feat: Paseo-like orchestrator Phase 1-2 — trace system, session persistence, timeline, run_command, auto-fix loop

Phase 1: Trace System + Observability
- tool_traces DB table + insert/update service
- tool_trace_start/tool_trace_finish WS frames (contracts + FE types)
- Instrumented tool-phase.ts with timing around every tool call
- GET /api/chats/:id/traces paginated endpoint
- Trace viewer frontend (collapsible panel with timing bars + token breakdown)

Phase 2: Session Persistence + Resume
- agent_snapshots table (UPSERT per chat, persisted on turn boundaries)
- save/load/delete service functions
- Agent snapshot sent on WS reconnect
- Session timeline view (vertical timeline with scroll-to + restore)

Tooling:
- run_command tool (execFile, 30s timeout, 32KB cap, path-guarded)
- Auto-fix loop: after write tools, runs pnpm build, injects errors into next turn

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

@@ -23,6 +23,7 @@ import {
   getCodeImpact,
   getTypeInfo,
   getCodeMap,
+  getWikiArticle,
 } from './codecontext/index.js';
 // v1.13.17-cross-repo-reads: cross-repo read grant request tool. Paired
 // with the pause-on-pending-grant branch in inference/tool-phase.ts and the
@@ -31,6 +32,14 @@ import { requestReadAccess } from '../request_read_access.js';
 // v2.6.x: read-only tool that reads a tab's transcript by its session-scoped
 // tab number. Needs DB/session context (ToolExecCtx 4th arg).
 import { readTabByNumber } from '../read_tab_by_number.js';
+// v2.x: memory management tools. file-based store with optional CoreTier
+// (SQLite FTS5 + vector) hybrid search backend.
+import { extractMemoryTool } from './extract_memory.js';
+import { manageMemoryTool } from './manage_memory.js';
+import { searchMemoryTool } from './search_memory.js';
+// vWhale: command execution tool. Spawns processes in the project worktree
+// with timeout and output cap. No shell — args are passed as array.
+import { runCommand } from './execute-command.js';
 
 // v1.13.3: alpha-sorted by tool.name at module load. llama.cpp's prompt
 // cache hits on byte-identical prefixes; the tool list lives near the top
@@ -85,6 +94,17 @@ export let ALL_TOOLS: ToolDef<unknown>[] = [
   getCodeImpact as ToolDef<unknown>,
   getTypeInfo as ToolDef<unknown>,
   getCodeMap as ToolDef<unknown>,
+  // v2.8.14-domain2-phase3: wiki mode + token-efficient scanning.
+  getWikiArticle as ToolDef<unknown>,
+  // v2.x: memory management tools. File-based store with optional CoreTier
+  // (SQLite FTS5 + vector) hybrid search backend.
+  extractMemoryTool as ToolDef<unknown>,
+  manageMemoryTool as ToolDef<unknown>,
+  searchMemoryTool as ToolDef<unknown>,
+  // vWhale: command execution. Spawns processes in the project worktree.
+  // Read-write; use with guard: restricted to project root via path_guard,
+  // no shell injection (execFile, not exec).
+  runCommand as ToolDef<unknown>,
 ].sort((a, b) => a.name.localeCompare(b.name));
 
 export let TOOLS_BY_NAME: Record<string, ToolDef<unknown>> = Object.fromEntries(