fix(coder): harden edit-apply pipeline against block duplication

Root cause: two proven corruption mechanisms — (M1) non-idempotent apply
stamped the same block N times when a quantized model re-emitted the same
edit_file call or a turn was retried; (M2) Levenshtein tier 4 was fail-open
with no uniqueness guard, silently splicing into the wrong location.

Fixes applied at every layer of the pipeline:

Matcher (fuzzy-match.ts): raise SIMILARITY_THRESHOLD 0.66 → 0.85; add
AMBIGUITY_EPSILON uniqueness guard — two windows within 0.05 of the top
score → ambiguous, not a guess; add block-anchor gate (≥3-line needles
require first+last line exact match before a window is scored).

Edit planner (pending_changes.ts): extract planEdit() as a pure function;
idempotency guards detect already-applied states (anchored insert re-stamp,
old-gone-but-new-present); findPendingDuplicate() collapses identical
pending rows at queue time so M1 never reaches applyOne.

Atomic writes (pending_changes.ts): temp-file + rename on the same
filesystem so a crash can't leave a half-written source file; realpath()
first so symlinks survive the rename.

Per-file mutex (pending_changes.ts): withFileLock() serializes concurrent
read-modify-write on the same path via a chained-Promise Map.

EOL preservation (pending_changes.ts): normalize CRLF → LF for matching,
restore native line ending on write so Windows-style files stay clean.

Context isolation (inference_context.ts): replace module-level singleton
with AsyncLocalStorage so concurrent inference runs (arena parallel
dispatch, dispatcher poll racing a user message) each get their own
scoped context with no clobbering.

Tests: plan-edit.test.ts (pure planEdit unit tests), extended fuzzy-match
and pending_changes_integration suites, ALS isolation test that proves
overlapping runs get correct session IDs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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';
@@ -174,22 +174,27 @@ async function main() {
     }
   );
 
-  // Wrap the inference runner to set/clear the write-tool context around each run.
-  // The inference runner calls enqueue() which fires asynchronously — we hook
-  // into the enqueue to set context before the run starts.
+  // Wrap the inference runner to bind the write-tool context around each run.
+  // enqueue() starts its async loop synchronously, so wrapping the call in
+  // 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) => {
-      // Set the inference context so write tools can access sql + sessionId.
-      // The context persists for the duration of the inference run. Since
-      // BooCoder is single-user and runs one inference at a time per session,
-      // this module-level state is safe.
-      setInferenceContext({ sql, sessionId, taskId: null });
+    enqueue: (
+      sessionId: string,
+      chatId: string,
+      assistantId: string,
+      user: string,
+      permissionMode?: 'plan' | 'ask' | 'bypass',
+    ) => {
+      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);
-      clearInferenceContext();
-      return result;
+      // No context to clear — AsyncLocalStorage scopes it to each run's own chain.
+      return inference.cancel(sessionId, chatId);
     },
     hasActive: (chatId: string) => inference.hasActive(chatId),
   };

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');
-
-      // Bypass permission mode (native BooCode): auto-apply staged edits to disk
-      // once the turn settles. `enqueue` registers synchronously, so hasActive is
-      // true immediately; poll until it clears, apply, then re-publish
-      // message_complete so the DiffPanel reflects the now-applied (non-pending)
-      // state. Best-effort — failures stay in the pending queue for manual apply.
-      if (mode_id === 'bypass') {
-        const projectId = sessionRows[0]!.project_id;
-        const assistantId = assistantMsg!.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 */
-          }
-        })();
-      }
+      // Native BooCode permission gate (plan/ask/bypass) — threaded into the
+      // write-tool context so create/edit/delete and apply_pending honor it.
+      // Plan = read-only, Ask = stage to the queue (agent can't self-apply),
+      // Bypass = apply each write immediately. Other mode ids (e.g. an external
+      // fallback's native mode) leave the gate undefined = legacy behavior.
+      req.log.info(
+        { provider, mode_id, permissionMode: asPermissionMode(mode_id), chatId },
+        'native enqueue — permission gate',
+      );
+      inference.enqueue(sessionId, chatId, assistantMsg!.id, 'default', asPermissionMode(mode_id));
 
       reply.code(202);
       return { user_message_id: userMsg!.id, assistant_message_id: assistantMsg!.id };

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/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
-      inference.enqueue(sessionId, chatId, assistantId, 'default');
+      // Enqueue inference — pass the native permission gate (plan/ask/bypass)
+      // 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/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;
-  let bestSpan: { start: number; end: number } | null = null;
+  // Block-anchor gate for multi-line needles: the first and last lines must match
+  // 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');
-    const score = similarity(windowJoined, needleJoined);
-    if (score > best) {
-      best = score;
-      bestSpan = { start: window[0]!.start, end: window[n - 1]!.end };
+    if (anchored) {
+      const winFirst = canonicalize(window[0]!.text.trim());
+      const winLast = canonicalize(window[n - 1]!.text.trim());
+      if (winFirst !== needleFirst || winLast !== needleLast) continue;
     }
+    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) {
-    return { kind: 'fuzzy', start: bestSpan.start, end: bestSpan.end };
-  }
-  return null;
+  if (scored.length === 0) return null;
+  scored.sort((a, b) => b.score - a.score);
+  const best = scored[0]!;
+  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/pending_changes.ts

@@ -1,9 +1,120 @@
-import { readFile, writeFile, unlink, mkdir } from 'node:fs/promises';
-import { dirname } from 'node:path';
+import { readFile, writeFile, unlink, mkdir, rename, realpath } from 'node:fs/promises';
+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})
@@ -110,31 +256,42 @@ export async function applyOne(
   }
 
   try {
+    return await withFileLock(change.file_path, async () => {
       // Re-validate path in case projectRoot has shifted
       resolveWritePath(projectRoot, change.file_path);
 
       switch (change.operation) {
         case 'create': {
           await mkdir(dirname(change.file_path), { recursive: true });
-        await writeFile(change.file_path, change.diff, 'utf8');
+          await writeFileAtomic(change.file_path, change.diff);
           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') {
+          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 ${match.count} locations — add surrounding context to disambiguate`,
+              `old_string matches ${plan.count} locations — add surrounding context to disambiguate`,
             );
           }
-        if (match.kind === 'not_found') {
+          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',
             );
           }
-        const updated = content.slice(0, match.start) + newStr + content.slice(match.end);
-        await writeFile(change.file_path, updated, 'utf8');
+          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;
         }
         case 'delete': {
@@ -152,6 +309,7 @@ export async function applyOne(
 
       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 };
+    });
   } 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/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 {
-      status: 'queued',
-      change_id: change.id,
-      file_path: change.file_path,
-      operation: 'create',
-      message: `File creation queued: ${change.file_path}. Use apply_pending to write changes to disk.`,
-    };
+    return finalizeWrite(
+      context,
+      projectRoot,
+      change,
+      `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 {
-      status: 'queued',
-      change_id: change.id,
-      file_path: change.file_path,
-      operation: 'delete',
-      message: `File deletion queued: ${change.file_path}. Use apply_pending to write changes to disk.`,
-    };
+    return finalizeWrite(
+      context,
+      projectRoot,
+      change,
+      `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 {
-      status: 'queued',
-      change_id: change.id,
-      file_path: change.file_path,
-      operation: 'edit',
-      message: `Edit queued for ${change.file_path}. Use apply_pending to write changes to disk.`,
-    };
+    return finalizeWrite(
+      context,
+      projectRoot,
+      change,
+      `Edit queued for ${change.file_path}. Use apply_pending to write changes to disk.`,
+    );
   },
 };

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 read it via `getInferenceContext()` during execute.
- * Same pattern as BooChat's `loadConfig()` singleton — tools need
- * ambient state that can't be threaded through the tool-phase execute
- * signature (which is `execute(input, projectRoot, extraRoots?)`).
+ * Write tools need ambient state (sql, sessionId, the permission gate) that the
+ * BooChat tool-phase `execute(input, projectRoot, extraRoots?)` signature can't
+ * carry. This used to be a single module-level `let current` — but the inference
+ * runner's `enqueue()` is fire-and-forget, so two overlapping runs (a user
+ * 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;
-}
-
-export function clearInferenceContext(): void {
-  current = null;
+/**
+ * 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
+ * same store. Concurrent runs each get their own; nothing is shared or cleared
+ * 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/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,
+  };
+}