gsd-pi 2.80.0-dev.4ea7d80e7 → 2.80.0-dev.7582bf37a

package/packages/pi-coding-agent/dist/resources/extensions/memory/storage-safety-guard.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=storage-safety-guard.test.d.ts.map

package/packages/pi-coding-agent/dist/resources/extensions/memory/storage-safety-guard.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"storage-safety-guard.test.d.ts","sourceRoot":"","sources":["../../../../src/resources/extensions/memory/storage-safety-guard.test.ts"],"names":[],"mappings":""}

package/packages/pi-coding-agent/dist/resources/extensions/memory/storage-safety-guard.test.js

@@ -0,0 +1,28 @@
+import assert from "node:assert/strict";
+import { lstatSync, mkdtempSync, readFileSync, rmSync, symlinkSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import test from "node:test";
+import { MemoryStorage } from "./storage.js";
+test("MemoryStorage replaces a symlinked DB path instead of overwriting the symlink target", async (t) => {
+    const dir = mkdtempSync(join(tmpdir(), "memory-storage-atomic-"));
+    t.after(() => rmSync(dir, { recursive: true, force: true }));
+    const canaryPath = join(dir, "canary.txt");
+    const dbPath = join(dir, "memory.db");
+    const canaryStorage = await MemoryStorage.create(canaryPath);
+    canaryStorage.close();
+    const originalCanary = readFileSync(canaryPath);
+    symlinkSync(canaryPath, dbPath);
+    const storage = await MemoryStorage.create(dbPath);
+    storage.upsertThreads([{
+            threadId: "thread-1",
+            filePath: join(dir, "thread.jsonl"),
+            fileSize: 1,
+            fileMtime: 1,
+            cwd: dir,
+        }]);
+    storage.close();
+    assert.deepEqual(readFileSync(canaryPath), originalCanary);
+    assert.equal(lstatSync(dbPath).isSymbolicLink(), false, "atomic snapshot write should replace the symlink");
+});
+//# sourceMappingURL=storage-safety-guard.test.js.map

package/packages/pi-coding-agent/dist/resources/extensions/memory/storage-safety-guard.test.js.map

@@ -0,0 +1 @@
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package/packages/pi-coding-agent/dist/resources/extensions/memory/storage.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"storage.d.ts","sourceRoot":"","sources":["../../../../src/resources/extensions/memory/storage.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAQH,MAAM,WAAW,SAAS;IACzB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC;IACnB,GAAG,EAAE,MAAM,CAAC;IACZ,MAAM,EAAE,SAAS,GAAG,YAAY,GAAG,MAAM,GAAG,OAAO,CAAC;IACpD,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,eAAe;IAC/B,SAAS,EAAE,MAAM,CAAC;IAClB,eAAe,EAAE,MAAM,CAAC;IACxB,UAAU,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,MAAM;IACtB,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAAC;IAC3B,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,MAAM,EAAE,SAAS,GAAG,SAAS,GAAG,MAAM,GAAG,OAAO,CAAC;IACjD,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IAC/B,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;CACnB;AAED,qBAAa,aAAa;IACzB,OAAO,CAAC,EAAE,CAAgB;IAC1B,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,YAAY,CAA8C;IAElE,OAAO;WAKM,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,aAAa,CAAC;IAmB3D,OAAO,CAAC,OAAO;IAKf,OAAO,CAAC,eAAe;IAUvB,OAAO,CAAC,UAAU;IA0ClB,OAAO,CAAC,QAAQ;IAWhB,OAAO,CAAC,QAAQ;IAKhB;;;OAGG;IACH,aAAa,CACZ,OAAO,EAAE,KAAK,CAAC;QACd,QAAQ,EAAE,MAAM,CAAC;QACjB,QAAQ,EAAE,MAAM,CAAC;QACjB,QAAQ,EAAE,MAAM,CAAC;QACjB,SAAS,EAAE,MAAM,CAAC;QAClB,GAAG,EAAE,MAAM,CAAC;KACZ,CAAC,GACA;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE;IA0CzD;;;OAGG;IACH,eAAe,CACd,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,MAAM,EACb,YAAY,EAAE,MAAM,GAClB,KAAK,CAAC;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAC;QAAC,cAAc,EAAE,MAAM,CAAA;KAAE,CAAC;IAkCrE;;OAEG;IACH,iBAAiB,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI;IAgBzD;;OAEG;IACH,aAAa,CAAC,QAAQ,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,GAAG,IAAI;IAY3D;;;OAGG;IACH,uBAAuB,CACtB,QAAQ,EAAE,MAAM,EAChB,YAAY,EAAE,MAAM,GAClB;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,cAAc,EAAE,MAAM,CAAA;KAAE,GAAG,IAAI;IAsCnD;;OAEG;IACH,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAQtC;;OAEG;IACH,gBAAgB,IAAI,KAAK,CAAC;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,cAAc,EAAE,MAAM,CAAA;KAAE,CAAC;IAWvE;;OAEG;IACH,sBAAsB,CAAC,GAAG,EAAE,MAAM,GAAG,KAAK,CAAC;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,cAAc,EAAE,MAAM,CAAA;KAAE,CAAC;IAcxF;;OAEG;IACH,SAAS,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,GAAG,SAAS;IAOlD;;OAEG;IACH,QAAQ,IAAI;QACX,YAAY,EAAE,MAAM,CAAC;QACrB,cAAc,EAAE,MAAM,CAAC;QACvB,WAAW,EAAE,MAAM,CAAC;QACpB,YAAY,EAAE,MAAM,CAAC;QACrB,kBAAkB,EAAE,MAAM,CAAC;QAC3B,iBAAiB,EAAE,MAAM,CAAC;KAC1B;IA4BD;;OAEG;IACH,QAAQ,IAAI,IAAI;IAOhB;;OAEG;IACH,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI;IAa9B;;OAEG;IACH,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI;IA4BjC,KAAK,IAAI,IAAI;CAQb"}

package/packages/pi-coding-agent/dist/resources/extensions/memory/storage.js

@@ -8,8 +8,9 @@
  */
 import initSqlJs from "sql.js";
 import { randomUUID } from "crypto";
-import { existsSync, mkdirSync, readFileSync, writeFileSync } from "fs";
+import { existsSync, mkdirSync, readFileSync } from "fs";
 import { dirname } from "path";
+import { atomicWriteDbSnapshotSync } from "../../../core/db-snapshot.js";
 export class MemoryStorage {
     constructor(db, dbPath) {
         this.persistTimer = null;
@@ -33,7 +34,7 @@ export class MemoryStorage {
     }
     persist() {
         const data = this.db.export();
-        writeFileSync(this.dbPath, Buffer.from(data));
+        atomicWriteDbSnapshotSync(this.dbPath, data);
     }
     schedulePersist() {
         if (this.persistTimer) {

package/packages/pi-coding-agent/dist/resources/extensions/memory/storage.js.map

@@ -1 +1 @@
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\"pending\" | \"claimed\" | \"done\" | \"error\";\n\tworker_id: string | null;\n\townership_token: string | null;\n\tlease_expires_at: string | null;\n\terror_message: string | null;\n\tcreated_at: string;\n\tupdated_at: string;\n}\n\nexport class MemoryStorage {\n\tprivate db: SqlJsDatabase;\n\tprivate dbPath: string;\n\tprivate persistTimer: ReturnType<typeof setTimeout> | null = null;\n\n\tprivate constructor(db: SqlJsDatabase, dbPath: string) {\n\t\tthis.db = db;\n\t\tthis.dbPath = dbPath;\n\t}\n\n\tstatic async create(dbPath: string): Promise<MemoryStorage> {\n\t\tconst dir = dirname(dbPath);\n\t\tif (!existsSync(dir)) {\n\t\t\tmkdirSync(dir, { recursive: true });\n\t\t}\n\n\t\tconst SQL = await initSqlJs();\n\t\tconst buffer = existsSync(dbPath) ? readFileSync(dbPath) : undefined;\n\t\tconst db = buffer ? new SQL.Database(buffer) : new SQL.Database();\n\n\t\tdb.run(\"PRAGMA journal_mode = WAL\");\n\t\tdb.run(\"PRAGMA synchronous = NORMAL\");\n\t\tdb.run(\"PRAGMA busy_timeout = 5000\");\n\n\t\tconst storage = new MemoryStorage(db, dbPath);\n\t\tstorage.initSchema();\n\t\treturn storage;\n\t}\n\n\tprivate persist(): void {\n\t\tconst data = this.db.export();\n\t\twriteFileSync(this.dbPath, Buffer.from(data));\n\t}\n\n\tprivate schedulePersist(): void {\n\t\tif (this.persistTimer) {\n\t\t\tclearTimeout(this.persistTimer);\n\t\t}\n\t\tthis.persistTimer = setTimeout(() => {\n\t\t\tthis.persistTimer = null;\n\t\t\tthis.persist();\n\t\t}, 500);\n\t}\n\n\tprivate initSchema(): void {\n\t\tthis.db.run(`\n\t\t\tCREATE TABLE IF NOT EXISTS threads (\n\t\t\t\tthread_id TEXT PRIMARY KEY,\n\t\t\t\tfile_path TEXT NOT NULL,\n\t\t\t\tfile_size INTEGER NOT NULL DEFAULT 0,\n\t\t\t\tfile_mtime INTEGER NOT NULL DEFAULT 0,\n\t\t\t\tcwd TEXT NOT NULL DEFAULT '',\n\t\t\t\tstatus TEXT NOT NULL DEFAULT 'pending',\n\t\t\t\terror_message TEXT,\n\t\t\t\tcreated_at TEXT NOT NULL DEFAULT (datetime('now')),\n\t\t\t\tupdated_at TEXT NOT NULL DEFAULT (datetime('now'))\n\t\t\t)\n\t\t`);\n\t\tthis.db.run(`\n\t\t\tCREATE TABLE IF NOT EXISTS stage1_outputs (\n\t\t\t\tthread_id TEXT PRIMARY KEY,\n\t\t\t\textraction_json TEXT NOT NULL,\n\t\t\t\tcreated_at TEXT NOT NULL DEFAULT (datetime('now')),\n\t\t\t\tFOREIGN KEY (thread_id) REFERENCES threads(thread_id) ON DELETE CASCADE\n\t\t\t)\n\t\t`);\n\t\tthis.db.run(`\n\t\t\tCREATE TABLE IF NOT EXISTS jobs (\n\t\t\t\tid TEXT PRIMARY KEY,\n\t\t\t\tphase TEXT NOT NULL,\n\t\t\t\tthread_id TEXT,\n\t\t\t\tstatus TEXT NOT NULL DEFAULT 'pending',\n\t\t\t\tworker_id TEXT,\n\t\t\t\townership_token TEXT,\n\t\t\t\tlease_expires_at TEXT,\n\t\t\t\terror_message TEXT,\n\t\t\t\tcreated_at TEXT NOT NULL DEFAULT (datetime('now')),\n\t\t\t\tupdated_at TEXT NOT NULL DEFAULT (datetime('now'))\n\t\t\t)\n\t\t`);\n\t\tthis.db.run(\"CREATE INDEX IF NOT EXISTS idx_jobs_phase_status ON jobs(phase, status)\");\n\t\tthis.db.run(\"CREATE INDEX IF NOT EXISTS idx_threads_status ON threads(status)\");\n\t\tthis.db.run(\"CREATE INDEX IF NOT EXISTS idx_threads_cwd ON threads(cwd)\");\n\t\tthis.persist();\n\t}\n\n\tprivate queryAll<T>(sql: string, params: unknown[] = []): T[] {\n\t\tconst stmt = this.db.prepare(sql);\n\t\tstmt.bind(params as (string | number | null | Uint8Array)[]);\n\t\tconst rows: T[] = [];\n\t\twhile (stmt.step()) {\n\t\t\trows.push(stmt.getAsObject() as T);\n\t\t}\n\t\tstmt.free();\n\t\treturn rows;\n\t}\n\n\tprivate queryOne<T>(sql: string, params: unknown[] = []): T | undefined {\n\t\tconst rows = this.queryAll<T>(sql, params);\n\t\treturn rows[0];\n\t}\n\n\t/**\n\t * Insert or update thread records. Skips threads whose file hasn't changed\n\t * (same size + mtime = watermark match).\n\t */\n\tupsertThreads(\n\t\tthreads: Array<{\n\t\t\tthreadId: string;\n\t\t\tfilePath: string;\n\t\t\tfileSize: number;\n\t\t\tfileMtime: number;\n\t\t\tcwd: string;\n\t\t}>,\n\t): { inserted: number; updated: number; skipped: number } {\n\t\tlet inserted = 0;\n\t\tlet updated = 0;\n\t\tlet skipped = 0;\n\n\t\tfor (const t of threads) {\n\t\t\tconst existing = this.queryOne<{ file_size: number; file_mtime: number; status: string }>(\n\t\t\t\t\"SELECT file_size, file_mtime, status FROM threads WHERE thread_id = ?\",\n\t\t\t\t[t.threadId],\n\t\t\t);\n\n\t\t\tif (!existing) {\n\t\t\t\tthis.db.run(\n\t\t\t\t\t\"INSERT INTO threads (thread_id, file_path, file_size, file_mtime, cwd, status) VALUES (?, ?, ?, ?, ?, 'pending')\",\n\t\t\t\t\t[t.threadId, t.filePath, t.fileSize, t.fileMtime, t.cwd],\n\t\t\t\t);\n\t\t\t\tthis.db.run(\n\t\t\t\t\t\"INSERT OR IGNORE INTO jobs (id, phase, thread_id, status) VALUES (?, 'stage1', ?, 'pending')\",\n\t\t\t\t\t[randomUUID(), t.threadId],\n\t\t\t\t);\n\t\t\t\tinserted++;\n\t\t\t} else if (existing.file_size !== t.fileSize || existing.file_mtime !== t.fileMtime) {\n\t\t\t\tthis.db.run(\n\t\t\t\t\t\"UPDATE threads SET file_path = ?, file_size = ?, file_mtime = ?, cwd = ?, status = 'pending', updated_at = datetime('now') WHERE thread_id = ?\",\n\t\t\t\t\t[t.filePath, t.fileSize, t.fileMtime, t.cwd, t.threadId],\n\t\t\t\t);\n\t\t\t\tif (existing.status === \"done\" || existing.status === \"error\") {\n\t\t\t\t\tthis.db.run(\n\t\t\t\t\t\t\"INSERT OR IGNORE INTO jobs (id, phase, thread_id, status) VALUES (?, 'stage1', ?, 'pending')\",\n\t\t\t\t\t\t[randomUUID(), t.threadId],\n\t\t\t\t\t);\n\t\t\t\t}\n\t\t\t\tupdated++;\n\t\t\t} else {\n\t\t\t\tskipped++;\n\t\t\t}\n\t\t}\n\n\t\tthis.schedulePersist();\n\t\treturn { inserted, updated, skipped };\n\t}\n\n\t/**\n\t * Claim up to `limit` stage1 jobs for the given worker.\n\t * Uses lease-based ownership with an ownership_token UUID.\n\t */\n\tclaimStage1Jobs(\n\t\tworkerId: string,\n\t\tlimit: number,\n\t\tleaseSeconds: number,\n\t): Array<{ jobId: string; threadId: string; ownershipToken: string }> {\n\t\tconst token = randomUUID();\n\t\tconst expiresAt = new Date(Date.now() + leaseSeconds * 1000).toISOString();\n\n\t\tthis.db.run(\n\t\t\t`UPDATE jobs SET\n\t\t\t\tstatus = 'claimed',\n\t\t\t\tworker_id = ?,\n\t\t\t\townership_token = ?,\n\t\t\t\tlease_expires_at = ?,\n\t\t\t\tupdated_at = datetime('now')\n\t\t\tWHERE id IN (\n\t\t\t\tSELECT id FROM jobs\n\t\t\t\tWHERE phase = 'stage1'\n\t\t\t\t\tAND (status = 'pending' OR (status = 'claimed' AND lease_expires_at < datetime('now')))\n\t\t\t\tLIMIT ?\n\t\t\t)`,\n\t\t\t[workerId, token, expiresAt, limit],\n\t\t);\n\n\t\tconst rows = this.queryAll<{ id: string; thread_id: string }>(\n\t\t\t\"SELECT id, thread_id FROM jobs WHERE ownership_token = ? AND status = 'claimed'\",\n\t\t\t[token],\n\t\t);\n\n\t\tthis.schedulePersist();\n\n\t\treturn rows.map((r) => ({\n\t\t\tjobId: r.id,\n\t\t\tthreadId: r.thread_id,\n\t\t\townershipToken: token,\n\t\t}));\n\t}\n\n\t/**\n\t * Mark a stage1 job as complete and store the extraction output.\n\t */\n\tcompleteStage1Job(threadId: string, output: string): void {\n\t\tthis.db.run(\n\t\t\t\"UPDATE jobs SET status = 'done', updated_at = datetime('now') WHERE thread_id = ? AND phase = 'stage1' AND status = 'claimed'\",\n\t\t\t[threadId],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"INSERT OR REPLACE INTO stage1_outputs (thread_id, extraction_json, created_at) VALUES (?, ?, datetime('now'))\",\n\t\t\t[threadId, output],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"UPDATE threads SET status = 'done', updated_at = datetime('now') WHERE thread_id = ?\",\n\t\t\t[threadId],\n\t\t);\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Mark a stage1 job as errored.\n\t */\n\tfailStage1Job(threadId: string, errorMessage: string): void {\n\t\tthis.db.run(\n\t\t\t\"UPDATE jobs SET status = 'error', error_message = ?, updated_at = datetime('now') WHERE thread_id = ? AND phase = 'stage1' AND status = 'claimed'\",\n\t\t\t[errorMessage, threadId],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"UPDATE threads SET status = 'error', error_message = ?, updated_at = datetime('now') WHERE thread_id = ?\",\n\t\t\t[errorMessage, threadId],\n\t\t);\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Try to claim the global phase 2 consolidation job.\n\t * Only one worker can hold this at a time.\n\t */\n\ttryClaimGlobalPhase2Job(\n\t\tworkerId: string,\n\t\tleaseSeconds: number,\n\t): { jobId: string; ownershipToken: string } | null {\n\t\tconst token = randomUUID();\n\t\tconst expiresAt = new Date(Date.now() + leaseSeconds * 1000).toISOString();\n\n\t\tconst pendingStage1 = this.queryOne<{ cnt: number }>(\n\t\t\t\"SELECT COUNT(*) as cnt FROM jobs WHERE phase = 'stage1' AND status IN ('pending', 'claimed')\",\n\t\t);\n\n\t\tif (pendingStage1 && pendingStage1.cnt > 0) {\n\t\t\treturn null;\n\t\t}\n\n\t\tconst existingPhase2 = this.queryOne<{ id: string }>(\n\t\t\t\"SELECT id FROM jobs WHERE phase = 'stage2' AND status = 'claimed' AND lease_expires_at > datetime('now')\",\n\t\t);\n\n\t\tif (existingPhase2) {\n\t\t\treturn null;\n\t\t}\n\n\t\tconst outputCount = this.queryOne<{ cnt: number }>(\n\t\t\t\"SELECT COUNT(*) as cnt FROM stage1_outputs\",\n\t\t);\n\n\t\tif (!outputCount || outputCount.cnt === 0) {\n\t\t\treturn null;\n\t\t}\n\n\t\tconst jobId = randomUUID();\n\t\tthis.db.run(\n\t\t\t\"INSERT INTO jobs (id, phase, status, worker_id, ownership_token, lease_expires_at) VALUES (?, 'stage2', 'claimed', ?, ?, ?)\",\n\t\t\t[jobId, workerId, token, expiresAt],\n\t\t);\n\n\t\tthis.schedulePersist();\n\t\treturn { jobId, ownershipToken: token };\n\t}\n\n\t/**\n\t * Complete the phase 2 consolidation job.\n\t */\n\tcompletePhase2Job(jobId: string): void {\n\t\tthis.db.run(\n\t\t\t\"UPDATE jobs SET status = 'done', updated_at = datetime('now') WHERE id = ? AND phase = 'stage2'\",\n\t\t\t[jobId],\n\t\t);\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Get all stage1 extraction outputs.\n\t */\n\tgetStage1Outputs(): Array<{ threadId: string; extractionJson: string }> {\n\t\tconst rows = this.queryAll<{ thread_id: string; extraction_json: string }>(\n\t\t\t\"SELECT thread_id, extraction_json FROM stage1_outputs\",\n\t\t);\n\n\t\treturn rows.map((r) => ({\n\t\t\tthreadId: r.thread_id,\n\t\t\textractionJson: r.extraction_json,\n\t\t}));\n\t}\n\n\t/**\n\t * Get all stage1 outputs for a specific cwd.\n\t */\n\tgetStage1OutputsForCwd(cwd: string): Array<{ threadId: string; extractionJson: string }> {\n\t\tconst rows = this.queryAll<{ thread_id: string; extraction_json: string }>(\n\t\t\t`SELECT s.thread_id, s.extraction_json FROM stage1_outputs s\n\t\t\tINNER JOIN threads t ON t.thread_id = s.thread_id\n\t\t\tWHERE t.cwd = ?`,\n\t\t\t[cwd],\n\t\t);\n\n\t\treturn rows.map((r) => ({\n\t\t\tthreadId: r.thread_id,\n\t\t\textractionJson: r.extraction_json,\n\t\t}));\n\t}\n\n\t/**\n\t * Get thread info by ID.\n\t */\n\tgetThread(threadId: string): ThreadRow | undefined {\n\t\treturn this.queryOne<ThreadRow>(\n\t\t\t\"SELECT * FROM threads WHERE thread_id = ?\",\n\t\t\t[threadId],\n\t\t);\n\t}\n\n\t/**\n\t * Get pipeline statistics.\n\t */\n\tgetStats(): {\n\t\ttotalThreads: number;\n\t\tpendingThreads: number;\n\t\tdoneThreads: number;\n\t\terrorThreads: number;\n\t\ttotalStage1Outputs: number;\n\t\tpendingStage1Jobs: number;\n\t} {\n\t\tconst threads = this.queryOne<{ total: number; pending: number; done: number; errors: number }>(`\n\t\t\tSELECT\n\t\t\t\tCOUNT(*) as total,\n\t\t\t\tSUM(CASE WHEN status = 'pending' THEN 1 ELSE 0 END) as pending,\n\t\t\t\tSUM(CASE WHEN status = 'done' THEN 1 ELSE 0 END) as done,\n\t\t\t\tSUM(CASE WHEN status = 'error' THEN 1 ELSE 0 END) as errors\n\t\t\tFROM threads\n\t\t`)!;\n\n\t\tconst outputs = this.queryOne<{ cnt: number }>(\n\t\t\t\"SELECT COUNT(*) as cnt FROM stage1_outputs\",\n\t\t)!;\n\n\t\tconst pendingJobs = this.queryOne<{ cnt: number }>(\n\t\t\t\"SELECT COUNT(*) as cnt FROM jobs WHERE phase = 'stage1' AND status IN ('pending', 'claimed')\",\n\t\t)!;\n\n\t\treturn {\n\t\t\ttotalThreads: threads.total,\n\t\t\tpendingThreads: threads.pending,\n\t\t\tdoneThreads: threads.done,\n\t\t\terrorThreads: threads.errors,\n\t\t\ttotalStage1Outputs: outputs.cnt,\n\t\t\tpendingStage1Jobs: pendingJobs.cnt,\n\t\t};\n\t}\n\n\t/**\n\t * Clear all data (for /memory clear).\n\t */\n\tclearAll(): void {\n\t\tthis.db.run(\"DELETE FROM stage1_outputs\");\n\t\tthis.db.run(\"DELETE FROM jobs\");\n\t\tthis.db.run(\"DELETE FROM threads\");\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Clear data for a specific cwd (for /memory clear in project scope).\n\t */\n\tclearForCwd(cwd: string): void {\n\t\tthis.db.run(\n\t\t\t\"DELETE FROM stage1_outputs WHERE thread_id IN (SELECT thread_id FROM threads WHERE cwd = ?)\",\n\t\t\t[cwd],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"DELETE FROM jobs WHERE thread_id IN (SELECT thread_id FROM threads WHERE cwd = ?)\",\n\t\t\t[cwd],\n\t\t);\n\t\tthis.db.run(\"DELETE FROM threads WHERE cwd = ?\", [cwd]);\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Reset all threads to pending (for /memory rebuild).\n\t */\n\tresetAllForCwd(cwd: string): void {\n\t\tthis.db.run(\n\t\t\t\"DELETE FROM stage1_outputs WHERE thread_id IN (SELECT thread_id FROM threads WHERE cwd = ?)\",\n\t\t\t[cwd],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"DELETE FROM jobs WHERE thread_id IN (SELECT thread_id FROM threads WHERE cwd = ?)\",\n\t\t\t[cwd],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"UPDATE threads SET status = 'pending', updated_at = datetime('now') WHERE cwd = ?\",\n\t\t\t[cwd],\n\t\t);\n\n\t\tconst threads = this.queryAll<{ thread_id: string }>(\n\t\t\t\"SELECT thread_id FROM threads WHERE cwd = ?\",\n\t\t\t[cwd],\n\t\t);\n\n\t\tfor (const t of threads) {\n\t\t\tthis.db.run(\n\t\t\t\t\"INSERT INTO jobs (id, phase, thread_id, status) VALUES (?, 'stage1', ?, 'pending')\",\n\t\t\t\t[randomUUID(), t.thread_id],\n\t\t\t);\n\t\t}\n\t\tthis.schedulePersist();\n\t}\n\n\tclose(): void {\n\t\tif (this.persistTimer) {\n\t\t\tclearTimeout(this.persistTimer);\n\t\t\tthis.persistTimer = null;\n\t\t}\n\t\tthis.persist();\n\t\tthis.db.close();\n\t}\n}\n"]}
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* SQLite storage for the memory extraction pipeline.\n *\n * Tables:\n * - threads: tracks session files and their processing state\n * - stage1_outputs: stores per-thread extraction results\n * - jobs: lease-based job queue for pipeline phases\n */\n\nimport initSqlJs, { type Database as SqlJsDatabase } from \"sql.js\";\nimport { randomUUID } from \"crypto\";\nimport { existsSync, mkdirSync, readFileSync } from \"fs\";\nimport { dirname } from \"path\";\nimport { atomicWriteDbSnapshotSync } from \"../../../core/db-snapshot.js\";\n\nexport interface ThreadRow {\n\tthread_id: string;\n\tfile_path: string;\n\tfile_size: number;\n\tfile_mtime: number;\n\tcwd: string;\n\tstatus: \"pending\" | \"processing\" | \"done\" | \"error\";\n\terror_message: string | null;\n\tcreated_at: string;\n\tupdated_at: string;\n}\n\nexport interface Stage1OutputRow {\n\tthread_id: string;\n\textraction_json: string;\n\tcreated_at: string;\n}\n\nexport interface JobRow {\n\tid: string;\n\tphase: \"stage1\" | \"stage2\";\n\tthread_id: string | null;\n\tstatus: \"pending\" | \"claimed\" | \"done\" | \"error\";\n\tworker_id: string | null;\n\townership_token: string | null;\n\tlease_expires_at: string | null;\n\terror_message: string | null;\n\tcreated_at: string;\n\tupdated_at: string;\n}\n\nexport class MemoryStorage {\n\tprivate db: SqlJsDatabase;\n\tprivate dbPath: string;\n\tprivate persistTimer: ReturnType<typeof setTimeout> | null = null;\n\n\tprivate constructor(db: SqlJsDatabase, dbPath: string) {\n\t\tthis.db = db;\n\t\tthis.dbPath = dbPath;\n\t}\n\n\tstatic async create(dbPath: string): Promise<MemoryStorage> {\n\t\tconst dir = dirname(dbPath);\n\t\tif (!existsSync(dir)) {\n\t\t\tmkdirSync(dir, { recursive: true });\n\t\t}\n\n\t\tconst SQL = await initSqlJs();\n\t\tconst buffer = existsSync(dbPath) ? readFileSync(dbPath) : undefined;\n\t\tconst db = buffer ? new SQL.Database(buffer) : new SQL.Database();\n\n\t\tdb.run(\"PRAGMA journal_mode = WAL\");\n\t\tdb.run(\"PRAGMA synchronous = NORMAL\");\n\t\tdb.run(\"PRAGMA busy_timeout = 5000\");\n\n\t\tconst storage = new MemoryStorage(db, dbPath);\n\t\tstorage.initSchema();\n\t\treturn storage;\n\t}\n\n\tprivate persist(): void {\n\t\tconst data = this.db.export();\n\t\tatomicWriteDbSnapshotSync(this.dbPath, data);\n\t}\n\n\tprivate schedulePersist(): void {\n\t\tif (this.persistTimer) {\n\t\t\tclearTimeout(this.persistTimer);\n\t\t}\n\t\tthis.persistTimer = setTimeout(() => {\n\t\t\tthis.persistTimer = null;\n\t\t\tthis.persist();\n\t\t}, 500);\n\t}\n\n\tprivate initSchema(): void {\n\t\tthis.db.run(`\n\t\t\tCREATE TABLE IF NOT EXISTS threads (\n\t\t\t\tthread_id TEXT PRIMARY KEY,\n\t\t\t\tfile_path TEXT NOT NULL,\n\t\t\t\tfile_size INTEGER NOT NULL DEFAULT 0,\n\t\t\t\tfile_mtime INTEGER NOT NULL DEFAULT 0,\n\t\t\t\tcwd TEXT NOT NULL DEFAULT '',\n\t\t\t\tstatus TEXT NOT NULL DEFAULT 'pending',\n\t\t\t\terror_message TEXT,\n\t\t\t\tcreated_at TEXT NOT NULL DEFAULT (datetime('now')),\n\t\t\t\tupdated_at TEXT NOT NULL DEFAULT (datetime('now'))\n\t\t\t)\n\t\t`);\n\t\tthis.db.run(`\n\t\t\tCREATE TABLE IF NOT EXISTS stage1_outputs (\n\t\t\t\tthread_id TEXT PRIMARY KEY,\n\t\t\t\textraction_json TEXT NOT NULL,\n\t\t\t\tcreated_at TEXT NOT NULL DEFAULT (datetime('now')),\n\t\t\t\tFOREIGN KEY (thread_id) REFERENCES threads(thread_id) ON DELETE CASCADE\n\t\t\t)\n\t\t`);\n\t\tthis.db.run(`\n\t\t\tCREATE TABLE IF NOT EXISTS jobs (\n\t\t\t\tid TEXT PRIMARY KEY,\n\t\t\t\tphase TEXT NOT NULL,\n\t\t\t\tthread_id TEXT,\n\t\t\t\tstatus TEXT NOT NULL DEFAULT 'pending',\n\t\t\t\tworker_id TEXT,\n\t\t\t\townership_token TEXT,\n\t\t\t\tlease_expires_at TEXT,\n\t\t\t\terror_message TEXT,\n\t\t\t\tcreated_at TEXT NOT NULL DEFAULT (datetime('now')),\n\t\t\t\tupdated_at TEXT NOT NULL DEFAULT (datetime('now'))\n\t\t\t)\n\t\t`);\n\t\tthis.db.run(\"CREATE INDEX IF NOT EXISTS idx_jobs_phase_status ON jobs(phase, status)\");\n\t\tthis.db.run(\"CREATE INDEX IF NOT EXISTS idx_threads_status ON threads(status)\");\n\t\tthis.db.run(\"CREATE INDEX IF NOT EXISTS idx_threads_cwd ON threads(cwd)\");\n\t\tthis.persist();\n\t}\n\n\tprivate queryAll<T>(sql: string, params: unknown[] = []): T[] {\n\t\tconst stmt = this.db.prepare(sql);\n\t\tstmt.bind(params as (string | number | null | Uint8Array)[]);\n\t\tconst rows: T[] = [];\n\t\twhile (stmt.step()) {\n\t\t\trows.push(stmt.getAsObject() as T);\n\t\t}\n\t\tstmt.free();\n\t\treturn rows;\n\t}\n\n\tprivate queryOne<T>(sql: string, params: unknown[] = []): T | undefined {\n\t\tconst rows = this.queryAll<T>(sql, params);\n\t\treturn rows[0];\n\t}\n\n\t/**\n\t * Insert or update thread records. Skips threads whose file hasn't changed\n\t * (same size + mtime = watermark match).\n\t */\n\tupsertThreads(\n\t\tthreads: Array<{\n\t\t\tthreadId: string;\n\t\t\tfilePath: string;\n\t\t\tfileSize: number;\n\t\t\tfileMtime: number;\n\t\t\tcwd: string;\n\t\t}>,\n\t): { inserted: number; updated: number; skipped: number } {\n\t\tlet inserted = 0;\n\t\tlet updated = 0;\n\t\tlet skipped = 0;\n\n\t\tfor (const t of threads) {\n\t\t\tconst existing = this.queryOne<{ file_size: number; file_mtime: number; status: string }>(\n\t\t\t\t\"SELECT file_size, file_mtime, status FROM threads WHERE thread_id = ?\",\n\t\t\t\t[t.threadId],\n\t\t\t);\n\n\t\t\tif (!existing) {\n\t\t\t\tthis.db.run(\n\t\t\t\t\t\"INSERT INTO threads (thread_id, file_path, file_size, file_mtime, cwd, status) VALUES (?, ?, ?, ?, ?, 'pending')\",\n\t\t\t\t\t[t.threadId, t.filePath, t.fileSize, t.fileMtime, t.cwd],\n\t\t\t\t);\n\t\t\t\tthis.db.run(\n\t\t\t\t\t\"INSERT OR IGNORE INTO jobs (id, phase, thread_id, status) VALUES (?, 'stage1', ?, 'pending')\",\n\t\t\t\t\t[randomUUID(), t.threadId],\n\t\t\t\t);\n\t\t\t\tinserted++;\n\t\t\t} else if (existing.file_size !== t.fileSize || existing.file_mtime !== t.fileMtime) {\n\t\t\t\tthis.db.run(\n\t\t\t\t\t\"UPDATE threads SET file_path = ?, file_size = ?, file_mtime = ?, cwd = ?, status = 'pending', updated_at = datetime('now') WHERE thread_id = ?\",\n\t\t\t\t\t[t.filePath, t.fileSize, t.fileMtime, t.cwd, t.threadId],\n\t\t\t\t);\n\t\t\t\tif (existing.status === \"done\" || existing.status === \"error\") {\n\t\t\t\t\tthis.db.run(\n\t\t\t\t\t\t\"INSERT OR IGNORE INTO jobs (id, phase, thread_id, status) VALUES (?, 'stage1', ?, 'pending')\",\n\t\t\t\t\t\t[randomUUID(), t.threadId],\n\t\t\t\t\t);\n\t\t\t\t}\n\t\t\t\tupdated++;\n\t\t\t} else {\n\t\t\t\tskipped++;\n\t\t\t}\n\t\t}\n\n\t\tthis.schedulePersist();\n\t\treturn { inserted, updated, skipped };\n\t}\n\n\t/**\n\t * Claim up to `limit` stage1 jobs for the given worker.\n\t * Uses lease-based ownership with an ownership_token UUID.\n\t */\n\tclaimStage1Jobs(\n\t\tworkerId: string,\n\t\tlimit: number,\n\t\tleaseSeconds: number,\n\t): Array<{ jobId: string; threadId: string; ownershipToken: string }> {\n\t\tconst token = randomUUID();\n\t\tconst expiresAt = new Date(Date.now() + leaseSeconds * 1000).toISOString();\n\n\t\tthis.db.run(\n\t\t\t`UPDATE jobs SET\n\t\t\t\tstatus = 'claimed',\n\t\t\t\tworker_id = ?,\n\t\t\t\townership_token = ?,\n\t\t\t\tlease_expires_at = ?,\n\t\t\t\tupdated_at = datetime('now')\n\t\t\tWHERE id IN (\n\t\t\t\tSELECT id FROM jobs\n\t\t\t\tWHERE phase = 'stage1'\n\t\t\t\t\tAND (status = 'pending' OR (status = 'claimed' AND lease_expires_at < datetime('now')))\n\t\t\t\tLIMIT ?\n\t\t\t)`,\n\t\t\t[workerId, token, expiresAt, limit],\n\t\t);\n\n\t\tconst rows = this.queryAll<{ id: string; thread_id: string }>(\n\t\t\t\"SELECT id, thread_id FROM jobs WHERE ownership_token = ? AND status = 'claimed'\",\n\t\t\t[token],\n\t\t);\n\n\t\tthis.schedulePersist();\n\n\t\treturn rows.map((r) => ({\n\t\t\tjobId: r.id,\n\t\t\tthreadId: r.thread_id,\n\t\t\townershipToken: token,\n\t\t}));\n\t}\n\n\t/**\n\t * Mark a stage1 job as complete and store the extraction output.\n\t */\n\tcompleteStage1Job(threadId: string, output: string): void {\n\t\tthis.db.run(\n\t\t\t\"UPDATE jobs SET status = 'done', updated_at = datetime('now') WHERE thread_id = ? AND phase = 'stage1' AND status = 'claimed'\",\n\t\t\t[threadId],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"INSERT OR REPLACE INTO stage1_outputs (thread_id, extraction_json, created_at) VALUES (?, ?, datetime('now'))\",\n\t\t\t[threadId, output],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"UPDATE threads SET status = 'done', updated_at = datetime('now') WHERE thread_id = ?\",\n\t\t\t[threadId],\n\t\t);\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Mark a stage1 job as errored.\n\t */\n\tfailStage1Job(threadId: string, errorMessage: string): void {\n\t\tthis.db.run(\n\t\t\t\"UPDATE jobs SET status = 'error', error_message = ?, updated_at = datetime('now') WHERE thread_id = ? AND phase = 'stage1' AND status = 'claimed'\",\n\t\t\t[errorMessage, threadId],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"UPDATE threads SET status = 'error', error_message = ?, updated_at = datetime('now') WHERE thread_id = ?\",\n\t\t\t[errorMessage, threadId],\n\t\t);\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Try to claim the global phase 2 consolidation job.\n\t * Only one worker can hold this at a time.\n\t */\n\ttryClaimGlobalPhase2Job(\n\t\tworkerId: string,\n\t\tleaseSeconds: number,\n\t): { jobId: string; ownershipToken: string } | null {\n\t\tconst token = randomUUID();\n\t\tconst expiresAt = new Date(Date.now() + leaseSeconds * 1000).toISOString();\n\n\t\tconst pendingStage1 = this.queryOne<{ cnt: number }>(\n\t\t\t\"SELECT COUNT(*) as cnt FROM jobs WHERE phase = 'stage1' AND status IN ('pending', 'claimed')\",\n\t\t);\n\n\t\tif (pendingStage1 && pendingStage1.cnt > 0) {\n\t\t\treturn null;\n\t\t}\n\n\t\tconst existingPhase2 = this.queryOne<{ id: string }>(\n\t\t\t\"SELECT id FROM jobs WHERE phase = 'stage2' AND status = 'claimed' AND lease_expires_at > datetime('now')\",\n\t\t);\n\n\t\tif (existingPhase2) {\n\t\t\treturn null;\n\t\t}\n\n\t\tconst outputCount = this.queryOne<{ cnt: number }>(\n\t\t\t\"SELECT COUNT(*) as cnt FROM stage1_outputs\",\n\t\t);\n\n\t\tif (!outputCount || outputCount.cnt === 0) {\n\t\t\treturn null;\n\t\t}\n\n\t\tconst jobId = randomUUID();\n\t\tthis.db.run(\n\t\t\t\"INSERT INTO jobs (id, phase, status, worker_id, ownership_token, lease_expires_at) VALUES (?, 'stage2', 'claimed', ?, ?, ?)\",\n\t\t\t[jobId, workerId, token, expiresAt],\n\t\t);\n\n\t\tthis.schedulePersist();\n\t\treturn { jobId, ownershipToken: token };\n\t}\n\n\t/**\n\t * Complete the phase 2 consolidation job.\n\t */\n\tcompletePhase2Job(jobId: string): void {\n\t\tthis.db.run(\n\t\t\t\"UPDATE jobs SET status = 'done', updated_at = datetime('now') WHERE id = ? AND phase = 'stage2'\",\n\t\t\t[jobId],\n\t\t);\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Get all stage1 extraction outputs.\n\t */\n\tgetStage1Outputs(): Array<{ threadId: string; extractionJson: string }> {\n\t\tconst rows = this.queryAll<{ thread_id: string; extraction_json: string }>(\n\t\t\t\"SELECT thread_id, extraction_json FROM stage1_outputs\",\n\t\t);\n\n\t\treturn rows.map((r) => ({\n\t\t\tthreadId: r.thread_id,\n\t\t\textractionJson: r.extraction_json,\n\t\t}));\n\t}\n\n\t/**\n\t * Get all stage1 outputs for a specific cwd.\n\t */\n\tgetStage1OutputsForCwd(cwd: string): Array<{ threadId: string; extractionJson: string }> {\n\t\tconst rows = this.queryAll<{ thread_id: string; extraction_json: string }>(\n\t\t\t`SELECT s.thread_id, s.extraction_json FROM stage1_outputs s\n\t\t\tINNER JOIN threads t ON t.thread_id = s.thread_id\n\t\t\tWHERE t.cwd = ?`,\n\t\t\t[cwd],\n\t\t);\n\n\t\treturn rows.map((r) => ({\n\t\t\tthreadId: r.thread_id,\n\t\t\textractionJson: r.extraction_json,\n\t\t}));\n\t}\n\n\t/**\n\t * Get thread info by ID.\n\t */\n\tgetThread(threadId: string): ThreadRow | undefined {\n\t\treturn this.queryOne<ThreadRow>(\n\t\t\t\"SELECT * FROM threads WHERE thread_id = ?\",\n\t\t\t[threadId],\n\t\t);\n\t}\n\n\t/**\n\t * Get pipeline statistics.\n\t */\n\tgetStats(): {\n\t\ttotalThreads: number;\n\t\tpendingThreads: number;\n\t\tdoneThreads: number;\n\t\terrorThreads: number;\n\t\ttotalStage1Outputs: number;\n\t\tpendingStage1Jobs: number;\n\t} {\n\t\tconst threads = this.queryOne<{ total: number; pending: number; done: number; errors: number }>(`\n\t\t\tSELECT\n\t\t\t\tCOUNT(*) as total,\n\t\t\t\tSUM(CASE WHEN status = 'pending' THEN 1 ELSE 0 END) as pending,\n\t\t\t\tSUM(CASE WHEN status = 'done' THEN 1 ELSE 0 END) as done,\n\t\t\t\tSUM(CASE WHEN status = 'error' THEN 1 ELSE 0 END) as errors\n\t\t\tFROM threads\n\t\t`)!;\n\n\t\tconst outputs = this.queryOne<{ cnt: number }>(\n\t\t\t\"SELECT COUNT(*) as cnt FROM stage1_outputs\",\n\t\t)!;\n\n\t\tconst pendingJobs = this.queryOne<{ cnt: number }>(\n\t\t\t\"SELECT COUNT(*) as cnt FROM jobs WHERE phase = 'stage1' AND status IN ('pending', 'claimed')\",\n\t\t)!;\n\n\t\treturn {\n\t\t\ttotalThreads: threads.total,\n\t\t\tpendingThreads: threads.pending,\n\t\t\tdoneThreads: threads.done,\n\t\t\terrorThreads: threads.errors,\n\t\t\ttotalStage1Outputs: outputs.cnt,\n\t\t\tpendingStage1Jobs: pendingJobs.cnt,\n\t\t};\n\t}\n\n\t/**\n\t * Clear all data (for /memory clear).\n\t */\n\tclearAll(): void {\n\t\tthis.db.run(\"DELETE FROM stage1_outputs\");\n\t\tthis.db.run(\"DELETE FROM jobs\");\n\t\tthis.db.run(\"DELETE FROM threads\");\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Clear data for a specific cwd (for /memory clear in project scope).\n\t */\n\tclearForCwd(cwd: string): void {\n\t\tthis.db.run(\n\t\t\t\"DELETE FROM stage1_outputs WHERE thread_id IN (SELECT thread_id FROM threads WHERE cwd = ?)\",\n\t\t\t[cwd],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"DELETE FROM jobs WHERE thread_id IN (SELECT thread_id FROM threads WHERE cwd = ?)\",\n\t\t\t[cwd],\n\t\t);\n\t\tthis.db.run(\"DELETE FROM threads WHERE cwd = ?\", [cwd]);\n\t\tthis.schedulePersist();\n\t}\n\n\t/**\n\t * Reset all threads to pending (for /memory rebuild).\n\t */\n\tresetAllForCwd(cwd: string): void {\n\t\tthis.db.run(\n\t\t\t\"DELETE FROM stage1_outputs WHERE thread_id IN (SELECT thread_id FROM threads WHERE cwd = ?)\",\n\t\t\t[cwd],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"DELETE FROM jobs WHERE thread_id IN (SELECT thread_id FROM threads WHERE cwd = ?)\",\n\t\t\t[cwd],\n\t\t);\n\t\tthis.db.run(\n\t\t\t\"UPDATE threads SET status = 'pending', updated_at = datetime('now') WHERE cwd = ?\",\n\t\t\t[cwd],\n\t\t);\n\n\t\tconst threads = this.queryAll<{ thread_id: string }>(\n\t\t\t\"SELECT thread_id FROM threads WHERE cwd = ?\",\n\t\t\t[cwd],\n\t\t);\n\n\t\tfor (const t of threads) {\n\t\t\tthis.db.run(\n\t\t\t\t\"INSERT INTO jobs (id, phase, thread_id, status) VALUES (?, 'stage1', ?, 'pending')\",\n\t\t\t\t[randomUUID(), t.thread_id],\n\t\t\t);\n\t\t}\n\t\tthis.schedulePersist();\n\t}\n\n\tclose(): void {\n\t\tif (this.persistTimer) {\n\t\t\tclearTimeout(this.persistTimer);\n\t\t\tthis.persistTimer = null;\n\t\t}\n\t\tthis.persist();\n\t\tthis.db.close();\n\t}\n}\n"]}

package/packages/pi-coding-agent/src/core/agent-session-abort-order.test.ts

@@ -120,6 +120,7 @@ describe("#4243 — abort() must run before _disconnectFromAgent()", () => {
 
 	it("newSession() invokes abort() before _disconnectFromAgent()", async () => {
 		const session = await createSession();
+		(session as any).agent.state.isStreaming = true;
 		const order = recordCallOrder(session as any, ["abort", "_disconnectFromAgent"]);
 
 		const ok = await session.newSession();
@@ -138,6 +139,40 @@ describe("#4243 — abort() must run before _disconnectFromAgent()", () => {
 		);
 	});
 
+	it("newSession() waits instead of aborting when the prior turn is idle but not settled", async () => {
+		const session = await createSession();
+		const order: string[] = [];
+		let releaseIdle!: () => void;
+		const idle = new Promise<void>((resolve) => {
+			releaseIdle = resolve;
+		});
+
+		(session as any).agent.state.isStreaming = false;
+		(session as any).agent.waitForIdle = () => {
+			order.push("waitForIdle");
+			return idle;
+		};
+		(session as any).abort = async () => {
+			order.push("abort");
+		};
+		const originalDisconnect = (session as any)._disconnectFromAgent.bind(session);
+		(session as any)._disconnectFromAgent = () => {
+			order.push("_disconnectFromAgent");
+			originalDisconnect();
+		};
+
+		const pendingNewSession = session.newSession();
+		await Promise.resolve();
+		assert.deepEqual(order, ["waitForIdle"]);
+		assert.equal(order.includes("abort"), false);
+
+		releaseIdle();
+		const ok = await pendingNewSession;
+		assert.equal(ok, true);
+		assert.deepEqual(order, ["waitForIdle", "_disconnectFromAgent"]);
+		assert.equal(order.includes("abort"), false);
+	});
+
 	it("newSession() waits instead of aborting while agent_end processing is still streaming", async () => {
 		const session = await createSession();
 		const order: string[] = [];
@@ -432,6 +467,7 @@ describe("#4243 — abort() must run before _disconnectFromAgent()", () => {
 		const sessionFile = session.sessionFile;
 		assert.ok(typeof sessionFile === "string" && sessionFile.length > 0, "need a session file to switch to");
 
+		(session as any).agent.state.isStreaming = true;
 		const order = recordCallOrder(session as any, ["abort", "_disconnectFromAgent"]);
 
 		const ok = await session.switchSession(sessionFile);

package/packages/pi-coding-agent/src/core/agent-session-tool-refresh.test.ts

@@ -1,3 +1,4 @@
+// GSD2 - Agent session workspace-root refresh regression tests
 // Regression test for #3616: newSession() must restore the full tool set
 // when cwd is unchanged.
 //
@@ -26,7 +27,7 @@ import { SettingsManager } from "./settings-manager.js";
 
 let testDir: string;
 
-async function createSession(): Promise<AgentSession> {
+async function createSession(options: { workspaceRootRef?: { current: string } } = {}): Promise<AgentSession> {
 	const agentDir = join(testDir, "agent-home");
 	const authStorage = AuthStorage.inMemory({});
 	const modelRegistry = new ModelRegistry(authStorage, join(agentDir, "models.json"));
@@ -48,6 +49,7 @@ async function createSession(): Promise<AgentSession> {
 		cwd: testDir,
 		resourceLoader,
 		modelRegistry,
+		workspaceRootRef: options.workspaceRootRef,
 	});
 }
 
@@ -130,4 +132,41 @@ describe("#3616 — newSession() restores narrowed tool set when cwd unchanged",
 			"cwd-changed branch must rebuild with includeAllExtensionTools: true",
 		);
 	});
+
+	it("uses explicit workspaceRoot option instead of process.cwd() when rebuilding runtime", async () => {
+		const session = await createSession();
+		const explicitWorkspaceRoot = mkdtempSync(join(testDir, "explicit-workspace-"));
+		(session as any)._cwd = process.cwd();
+
+		let buildRuntimeCalled = false;
+		let capturedBuildOptions: { includeAllExtensionTools?: boolean } | undefined;
+		const originalBuild = (session as any)._buildRuntime.bind(session);
+		(session as any)._buildRuntime = (options?: { includeAllExtensionTools?: boolean }) => {
+			buildRuntimeCalled = true;
+			capturedBuildOptions = options;
+			return originalBuild(options);
+		};
+
+		const ok = await session.newSession({ workspaceRoot: explicitWorkspaceRoot });
+		assert.equal(ok, true);
+		assert.equal((session as any)._cwd, explicitWorkspaceRoot);
+		assert.ok(buildRuntimeCalled, "explicit workspace root differing from prior root must rebuild runtime");
+		assert.strictEqual(
+			capturedBuildOptions?.includeAllExtensionTools,
+			true,
+			"explicit workspaceRoot rebuild must pass includeAllExtensionTools: true",
+		);
+	});
+
+	it("updates provider workspace root ref when newSession uses explicit workspaceRoot", async () => {
+		const workspaceRootRef = { current: "" };
+		const session = await createSession({ workspaceRootRef });
+		const explicitWorkspaceRoot = mkdtempSync(join(testDir, "provider-workspace-"));
+
+		assert.equal(workspaceRootRef.current, testDir);
+
+		const ok = await session.newSession({ workspaceRoot: explicitWorkspaceRoot });
+		assert.equal(ok, true);
+		assert.equal(workspaceRootRef.current, explicitWorkspaceRoot);
+	});
 });

package/packages/pi-coding-agent/src/core/agent-session.ts

@@ -1,3 +1,4 @@
+// GSD2 - Agent session lifecycle and workspace runtime coordination
 /**
  * AgentSession - Core abstraction for agent lifecycle and session management.
  *
@@ -167,6 +168,8 @@ export interface AgentSessionConfig {
 	baseToolsOverride?: Record<string, AgentTool>;
 	/** Mutable ref used by Agent to access the current ExtensionRunner */
 	extensionRunnerRef?: { current?: ExtensionRunner };
+	/** Mutable ref used by providers to access the current workspace root. */
+	workspaceRootRef?: { current: string };
 	/** Optional: check if the claude-code CLI provider is ready (installed + authed).
 	 * Passed through to RetryHandler for third-party block recovery (#3772). */
 	isClaudeCodeReady?: () => boolean;
@@ -284,6 +287,7 @@ export class AgentSession {
 	private _baseToolRegistry: Map<string, AgentTool> = new Map();
 	private _cwd: string;
 	private _extensionRunnerRef?: { current?: ExtensionRunner };
+	private _workspaceRootRef?: { current: string };
 	private _initialActiveToolNames?: string[];
 	private _baseToolsOverride?: Record<string, AgentTool>;
 	private _extensionUIContext?: ExtensionUIContext;
@@ -305,6 +309,8 @@ export class AgentSession {
 
 	// Base system prompt (without extension appends) - used to apply fresh appends each turn
 	private _baseSystemPrompt = "";
+	// Optional prompt-only skill catalog filter. Skills remain loaded and invocable by name.
+	private _visibleSkillNames: Set<string> | undefined = undefined;
 
 	constructor(config: AgentSessionConfig) {
 		this.agent = config.agent;
@@ -321,6 +327,10 @@ export class AgentSession {
 			this._modelRegistry,
 		);
 		this._extensionRunnerRef = config.extensionRunnerRef;
+		this._workspaceRootRef = config.workspaceRootRef;
+		if (this._workspaceRootRef) {
+			this._workspaceRootRef.current = this._cwd;
+		}
 		this._initialActiveToolNames = config.initialActiveToolNames;
 		this._baseToolsOverride = config.baseToolsOverride;
 
@@ -867,6 +877,25 @@ export class AgentSession {
 		this.agent.setSystemPrompt(this._baseSystemPrompt);
 	}
 
+	/**
+	 * Set or clear a prompt-only filter for the <available_skills> catalog.
+	 *
+	 * This does not unload skills or disable the Skill tool. It only controls
+	 * which loaded skills are advertised in the system prompt on rebuild.
+	 */
+	setVisibleSkillsByName(skillNames: string[] | undefined): void {
+		this._visibleSkillNames = skillNames === undefined
+			? undefined
+			: new Set(skillNames.map((name) => name.trim().toLowerCase()).filter(Boolean));
+		this._baseSystemPrompt = this._rebuildSystemPrompt(this.getActiveToolNames());
+		this.agent.setSystemPrompt(this._baseSystemPrompt);
+	}
+
+	/** Get the current prompt-only skill catalog filter, if one is active. */
+	getVisibleSkillNames(): string[] | undefined {
+		return this._visibleSkillNames ? [...this._visibleSkillNames] : undefined;
+	}
+
 	/** Whether compaction or branch summarization is currently running */
 	get isCompacting(): boolean {
 		return this._compactionOrchestrator.isCompacting;
@@ -1045,6 +1074,9 @@ export class AgentSession {
 		return buildSystemPrompt({
 			cwd: this._cwd,
 			skills: loadedSkills,
+			skillFilter: this._visibleSkillNames
+				? (skill) => this._visibleSkillNames!.has(skill.name.trim().toLowerCase())
+				: undefined,
 			contextFiles: loadedContextFiles,
 			customPrompt: loaderSystemPrompt,
 			appendSystemPrompt,
@@ -1626,6 +1658,11 @@ export class AgentSession {
 		// message_end/agent_end events fire while listeners are still connected.
 		// During agent_end handling the turn is already ending; aborting there can
 		// convert a successful auto-mode handoff into an aborted provider message.
+		if (!this.agent.state.isStreaming) {
+			this._retryHandler.abortRetry();
+			await this.agent.waitForIdle();
+			return;
+		}
 		await this.abort();
 	}
 
@@ -1640,6 +1677,8 @@ export class AgentSession {
 	async newSession(options?: {
 		parentSession?: string;
 		setup?: (sessionManager: SessionManager) => Promise<void>;
+		/** Explicit workspace root for the new session/tool runtime. */
+		workspaceRoot?: string;
 		/** See ExtensionCommandContext.newSession for docs (#3731). */
 		abortSignal?: AbortSignal;
 	}): Promise<boolean> {
@@ -1661,10 +1700,10 @@ export class AgentSession {
 		try {
 			await this._settleCurrentTurnForSessionTransition();
 
-			// #3731: If the caller aborted (e.g. runUnit() timed out and restored cwd to
-			// project root), discard this session before capturing process.cwd() and
-			// rebuilding the tool runtime. Without this check, the late newSession()
-			// would rebuild tools with root cwd, breaking worktree isolation.
+			// #3731: If the caller aborted (e.g. runUnit() timed out while the
+			// worktree was being torn down), discard this session before rebuilding
+			// the tool runtime. Without this check, the late newSession() could
+			// rebuild tools with a stale workspace root.
 			if (options?.abortSignal?.aborted) {
 				return false;
 			}
@@ -1674,15 +1713,21 @@ export class AgentSession {
 		} finally {
 			this._sessionSwitchPending = false;
 		}
-		// Update cwd to current process directory — auto-mode may have chdir'd
-		// into a worktree since the original session was created.
+		// Update the workspace root for the new tool runtime. Auto-mode passes
+		// this explicitly so session routing does not depend on global
+		// process.cwd() after worktree merge/teardown. Other callers keep the
+		// historical default.
 		const previousCwd = this._cwd;
-		this._cwd = process.cwd();
+		this._cwd = options?.workspaceRoot ?? process.cwd();
+		if (this._workspaceRootRef) {
+			this._workspaceRootRef.current = this._cwd;
+		}
 		this.sessionManager.newSession({ parentSession: options?.parentSession });
 		this.agent.sessionId = this.sessionManager.getSessionId();
 		this._steeringMessages = [];
 		this._followUpMessages = [];
 		this._pendingNextTurnMessages = [];
+		this._visibleSkillNames = undefined;
 
 		this.sessionManager.appendThinkingLevelChange(this.thinkingLevel);
 
@@ -2180,6 +2225,8 @@ export class AgentSession {
 				getActiveTools: () => this.getActiveToolNames(),
 				getAllTools: () => this.getAllTools(),
 				setActiveTools: (toolNames) => this.setActiveToolsByName(toolNames),
+				getVisibleSkills: () => this.getVisibleSkillNames(),
+				setVisibleSkills: (skillNames) => this.setVisibleSkillsByName(skillNames),
 				refreshTools: () => this._refreshToolRegistry(),
 				getCommands,
 				setModel: async (model, options) => {
@@ -2211,6 +2258,9 @@ export class AgentSession {
 					})();
 				},
 				getSystemPrompt: () => this.systemPrompt,
+				setCompactionThresholdOverride: (percent) => {
+					this.settingsManager.setCompactionThresholdOverride(percent);
+				},
 			},
 		);
 	}
@@ -2345,6 +2395,7 @@ export class AgentSession {
 		this.settingsManager.reload();
 		resetApiProviders();
 		await this._resourceLoader.reload();
+		this._visibleSkillNames = undefined;
 		this._buildRuntime({
 			activeToolNames: this.getActiveToolNames(),
 			flagValues: previousFlagValues,
@@ -2534,6 +2585,7 @@ export class AgentSession {
 		this._steeringMessages = [];
 		this._followUpMessages = [];
 		this._pendingNextTurnMessages = [];
+		this._visibleSkillNames = undefined;
 
 		// Set new session
 		this.sessionManager.setSessionFile(sessionPath);

package/packages/pi-coding-agent/src/core/chat-controller-ordering.test.ts

@@ -1049,7 +1049,9 @@ test("chat-controller rolls up only contiguous low-signal tool runs on message_e
 	assert.equal(host.chatContainer.children[1]?.constructor?.name, "AssistantMessageComponent");
 	assert.equal(host.chatContainer.children[2]?.constructor?.name, "ToolPhaseSummaryComponent");
 	assert.match(host.chatContainer.children[0].render(120).join("\n"), /Setup \/ shell 2 actions/);
-	assert.match(host.chatContainer.children[2].render(120).join("\n"), /Context reads 2 actions/);
+	const readSummary = host.chatContainer.children[2].render(120).join("\n");
+	assert.match(readSummary, /Context reads · 2 files/);
+	assert.match(readSummary, /\/tmp\/a · \/tmp\/b/);
 	assert.equal(host.chatContainer._prevRender, null, "summary reposition must invalidate the chat container render cache");
 });
 
@@ -1080,7 +1082,9 @@ test("chat-controller rolls up low-signal direct tool execution events on agent_
 		} as any);
 	}
 
-	assert.equal(host.chatContainer.children.length, 3, "direct tool events render as individual rows while running");
+	assert.equal(host.chatContainer.children.length, 1, "direct tool events roll up as they finish");
+	assert.equal(host.chatContainer.children[0]?.constructor?.name, "ToolPhaseSummaryComponent");
+	assert.match(host.chatContainer.children[0].render(120).join("\n"), /Setup \/ shell 3 actions/);
 
 	await handleAgentEvent(host, { type: "agent_end" } as any);
 

package/packages/pi-coding-agent/src/core/compaction/compaction.ts

@@ -86,6 +86,13 @@ export interface CompactionSettings {
 	enabled: boolean;
 	reserveTokens: number;
 	keepRecentTokens: number;
+	/**
+	 * Optional percent-of-context-window threshold (0 < value < 1). When set,
+	 * `shouldCompact()` fires once `contextTokens > contextWindow * thresholdPercent`,
+	 * overriding the absolute `reserveTokens` calculation. Lets host integrations
+	 * (e.g. GSD) express compaction policy as a fraction independent of model size.
+	 */
+	thresholdPercent?: number;
 }
 
 export const DEFAULT_COMPACTION_SETTINGS: CompactionSettings = {
@@ -185,9 +192,20 @@ export function estimateContextTokens(messages: AgentMessage[]): ContextUsageEst
 
 /**
  * Check if compaction should trigger based on context usage.
+ *
+ * When `thresholdPercent` is set (and within (0, 1)), it overrides the absolute
+ * `reserveTokens` calculation: compaction fires at `contextWindow * thresholdPercent`.
+ * Otherwise the legacy `contextWindow - reserveTokens` headroom is used.
  */
 export function shouldCompact(contextTokens: number, contextWindow: number, settings: CompactionSettings): boolean {
 	if (!settings.enabled) return false;
+	if (
+		settings.thresholdPercent !== undefined &&
+		settings.thresholdPercent > 0 &&
+		settings.thresholdPercent < 1
+	) {
+		return contextTokens > contextWindow * settings.thresholdPercent;
+	}
 	return contextTokens > contextWindow - settings.reserveTokens;
 }