gsd-pi 2.80.0 → 2.81.0-dev.3cddbbba2

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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gsd/pi-coding-agent",
-  "version": "2.80.0",
+  "version": "2.81.0",
   "description": "Coding agent CLI (vendored from pi-mono)",
   "type": "module",
   "gsd": {
@@ -25,6 +25,7 @@
     "copy-assets": "node scripts/copy-assets.cjs"
   },
   "dependencies": {
+    "@gsd-build/contracts": "^2.80.0",
     "@mariozechner/jiti": "^2.6.2",
     "@silvia-odwyer/photon-node": "^0.3.4",
     "chalk": "^5.5.0",

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[] = [];
@@ -200,6 +235,7 @@ describe("#4243 — abort() must run before _disconnectFromAgent()", () => {
 	it("abort() marks synthetic agent_end processing while extension handlers run", async () => {
 		const session = await createSession();
 		const observedProcessingStates: boolean[] = [];
+		const observedOrigins: unknown[] = [];
 
 		(session as any).agent.abort = () => {};
 		(session as any).agent.waitForIdle = async () => {};
@@ -207,6 +243,7 @@ describe("#4243 — abort() must run before _disconnectFromAgent()", () => {
 			emit: async (event: any) => {
 				if (event.type === "agent_end") {
 					observedProcessingStates.push((session as any)._processingAgentEnd);
+					observedOrigins.push(event.abortOrigin);
 				}
 			},
 			emitStop: async () => {
@@ -214,9 +251,10 @@ describe("#4243 — abort() must run before _disconnectFromAgent()", () => {
 			},
 		};
 
-		await session.abort();
+		await session.abort({ origin: "session-transition" });
 
 		assert.deepEqual(observedProcessingStates, [true, true]);
+		assert.deepEqual(observedOrigins, ["session-transition"]);
 		assert.equal((session as any)._processingAgentEnd, false);
 	});
 
@@ -432,6 +470,7 @@ 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.
  *
@@ -17,6 +18,7 @@ import { readFileSync } from "node:fs";
 import { basename, dirname, join } from "node:path";
 import type {
 	Agent,
+	AgentAbortOrigin,
 	AgentEvent,
 	AgentMessage,
 	AgentState,
@@ -167,6 +169,8 @@ 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 +288,7 @@ 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 +310,8 @@ 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 +328,10 @@ 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;
 
@@ -348,7 +359,7 @@ export class AgentSession {
 			emit: (event) => this._emit(event),
 			disconnectFromAgent: () => this._disconnectFromAgent(),
 			reconnectToAgent: () => this._reconnectToAgent(),
-			abort: () => this.abort(),
+			abort: () => this.abort({ origin: "user" }),
 		});
 
 		// Always subscribe to agent events for internal handling
@@ -655,11 +666,21 @@ export class AgentSession {
 
 		if (event.type === "agent_start") {
 			this._turnIndex = 0;
-			await extensionRunner.emit({ type: "agent_start" });
+			await extensionRunner.emit({
+				type: "agent_start",
+				sessionId: event.sessionId,
+				turnId: event.turnId,
+			});
 		} else if (event.type === "agent_end") {
 			this._processingAgentEnd = true;
 			try {
-				await extensionRunner.emit({ type: "agent_end", messages: event.messages });
+				await extensionRunner.emit({
+					type: "agent_end",
+					messages: event.messages,
+					sessionId: event.sessionId,
+					turnId: event.turnId,
+					abortOrigin: event.abortOrigin,
+				});
 				// `stop` fires on true quiescence: the agent cleanly completed and is now
 				// waiting for the user. Use the last assistant message's stopReason to
 				// distinguish clean completion from error/cancellation.
@@ -672,7 +693,13 @@ export class AgentSession {
 								? "error"
 								: "completed"
 						: "completed";
-				await extensionRunner.emitStop({ reason: stopReason, lastMessage: last });
+				await extensionRunner.emitStop({
+					reason: stopReason,
+					lastMessage: last,
+					sessionId: event.sessionId,
+					turnId: event.turnId,
+					abortOrigin: event.abortOrigin,
+				});
 			} finally {
 				this._processingAgentEnd = false;
 			}
@@ -681,6 +708,8 @@ export class AgentSession {
 				type: "turn_start",
 				turnIndex: this._turnIndex,
 				timestamp: Date.now(),
+				sessionId: event.sessionId,
+				turnId: event.turnId,
 			};
 			await extensionRunner.emit(extensionEvent);
 		} else if (event.type === "turn_end") {
@@ -689,6 +718,8 @@ export class AgentSession {
 				turnIndex: this._turnIndex,
 				message: event.message,
 				toolResults: event.toolResults,
+				sessionId: event.sessionId,
+				turnId: event.turnId,
 			};
 			await extensionRunner.emit(extensionEvent);
 			this._turnIndex++;
@@ -696,6 +727,8 @@ export class AgentSession {
 			const extensionEvent: MessageStartEvent = {
 				type: "message_start",
 				message: event.message,
+				sessionId: event.sessionId,
+				turnId: event.turnId,
 			};
 			await extensionRunner.emit(extensionEvent);
 		} else if (event.type === "message_update") {
@@ -703,12 +736,16 @@ export class AgentSession {
 				type: "message_update",
 				message: event.message,
 				assistantMessageEvent: event.assistantMessageEvent,
+				sessionId: event.sessionId,
+				turnId: event.turnId,
 			};
 			await extensionRunner.emit(extensionEvent);
 		} else if (event.type === "message_end") {
 			const extensionEvent: MessageEndEvent = {
 				type: "message_end",
 				message: event.message,
+				sessionId: event.sessionId,
+				turnId: event.turnId,
 			};
 			await extensionRunner.emit(extensionEvent);
 		} else if (event.type === "tool_execution_start") {
@@ -867,6 +904,25 @@ 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 +1101,9 @@ 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,
@@ -1572,9 +1631,9 @@ export class AgentSession {
 	/**
 	 * Abort current operation and wait for agent to become idle.
 	 */
-	async abort(): Promise<void> {
+	async abort(options?: { origin?: AgentAbortOrigin }): Promise<void> {
 		this._retryHandler.abortRetry();
-		this.agent.abort();
+		this.agent.abort(options?.origin);
 		await this.agent.waitForIdle();
 		// Ensure agent_end is emitted even when abort interrupts a tool call (#1414).
 		// The agent may go idle without emitting agent_end if the abort happens
@@ -1588,6 +1647,8 @@ export class AgentSession {
 				await this._extensionRunner.emit({
 					type: "agent_end",
 					messages,
+					sessionId: this.sessionId,
+					abortOrigin: options?.origin,
 				});
 				const last = messages[messages.length - 1];
 				const stopReason: "completed" | "cancelled" | "error" | "blocked" =
@@ -1598,7 +1659,12 @@ export class AgentSession {
 								? "error"
 								: "completed"
 						: "cancelled";
-				await this._extensionRunner.emitStop({ reason: stopReason, lastMessage: last });
+				await this._extensionRunner.emitStop({
+					reason: stopReason,
+					lastMessage: last,
+					sessionId: this.sessionId,
+					abortOrigin: options?.origin,
+				});
 			} finally {
 				this._processingAgentEnd = wasProcessingAgentEnd;
 			}
@@ -1626,7 +1692,12 @@ 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.
-		await this.abort();
+		if (!this.agent.state.isStreaming) {
+			this._retryHandler.abortRetry();
+			await this.agent.waitForIdle();
+			return;
+		}
+		await this.abort({ origin: "session-transition" });
 	}
 
 	/**
@@ -1640,6 +1711,8 @@ 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 +1734,10 @@ 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 +1747,21 @@ 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 +2259,8 @@ 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) => {
@@ -2193,7 +2274,7 @@ export class AgentSession {
 			{
 				getModel: () => this.model,
 				isIdle: () => !this.isStreaming,
-				abort: () => this.abort(),
+				abort: () => this.abort({ origin: "user" }),
 				hasPendingMessages: () => this.pendingMessageCount > 0,
 				shutdown: () => {
 					this._extensionShutdownHandler?.();
@@ -2211,6 +2292,9 @@ export class AgentSession {
 					})();
 				},
 				getSystemPrompt: () => this.systemPrompt,
+				setCompactionThresholdOverride: (percent) => {
+					this.settingsManager.setCompactionThresholdOverride(percent);
+				},
 			},
 		);
 	}
@@ -2345,6 +2429,7 @@ export class AgentSession {
 		this.settingsManager.reload();
 		resetApiProviders();
 		await this._resourceLoader.reload();
+		this._visibleSkillNames = undefined;
 		this._buildRuntime({
 			activeToolNames: this.getActiveToolNames(),
 			flagValues: previousFlagValues,
@@ -2534,6 +2619,7 @@ export class AgentSession {
 		this._steeringMessages = [];
 		this._followUpMessages = [];
 		this._pendingNextTurnMessages = [];
+		this._visibleSkillNames = undefined;
 
 		// Set new session
 		this.sessionManager.setSessionFile(sessionPath);