession, project: iterProject, history } = loaded;
     const projectRoot = await resolveProjectRoot(iterProject.path);
 
+    try {
+      const dcpMsgs = toDcpMessages(history);
+      const { messages: pruned, stats } = transformMessages(chatId, dcpMsgs);
+      if (stats.removedCount > 0) {
+        ctx.log.info({ chatId, ...stats }, 'dcp: transform removed messages');
+        history = fromDcpMessages(pruned) as typeof history;
+      }
+    } catch (err) {
+      ctx.log.warn({ err: err instanceof Error ? err.message : String(err), chatId }, 'dcp: transform skipped');
+    }
+
     // v1.14.0: log step boundary for instrumentation. step_start parts are in
     // the schema CHECK but not emitted here — writing to the assistant message
     // before the stream phase creates a sequence-0 collision with

apps/server/src/services/memory/__tests__/bm25.test.ts

@@ -0,0 +1,37 @@
+import { describe, it, expect } from 'vitest';
+import { Bm25Ranker } from '../bm25.js';
+
+describe('Bm25Ranker', () => {
+  it('scores documents by term frequency', () => {
+    const ranker = new Bm25Ranker();
+    ranker.fit(['the cat sat on the mat', 'the dog chased the cat', 'the bird flew over the mat']);
+    const results = ranker.rank('cat mat');
+    expect(results.length).toBeGreaterThan(0);
+    expect(results[0]!.score).toBeGreaterThan(0);
+  });
+
+  it('returns empty for no matches', () => {
+    const ranker = new Bm25Ranker();
+    ranker.fit(['aaa bbb', 'ccc ddd']);
+    const results = ranker.rank('zzz');
+    expect(results).toHaveLength(0);
+  });
+
+  it('handles single document corpus', () => {
+    const ranker = new Bm25Ranker();
+    ranker.fit(['only document here']);
+    const results = ranker.rank('document');
+    expect(results).toHaveLength(1);
+  });
+
+  it('ranks relevant docs higher', () => {
+    const ranker = new Bm25Ranker();
+    ranker.fit([
+      'javascript is a programming language',
+      'python is also a programming language',
+      'the weather is nice today',
+    ]);
+    const results = ranker.rank('javascript programming');
+    expect(results[0]!.index).toBe(0);
+  });
+});

apps/server/src/services/memory/__tests__/entries.test.ts

@@ -0,0 +1,31 @@
+import { describe, it, expect } from 'vitest';
+import { parseMemoryEntries } from '../entries.js';
+
+describe('parseMemoryEntries', () => {
+  it('parses a single entry with tags', () => {
+    const md = '## project: Indentation\n> tags: style\n\nUse two-space indentation\n';
+    const entries = parseMemoryEntries('style.md', md);
+    expect(entries).toHaveLength(1);
+    expect(entries[0].title).toBe('Indentation');
+    expect(entries[0].topic).toBe('project');
+    expect(entries[0].tags).toEqual(['style']);
+    expect(entries[0].content).toContain('two-space');
+  });
+
+  it('parses multiple entries', () => {
+    const md = [
+      '## project: Style',
+      '',
+      'Use tab indentation',
+      '',
+      '## user: Preference',
+      '',
+      'Prefer pnpm',
+      '',
+    ].join('\n');
+    const entries = parseMemoryEntries('mem.md', md);
+    expect(entries).toHaveLength(2);
+    expect(entries[0].topic).toBe('project');
+    expect(entries[1].topic).toBe('user');
+  });
+});

apps/server/src/services/memory/__tests__/paths.test.ts

@@ -0,0 +1,14 @@
+import { describe, it, expect } from 'vitest';
+import { getMemoryRoot, getTopicDir } from '../paths.js';
+
+describe('getMemoryRoot', () => {
+  it('returns .boocode/memory under project root', () => {
+    expect(getMemoryRoot('/proj')).toBe('/proj/.boocode/memory');
+  });
+});
+
+describe('getTopicDir', () => {
+  it('returns project/ under memory root', () => {
+    expect(getTopicDir('/r/.boocode/memory', 'project')).toBe('/r/.boocode/memory/project');
+  });
+});

apps/server/src/services/memory/__tests__/prompt.test.ts

@@ -0,0 +1,15 @@
+import { describe, it, expect } from 'vitest';
+import { formatMemoryBlock } from '../prompt.js';
+
+describe('formatMemoryBlock', () => {
+  it('wraps entries in boocode-memory tags', () => {
+    const block = formatMemoryBlock(['Use pnpm', 'Tests in vitest']);
+    expect(block).toContain('<boocode-memory>');
+    expect(block).toContain('Use pnpm');
+    expect(block).toContain('</boocode-memory>');
+  });
+
+  it('returns empty string for no entries', () => {
+    expect(formatMemoryBlock([])).toBe('');
+  });
+});

apps/server/src/services/memory/__tests__/recall.test.ts

@@ -0,0 +1,27 @@
+import { describe, it, expect } from 'vitest';
+import { rankByRelevance } from '../recall.js';
+import type { MemoryEntry } from '../entries.js';
+
+describe('rankByRelevance', () => {
+  it('returns entries matching query keywords', () => {
+    const entries: MemoryEntry[] = [
+      { id: '1', topic: 'project', title: 'Style', content: 'Use two-space indentation', tags: ['style'] },
+      { id: '2', topic: 'project', title: 'Tests', content: 'Use vitest for testing', tags: ['testing'] },
+    ];
+    const result = rankByRelevance('what indentation?', entries);
+    expect(result).toHaveLength(1);
+    expect(result[0].title).toBe('Style');
+  });
+});
+
+describe('rankByHybrid', () => {
+  it('falls back to BM25 when embeddings unavailable', async () => {
+    const entries: MemoryEntry[] = [
+      { id: '1', topic: 'project', title: 'Style', content: 'Use two-space indentation', tags: ['style'] },
+      { id: '2', topic: 'project', title: 'Tests', content: 'Use vitest for testing', tags: ['testing'] },
+    ];
+    const { rankByHybrid } = await import('../recall.js');
+    const result = await rankByHybrid('indentation style', entries);
+    expect(result.length).toBeGreaterThan(0);
+  });
+});

apps/server/src/services/memory/bm25.ts

@@ -0,0 +1,67 @@
+// BM25 ranker — pure Okapi BM25 scoring. No external deps.
+
+interface Bm25Config {
+  k1?: number;
+  b?: number;
+}
+
+export class Bm25Ranker {
+  private k1: number;
+  private b: number;
+  private corpus: string[];
+  private avgDocLen: number;
+  private idfCache: Map<string, number>;
+  private docCount: number;
+
+  constructor(config?: Bm25Config) {
+    this.k1 = config?.k1 ?? 1.5;
+    this.b = config?.b ?? 0.75;
+    this.corpus = [];
+    this.avgDocLen = 0;
+    this.idfCache = new Map();
+    this.docCount = 0;
+  }
+
+  fit(docs: string[]): void {
+    this.corpus = docs;
+    this.docCount = docs.length;
+    const lengths = docs.map((d) => d.split(/\s+/).length);
+    this.avgDocLen = lengths.reduce((a, b) => a + b, 0) / lengths.length;
+    this.idfCache.clear();
+  }
+
+  private tokenize(text: string): string[] {
+    return text.toLowerCase().split(/\s+/).filter((t) => t.length > 0);
+  }
+
+  private idf(term: string): number {
+    const cached = this.idfCache.get(term);
+    if (cached !== undefined) return cached;
+    const docsWithTerm = this.corpus.filter((d) => this.tokenize(d).includes(term)).length;
+    const idf = Math.log(1 + (this.docCount - docsWithTerm + 0.5) / (docsWithTerm + 0.5));
+    this.idfCache.set(term, idf);
+    return idf;
+  }
+
+  score(query: string, docIndex: number): number {
+    if (docIndex < 0 || docIndex >= this.corpus.length) return 0;
+    const doc = this.corpus[docIndex]!;
+    const queryTerms = this.tokenize(query);
+    const docTokens = this.tokenize(doc);
+    const docLen = docTokens.length;
+
+    let total = 0;
+    for (const term of queryTerms) {
+      const tf = docTokens.filter((t) => t === term).length;
+      if (tf === 0) continue;
+      const idfVal = this.idf(term);
+      total += idfVal * ((tf * (this.k1 + 1)) / (tf + this.k1 * (1 - this.b + this.b * docLen / this.avgDocLen)));
+    }
+    return total;
+  }
+
+  rank(query: string, topN: number = 10): Array<{ index: number; score: number }> {
+    const scores = this.corpus.map((_, i) => ({ index: i, score: this.score(query, i) }));
+    return scores.sort((a, b) => b.score - a.score).slice(0, topN).filter((s) => s.score > 0);
+  }
+}

apps/server/src/services/memory/embeddings.ts

@@ -0,0 +1,55 @@
+// Embedding module — ONNX-based local embeddings.
+// Falls back gracefully when the model file is not available.
+
+let model: any = null;
+let ortModule: any = null;
+
+export function isEmbeddingAvailable(): boolean {
+  return model !== null;
+}
+
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const dynamicRequire = typeof require !== 'undefined' ? require : null;
+
+export async function initEmbeddings(modelPath?: string): Promise<boolean> {
+  try {
+    if (dynamicRequire) {
+      try { ortModule = dynamicRequire('onnxruntime-node'); } catch { ortModule = null; }
+    }
+    if (!ortModule) {
+      try { ortModule = await import('onnxruntime-node' as any); } catch { ortModule = null; }
+    }
+    if (!ortModule) return false;
+    const path = modelPath ?? process.env['EMBEDDING_MODEL_PATH'] ?? '';
+    if (!path) return false;
+    model = await ortModule.InferenceSession.create(path);
+    return true;
+  } catch {
+    model = null;
+    return false;
+  }
+}
+
+export async function embed(texts: string[]): Promise<number[][] | null> {
+  if (!model) return null;
+  try {
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    const ort: { Tensor: new (...args: unknown[]) => unknown } | null = ortModule || null;
+    if (!ort) return null;
+    const input = new ort.Tensor('string', texts, [texts.length]);
+    const feeds: Record<string, any> = {};
+    feeds[model.inputNames[0]] = input;
+    const results = await model.run(feeds);
+    const output = results[model.outputNames[0]];
+    if (!output || !output.data) return null;
+    const dim = output.dims?.[1] ?? 384;
+    const data = output.data as Float32Array;
+    const vectors: number[][] = [];
+    for (let i = 0; i < texts.length; i++) {
+      vectors.push(Array.from(data.slice(i * dim, (i + 1) * dim)));
+    }
+    return vectors;
+  } catch {
+    return null;
+  }
+}

apps/server/src/services/memory/entries.ts

@@ -0,0 +1,54 @@
+export interface MemoryEntry {
+  id: string;
+  topic: string;
+  title: string;
+  content: string;
+  tags: string[];
+}
+
+export function parseMemoryEntries(fileName: string, markdown: string): MemoryEntry[] {
+  const entries: MemoryEntry[] = [];
+  const lines = markdown.split('\n');
+  let currentEntry: Partial<MemoryEntry> | null = null;
+  let currentContent: string[] = [];
+
+  for (const line of lines) {
+    const headingMatch = line.match(/^##\s+(.+):\s+(.+)$/);
+    if (headingMatch && headingMatch[1] && headingMatch[2]) {
+      if (currentEntry && currentEntry.title) {
+        entries.push({
+          id: `${fileName}-${entries.length}`,
+          topic: currentEntry.topic ?? '',
+          title: currentEntry.title,
+          content: currentContent.join('\n').trim(),
+          tags: currentEntry.tags ?? [],
+        });
+      }
+      currentEntry = { topic: headingMatch[1].trim(), title: headingMatch[2].trim(), tags: [] };
+      currentContent = [];
+      continue;
+    }
+
+    const tagsMatch = line.match(/^>\s*tags:\s*(.+)$/i);
+    if (tagsMatch && tagsMatch[1] && currentEntry) {
+      currentEntry.tags = tagsMatch[1].split(',').map((t) => t.trim());
+      continue;
+    }
+
+    if (currentEntry) {
+      currentContent.push(line);
+    }
+  }
+
+  if (currentEntry && currentEntry.title) {
+    entries.push({
+      id: `${fileName}-${entries.length}`,
+      topic: currentEntry.topic ?? '',
+      title: currentEntry.title,
+      content: currentContent.join('\n').trim(),
+      tags: currentEntry.tags ?? [],
+    });
+  }
+
+  return entries;
+}

apps/server/src/services/memory/index.ts

@@ -0,0 +1,6 @@
+export { loadMemoryForSession } from './recall.js';
+export { formatMemoryBlock } from './prompt.js';
+export { scanMemoryScopes } from './scan.js';
+export { parseMemoryEntries } from './entries.js';
+export { ensureMemoryScaffold, getMemoryRoot } from './paths.js';
+export type { MemoryEntry } from './entries.js';

apps/server/src/services/memory/paths.ts

@@ -0,0 +1,17 @@
+import { join } from 'node:path';
+import { mkdir } from 'node:fs/promises';
+
+const TOPICS = ['project', 'user', 'reference'] as const;
+export type MemoryTopic = (typeof TOPICS)[number];
+
+export function getMemoryRoot(projectRoot: string): string {
+  return join(projectRoot, '.boocode', 'memory');
+}
+
+export function getTopicDir(root: string, topic: MemoryTopic): string {
+  return join(root, topic);
+}
+
+export async function ensureMemoryScaffold(root: string): Promise<void> {
+  await Promise.all(TOPICS.map((t) => mkdir(join(root, t), { recursive: true })));
+}

apps/server/src/services/memory/prompt.ts

@@ -0,0 +1,5 @@
+export function formatMemoryBlock(entries: string[]): string {
+  if (entries.length === 0) return '';
+  const body = entries.map((e) => `- ${e}`).join('\n');
+  return `<boocode-memory>\n${body}\n</boocode-memory>`;
+}

apps/server/src/services/memory/recall.ts

@@ -0,0 +1,100 @@
+import type { MemoryEntry } from './entries.js';
+import { scanProjectMemory } from './scan.js';
+import { Bm25Ranker } from './bm25.js';
+import { embed, isEmbeddingAvailable } from './embeddings.js';
+
+const SEARCH_MODE = process.env['MEMORY_SEARCH'] ?? 'hybrid';
+
+function extractKeywords(query: string): string[] {
+  return query
+    .toLowerCase()
+    .replace(/[^a-z0-9\s]/g, '')
+    .split(/\s+/)
+    .filter((w) => w.length > 2);
+}
+
+export function rankByRelevance(query: string, entries: MemoryEntry[]): MemoryEntry[] {
+  const keywords = extractKeywords(query);
+  if (keywords.length === 0) return entries.slice(0, 5);
+
+  const scored = entries.map((entry) => {
+    let score = 0;
+    const searchText = `${entry.title} ${entry.content} ${entry.tags.join(' ')}`.toLowerCase();
+    for (const kw of keywords) {
+      if (entry.title.toLowerCase().includes(kw)) score += 3;
+      if (entry.tags.some((t) => t.toLowerCase().includes(kw))) score += 2;
+      if (entry.content.toLowerCase().includes(kw)) score += 1;
+    }
+    return { entry, score };
+  });
+
+  return scored
+    .filter((s) => s.score > 0)
+    .sort((a, b) => b.score - a.score)
+    .slice(0, 10)
+    .map((s) => s.entry);
+}
+
+export async function rankByHybrid(
+  query: string,
+  entries: MemoryEntry[],
+): Promise<MemoryEntry[]> {
+  if (entries.length === 0) return [];
+  const texts = entries.map((e) => `${e.title} ${e.content} ${e.tags.join(' ')}`);
+
+  const bm25 = new Bm25Ranker();
+  bm25.fit(texts);
+  const bm25Scores = texts.map((_, i) => bm25.score(query, i));
+  const maxBm25 = Math.max(...bm25Scores, 1);
+  const normBm25 = bm25Scores.map((s) => s / maxBm25);
+
+  let cosineScores: number[] = [];
+  if (isEmbeddingAvailable()) {
+    const vectors = await embed([query, ...texts]);
+    if (vectors) {
+      const queryVec = vectors[0]!;
+      cosineScores = texts.map((_, i) => {
+        const vec = vectors[i + 1];
+        if (!vec) return 0;
+        let dot = 0, nA = 0, nB = 0;
+        for (let j = 0; j < queryVec.length; j++) {
+          dot += queryVec[j]! * vec[j]!;
+          nA += queryVec[j]! * queryVec[j]!;
+          nB += vec[j]! * vec[j]!;
+        }
+        const denom = Math.sqrt(nA) * Math.sqrt(nB);
+        return denom === 0 ? 0 : dot / denom;
+      });
+    }
+  }
+
+  const scored = entries.map((entry, i) => {
+    const combined = (normBm25[i]! * 0.3) + ((cosineScores[i] ?? 0) * 0.7);
+    return { entry, score: combined };
+  });
+
+  return scored
+    .filter((s) => s.score >= 0.15)
+    .sort((a, b) => b.score - a.score)
+    .slice(0, 10)
+    .map((s) => s.entry);
+}
+
+export async function loadMemoryForSession(
+  projectRoot: string,
+  _sessionId?: string,
+  query?: string,
+): Promise<string[]> {
+  const entries = await scanProjectMemory(projectRoot);
+  if (entries.length === 0) return [];
+
+  const relevant = query
+    ? SEARCH_MODE === 'keyword'
+      ? rankByRelevance(query, entries)
+      : await rankByHybrid(query, entries)
+    : entries.slice(0, 5);
+
+  return relevant.map((e) => `[${e.topic}] ${e.title}: ${e.content}`);
+}
+
+export { initEmbeddings } from './embeddings.js';

apps/server/src/services/memory/scan.ts

@@ -0,0 +1,72 @@
+import { homedir } from 'node:os';
+import { join } from 'node:path';
+import { readFile, readdir } from 'node:fs/promises';
+import type { MemoryEntry } from './entries.js';
+import { parseMemoryEntries } from './entries.js';
+import { getMemoryRoot } from './paths.js';
+
+export interface MemoryScope {
+  projectRoot: string;
+  sessionDir?: string;
+  homeDir?: string;
+}
+
+async function scanDirectory(dir: string): Promise<MemoryEntry[]> {
+  const entries: MemoryEntry[] = [];
+  try {
+    const files = await readdir(dir, { withFileTypes: true });
+    for (const file of files) {
+      if (file.isFile() && file.name.endsWith('.md')) {
+        const content = await readFile(join(dir, file.name), 'utf8');
+        entries.push(...parseMemoryEntries(file.name, content));
+      }
+    }
+  } catch {
+    // Directory doesn't exist
+  }
+  return entries;
+}
+
+const MEMORY_TOPICS = ['project', 'user', 'reference'] as const;
+
+async function scanTopicDirs(root: string): Promise<MemoryEntry[]> {
+  const entries: MemoryEntry[] = [];
+  for (const topic of MEMORY_TOPICS) {
+    entries.push(...(await scanDirectory(join(root, topic))));
+  }
+  return entries;
+}
+
+export async function scanMemoryScopes(scope: MemoryScope): Promise<MemoryEntry[]> {
+  const allEntries: MemoryEntry[] = [];
+
+  // 1. Global (~/.boocode/memory/) - lowest priority
+  allEntries.push(...(await scanTopicDirs(getMemoryRoot(homedir()))));
+
+  // 2. Home ($HOME/.boocode/memory)
+  const homeDir = scope.homeDir ?? homedir();
+  const homeRoot = getMemoryRoot(homeDir);
+  if (homeRoot !== getMemoryRoot(homedir())) {
+    allEntries.push(...(await scanTopicDirs(homeRoot)));
+  }
+
+  // 3. Project (.boocode/memory/ under project root)
+  allEntries.push(...(await scanTopicDirs(getMemoryRoot(scope.projectRoot))));
+
+  // 4. Session (.boocode/sessions/<id>/memory.md) - highest priority
+  if (scope.sessionDir) {
+    try {
+      const sessionFile = join(scope.sessionDir, 'memory.md');
+      const content = await readFile(sessionFile, 'utf8');
+      allEntries.push(...parseMemoryEntries('session-memory', content));
+    } catch {
+      // No session memory file
+    }
+  }
+
+  return allEntries;
+}
+
+export async function scanProjectMemory(projectRoot: string): Promise<MemoryEntry[]> {
+  return scanMemoryScopes({ projectRoot });
+}

apps/server/src/services/memory/store.ts

@@ -0,0 +1,35 @@
+import { readFile, writeFile, readdir } from 'node:fs/promises';
+import { join } from 'node:path';
+import type { MemoryTopic } from './paths.js';
+import { getTopicDir } from './paths.js';
+
+export async function readTopicFiles(root: string, topic: MemoryTopic): Promise<Map<string, string>> {
+  const dir = getTopicDir(root, topic);
+  const files = new Map<string, string>();
+  try {
+    const entries = await readdir(dir, { withFileTypes: true });
+    for (const entry of entries) {
+      if (entry.isFile() && entry.name.endsWith('.md')) {
+        const content = await readFile(join(dir, entry.name), 'utf8');
+        files.set(entry.name, content);
+      }
+    }
+  } catch {
+    // Directory doesn't exist yet
+  }
+  return files;
+}
+
+export async function writeEntry(
+  root: string,
+  topic: MemoryTopic,
+  title: string,
+  content: string,
+  tags: string[],
+): Promise<void> {
+  const dir = getTopicDir(root, topic);
+  const tagLine = tags.length > 0 ? `> tags: ${tags.join(', ')}\n\n` : '\n';
+  const entry = `## ${topic}: ${title}\n${tagLine}${content}\n`;
+  const filename = title.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/(^-|-$)/g, '') + '.md';
+  await writeFile(join(dir, filename), entry, 'utf8');
+}

apps/server/src/services/synthesisPipeline.ts

@@ -35,6 +35,7 @@ export const SYNTHESIS_TOOLS: ReadonlySet<string> = new Set([
   'get_codebase_overview',
   'get_framework_analysis',
   'get_semantic_neighborhoods',
+  'get_blast_radius',
 ]);
 
 const TOP_N_FILES = 5;

apps/server/src/services/system-prompt.ts

@@ -22,6 +22,8 @@ import { readFile, stat } from 'node:fs/promises';
 import type { Agent, Project, Session } from '../types/api.js';
 import { getAgentsMtimes } from './agents.js';
 import { resolveRoute } from './inference/provider.js';
+import { loadMemoryForSession } from './memory/recall.js';
+import { formatMemoryBlock } from './memory/prompt.js';
 
 const BASE_SYSTEM_PROMPT = (projectPath: string) =>
   `You are BooCode Chat, a code investigation assistant. The user is working on a project located at ${projectPath}. Use the file-read tools (view_file, list_dir, grep, find_files) to investigate code when needed. Be concise. Cite file paths and line numbers when discussing code. Do not hallucinate file contents — read the file first. Tool results may be truncated; if so, narrow your query rather than guessing.`;
@@ -164,7 +166,11 @@ export async function buildSystemPromptWithFingerprint(
   let out = BASE_SYSTEM_PROMPT(project.path);
   const guidance = await getContainerGuidance();
   if (guidance) {
-    out += `\n\n--- Container guidance ---\n${guidance}\n--- end container guidance ---\n`;
+    out += '\n\n--- Container guidance ---\n' + guidance + '\n--- end container guidance ---\n';
+  }
+  const memory = await loadMemoryForSession(project.path, session.id).catch(() => []);
+  if (memory.length > 0) {
+    out += '\n\n' + formatMemoryBlock(memory);
   }
   if (agent && agent.system_prompt.trim().length > 0) {
     out += '\n\n' + agent.system_prompt.trim();

apps/server/src/services/tools/codecontext/get_call_graph.ts

@@ -0,0 +1,31 @@
+import { z } from 'zod';
+import { makeCodecontextTool } from './factory.js';
+
+export const GetCallGraphInput = z.object({
+  symbol: z.string().describe('Symbol name to analyze'),
+  depth: z.number().int().min(1).max(5).optional().describe('Max traversal depth (default 2)'),
+});
+export type GetCallGraphInputT = z.infer<typeof GetCallGraphInput>;
+
+const DESCRIPTION =
+  'Returns a call graph for a function or method: callers, callees, and transitive references. ' +
+  'Use to understand how a symbol is invoked and what it depends on.';
+
+const { toolDef: getCallGraph, execute: executeGetCallGraph } =
+  makeCodecontextTool<GetCallGraphInputT>({
+    name: 'get_call_graph',
+    schema: GetCallGraphInput,
+    description: DESCRIPTION,
+    jsonParameters: {
+      type: 'object',
+      properties: {
+        symbol: { type: 'string', description: 'Symbol name to analyze' },
+        depth: { type: 'number', description: 'Max traversal depth (default 2)' },
+      },
+      required: ['symbol'],
+      additionalProperties: false,
+    },
+    mapArgs: (input) => ({ symbol: input.symbol, depth: input.depth ?? 2 }),
+  });
+
+export { getCallGraph, executeGetCallGraph };

apps/server/src/services/tools/codecontext/get_symbol_details.ts

@@ -0,0 +1,31 @@
+import { z } from 'zod';
+import { makeCodecontextTool } from './factory.js';
+
+export const GetSymbolDetailsInput = z.object({
+  symbol: z.string().describe('Symbol name to resolve'),
+  file_path: z.string().optional().describe('Optional file path to narrow search'),
+});
+export type GetSymbolDetailsInputT = z.infer<typeof GetSymbolDetailsInput>;
+
+const DESCRIPTION =
+  'Returns type signature, definition location, and usage count for a named symbol. ' +
+  'Use after get_codebase_overview to dive deeper into specific functions, classes, or variables.';
+
+const { toolDef: getSymbolDetails, execute: executeGetSymbolDetails } =
+  makeCodecontextTool<GetSymbolDetailsInputT>({
+    name: 'get_symbol_details',
+    schema: GetSymbolDetailsInput,
+    description: DESCRIPTION,
+    jsonParameters: {
+      type: 'object',
+      properties: {
+        symbol: { type: 'string', description: 'Symbol name to resolve' },
+        file_path: { type: 'string', description: 'Optional file path to narrow search' },
+      },
+      required: ['symbol'],
+      additionalProperties: false,
+    },
+    mapArgs: (input) => ({ symbol: input.symbol, file_path: input.file_path }),
+  });
+
+export { getSymbolDetails, executeGetSymbolDetails };

apps/server/src/services/tools/extract_memory.ts

@@ -0,0 +1,44 @@
+import { z } from 'zod';
+import type { ToolDef } from '../tools/types.js';
+import { ensureMemoryScaffold, getMemoryRoot } from '../memory/paths.js';
+import { writeEntry } from '../memory/store.js';
+
+const ExtractMemoryInput = z.object({
+  topic: z.enum(['project', 'user', 'reference']).describe('Memory topic category'),
+  title: z.string().min(1).max(200).describe('Entry title (will be normalized to filename)'),
+  content: z.string().min(1).describe('Memory content body'),
+  tags: z.array(z.string()).optional().describe('Optional tags for search'),
+});
+
+type InputT = z.infer<typeof ExtractMemoryInput>;
+
+export const extractMemoryTool: ToolDef<InputT> = {
+  name: 'extract_memory',
+  description: 'Persist a memory entry to .boocode/memory/ for cross-session recall. Use for project conventions, user preferences, and architectural decisions.',
+  inputSchema: ExtractMemoryInput,
+  jsonSchema: {
+    type: 'function',
+    function: {
+      name: 'extract_memory',
+      description: 'Persist a memory entry for cross-session recall',
+      parameters: {
+        type: 'object',
+        properties: {
+          topic: { type: 'string', enum: ['project', 'user', 'reference'] },
+          title: { type: 'string', description: 'Entry title' },
+          content: { type: 'string', description: 'Memory content' },
+          tags: { type: 'array', items: { type: 'string' }, description: 'Search tags' },
+        },
+        required: ['topic', 'title', 'content'],
+      },
+    },
+  },
+  async execute(input: InputT, projectRoot: string): Promise<unknown> {
+    const root = getMemoryRoot(projectRoot);
+    await ensureMemoryScaffold(root);
+    await writeEntry(root, input.topic, input.title, input.content, input.tags ?? []);
+    return {
+      result: `Memory entry "${input.title}" saved to .boocode/memory/${input.topic}/`,
+    };
+  },
+};

apps/server/src/services/tools/search_memory.ts

@@ -0,0 +1,40 @@
+import { z } from 'zod';
+import type { ToolDef } from '../tools/types.js';
+import { scanProjectMemory } from '../memory/scan.js';
+import { rankByHybrid } from '../memory/recall.js';
+
+const SearchMemoryInput = z.object({
+  query: z.string().min(1).describe('Search query to match against memory entries'),
+});
+
+type InputT = z.infer<typeof SearchMemoryInput>;
+
+export const searchMemoryTool: ToolDef<InputT> = {
+  name: 'search_memory',
+  description: 'Search the .boocode/memory/ store for relevant entries. Returns ranked results matching the query. Use before asking about project conventions or preferences.',
+  inputSchema: SearchMemoryInput,
+  jsonSchema: {
+    type: 'function',
+    function: {
+      name: 'search_memory',
+      description: 'Search memory store for relevant entries',
+      parameters: {
+        type: 'object',
+        properties: {
+          query: { type: 'string', description: 'Search query' },
+        },
+        required: ['query'],
+      },
+    },
+  },
+  async execute(input: InputT, projectRoot: string): Promise<unknown> {
+    const entries = await scanProjectMemory(projectRoot);
+    if (entries.length === 0) return { result: 'No memory entries found.' };
+
+    const relevant = await rankByHybrid(input.query, entries);
+    if (relevant.length === 0) return { result: 'No matching memory entries.' };
+
+    const lines = relevant.map((e) => `[${e.topic}] ${e.title}: ${e.content}`);
+    return { result: `Found ${relevant.length} entry(ies):\n${lines.join('\n')}` };
+  },
+};

apps/web/src/App.tsx

@@ -7,6 +7,8 @@ import { Home } from '@/pages/Home';
 import { Project } from '@/pages/Project';
 import { Session } from '@/pages/Session';
 import { Settings } from '@/pages/Settings';
+import { Analytics } from '@/pages/Analytics';
+import { Results } from '@/pages/Results';
 import { Toaster } from '@/components/ui/sonner';
 import { useUserEvents } from '@/hooks/useUserEvents';
 import { useCoderUserEvents } from '@/hooks/useCoderUserEvents';
@@ -95,6 +97,8 @@ function AppShell() {
             <Route path="/project/:id" element={<Project />} />
             <Route path="/session/:id" element={<Session />} />
             <Route path="/settings" element={<Settings />} />
+            <Route path="/analytics" element={<Analytics />} />
+            <Route path="/results" element={<Results />} />
           </Routes>
         </main>
         <MobileRightRailBackdrop />

apps/web/src/api/client.ts

@@ -30,6 +30,10 @@ import type {
   BattleShape,
   ContestantShape,
   CrossExaminationShape,
+  AnalyticsSummary,
+  SessionAnalyticsRow,
+  ContextWindowStats,
+  TokenBreakdownAgg,
 } from './types';
 
 // v2.6 Phase 1-UX §9b: chat-scoped agent-session rows. Returned by
@@ -159,12 +163,13 @@ export const api = {
       request<{ files: string[] }>(`/api/projects/${id}/files`),
     git: (id: string) =>
       request<GitMeta>(`/api/projects/${id}/git`),
-    gitDiff: (id: string, mode: GitDiffMode | null) =>
+    gitDiff: (id: string, mode: GitDiffMode | null, hideWhitespace?: boolean) => {
-      request<GitDiffResult>(
+      const params: string[] = [];
-        mode !== null
+      if (mode !== null) params.push(`mode=${mode}`);
-          ? `/api/projects/${id}/git/diff?mode=${mode}`
+      if (hideWhitespace) params.push('whitespace=1');
-          : `/api/projects/${id}/git/diff`,
+      const qs = params.length > 0 ? `?${params.join('&')}` : '';
-      ),
+      return request<GitDiffResult>(`/api/projects/${id}/git/diff${qs}`);
+    },
     gitStage: (id: string, files: string[]) =>
       request<{ ok: boolean }>(`/api/projects/${id}/git/stage`, {
         method: 'POST',
@@ -185,6 +190,11 @@ export const api = {
         method: 'POST',
         body: JSON.stringify({ files }),
       }),
+    writeFile: (id: string, filePath: string, content: string) =>
+      request<{ ok: boolean }>(`/api/projects/${id}/write_file`, {
+        method: 'POST',
+        body: JSON.stringify({ path: filePath, content }),
+      }),
   },
 
   sessions: {
@@ -590,6 +600,14 @@ export const api = {
     costStats: () => request<{ stats: ToolCostStat[] }>('/api/tools/cost_stats'),
   },
 
+  // token-analyzer-ui: analytics aggregate endpoints.
+  analytics: {
+    summary: () => request<AnalyticsSummary>('/api/coder/analytics/summary'),
+    sessions: () => request<{ sessions: SessionAnalyticsRow[] }>('/api/coder/analytics/sessions'),
+    context: () => request<ContextWindowStats>('/api/analytics/context'),
+    tokenBreakdown: () => request<{ categories: TokenBreakdownAgg[] }>('/api/coder/analytics/token-breakdown'),
+  },
+
   settings: {
     get: () => request<Record<string, unknown>>('/api/settings'),
     patch: (body: Record<string, unknown>) =>