@goondocks/myco 0.12.10 → 0.14.0

package/dist/{chunk-J3L2RTYK.js → chunk-RBFECYNA.js}

@@ -1,7 +1,7 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   CloudEmbeddingBase
-} from "./chunk-QL2RBFIC.js";
+} from "./chunk-5YQ6VOFZ.js";
 
 // src/cli/providers/openrouter.ts
 var OPENROUTER_API_KEY_ENV = "MYCO_OPENROUTER_API_KEY";
@@ -23,4 +23,4 @@ export {
   OPENROUTER_API_KEY_ENV,
   OpenRouterEmbeddingProvider
 };
-//# sourceMappingURL=chunk-J3L2RTYK.js.map
+//# sourceMappingURL=chunk-RBFECYNA.js.map

package/dist/{chunk-4VSNNMEU.js → chunk-S66YG6QK.js}

@@ -4,7 +4,7 @@ import {
 } from "./chunk-MYX5NCRH.js";
 import {
   DEFAULT_MACHINE_ID
-} from "./chunk-PIRWYDOH.js";
+} from "./chunk-TRA3R4EC.js";
 
 // src/daemon/team-context.ts
 var teamSyncEnabled = false;
@@ -122,8 +122,27 @@ var BACKFILL_TABLES = [
   "resolution_events",
   "plans",
   "artifacts",
-  "digest_extracts"
+  "digest_extracts",
+  "skill_candidates",
+  "skill_records"
 ];
+var BACKFILL_TABLE_SET = new Set(BACKFILL_TABLES);
+function markSourceRowsSynced(records, syncedAt) {
+  const db = getDatabase();
+  const byTable = /* @__PURE__ */ new Map();
+  for (const rec of records) {
+    if (!BACKFILL_TABLE_SET.has(rec.table_name)) continue;
+    const ids = byTable.get(rec.table_name) ?? [];
+    ids.push(rec.row_id);
+    byTable.set(rec.table_name, ids);
+  }
+  for (const [table, ids] of byTable) {
+    const placeholders = ids.map(() => "?").join(", ");
+    db.prepare(
+      `UPDATE ${table} SET synced_at = ? WHERE id IN (${placeholders}) AND synced_at IS NULL`
+    ).run(syncedAt, ...ids);
+  }
+}
 function backfillUnsynced(machineId) {
   const db = getDatabase();
   let total = 0;
@@ -155,11 +174,15 @@ function backfillUnsynced(machineId) {
 
 export {
   initTeamContext,
+  isTeamSyncEnabled,
+  getTeamMachineId,
   syncRow,
+  enqueueOutbox,
   listPending,
   markSent,
   pruneOld,
   countPending,
+  markSourceRowsSynced,
   backfillUnsynced
 };
-//# sourceMappingURL=chunk-4VSNNMEU.js.map
+//# sourceMappingURL=chunk-S66YG6QK.js.map

package/dist/{chunk-4VSNNMEU.js.map → chunk-S66YG6QK.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/daemon/team-context.ts","../src/db/queries/team-outbox.ts"],"sourcesContent":["/**\n * Module-level state for team sync.\n *\n * Initialized once by the daemon on startup. Query modules import\n * `isTeamSyncEnabled()` and `getTeamMachineId()` to decide whether\n * to enqueue outbox records on write.\n */\n\nimport { SYNC_PROTOCOL_VERSION, DEFAULT_MACHINE_ID } from '@myco/constants.js';\n\n// ---------------------------------------------------------------------------\n// Module state\n// ---------------------------------------------------------------------------\n\nlet teamSyncEnabled = false;\nlet teamMachineId = DEFAULT_MACHINE_ID;\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Initialize team context. Called once on daemon startup.\n */\nexport function initTeamContext(enabled: boolean, machineId: string): void {\n  teamSyncEnabled = enabled;\n  teamMachineId = machineId;\n}\n\n/**\n * Whether team sync is currently enabled.\n *\n * Query modules check this before enqueuing outbox records.\n */\nexport function isTeamSyncEnabled(): boolean {\n  return teamSyncEnabled;\n}\n\n/**\n * The machine ID for this instance.\n */\nexport function getTeamMachineId(): string {\n  return teamMachineId;\n}\n\n/**\n * The sync protocol version in use.\n */\nexport function getTeamSyncProtocolVersion(): number {\n  return SYNC_PROTOCOL_VERSION;\n}\n\n/**\n * Reset team context (for testing).\n */\nexport function resetTeamContext(): void {\n  teamSyncEnabled = false;\n  teamMachineId = DEFAULT_MACHINE_ID;\n}\n","/**\n * Team outbox CRUD query helpers.\n *\n * The outbox pattern: write paths enqueue records here when team sync is enabled.\n * The sync client flushes pending records in batches to the Cloudflare Worker.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport { isTeamSyncEnabled, getTeamMachineId } from '@myco/daemon/team-context.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Max records returned per listPending call. */\nconst BURST_BATCH_SIZE = 200;\n\n/** Age in seconds after which sent records are pruned (24 hours). */\nconst SENT_PRUNE_AGE_SECONDS = 86_400;\n\n/** Milliseconds-per-second multiplier for epoch math. */\nconst MS_PER_SECOND = 1000;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required when enqueuing an outbox record. */\nexport interface OutboxInsert {\n  table_name: string;\n  row_id: string;\n  operation?: string;\n  payload: string;\n  machine_id: string;\n  created_at: number;\n}\n\n/** Row shape returned from outbox queries. */\nexport interface OutboxRow {\n  id: number;\n  table_name: string;\n  row_id: string;\n  operation: string;\n  payload: string;\n  machine_id: string;\n  created_at: number;\n  sent_at: number | null;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst OUTBOX_COLUMNS = [\n  'id',\n  'table_name',\n  'row_id',\n  'operation',\n  'payload',\n  'machine_id',\n  'created_at',\n  'sent_at',\n] as const;\n\nconst SELECT_COLUMNS = OUTBOX_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed OutboxRow. */\nfunction toOutboxRow(row: Record<string, unknown>): OutboxRow {\n  return {\n    id: row.id as number,\n    table_name: row.table_name as string,\n    row_id: row.row_id as string,\n    operation: row.operation as string,\n    payload: row.payload as string,\n    machine_id: row.machine_id as string,\n    created_at: row.created_at as number,\n    sent_at: (row.sent_at as number) ?? null,\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Convenience helper — used by query modules\n// ---------------------------------------------------------------------------\n\n/**\n * Enqueue a row for team sync if sync is enabled.\n *\n * Centralizes the if-enabled / enqueue / serialize pattern that every\n * write-path query module previously duplicated inline.\n */\nexport function syncRow(tableName: string, row: { id: string | number; created_at?: number }): void {\n  if (!isTeamSyncEnabled()) return;\n  enqueueOutbox({\n    table_name: tableName,\n    row_id: String(row.id),\n    payload: JSON.stringify(row),\n    machine_id: getTeamMachineId(),\n    created_at: row.created_at ?? Math.floor(Date.now() / 1000),\n  });\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Enqueue a record into the team outbox for later sync.\n *\n * Inserted with `sent_at = NULL` (pending).\n */\nexport function enqueueOutbox(data: OutboxInsert): OutboxRow {\n  const db = getDatabase();\n\n  const info = db.prepare(\n    `INSERT INTO team_outbox (\n       table_name, row_id, operation, payload, machine_id, created_at\n     ) VALUES (?, ?, ?, ?, ?, ?)`,\n  ).run(\n    data.table_name,\n    data.row_id,\n    data.operation ?? 'upsert',\n    data.payload,\n    data.machine_id,\n    data.created_at,\n  );\n\n  const id = Number(info.lastInsertRowid);\n\n  return toOutboxRow(\n    db.prepare(`SELECT ${SELECT_COLUMNS} FROM team_outbox WHERE id = ?`).get(id) as Record<string, unknown>,\n  );\n}\n\n/**\n * List pending outbox records (oldest-first).\n *\n * Uses burst sizing: fetches BURST_BATCH_SIZE rows and returns them all.\n * If fewer than BURST_THRESHOLD rows come back, callers get a normal-size\n * batch; if more, the full burst. This avoids a separate COUNT query.\n */\nexport function listPending(limit?: number): OutboxRow[] {\n  const db = getDatabase();\n\n  const rows = db.prepare(\n    `SELECT ${SELECT_COLUMNS}\n     FROM team_outbox\n     WHERE sent_at IS NULL\n     ORDER BY created_at ASC\n     LIMIT ?`,\n  ).all(limit ?? BURST_BATCH_SIZE) as Record<string, unknown>[];\n\n  return rows.map(toOutboxRow);\n}\n\n/**\n * Mark outbox records as sent by setting sent_at.\n */\nexport function markSent(ids: number[], sentAt: number): void {\n  if (ids.length === 0) return;\n\n  const db = getDatabase();\n  const placeholders = ids.map(() => '?').join(', ');\n\n  db.prepare(\n    `UPDATE team_outbox\n     SET sent_at = ?\n     WHERE id IN (${placeholders})`,\n  ).run(sentAt, ...ids);\n}\n\n/**\n * Reset sent_at to NULL for records that need to be retried.\n *\n * This allows the sync client to re-enqueue specific records for retry.\n */\nexport function markForRetry(ids: number[]): void {\n  if (ids.length === 0) return;\n\n  const db = getDatabase();\n  const placeholders = ids.map(() => '?').join(', ');\n\n  db.prepare(\n    `UPDATE team_outbox\n     SET sent_at = NULL\n     WHERE id IN (${placeholders})`,\n  ).run(...ids);\n}\n\n/**\n * Prune old outbox records.\n *\n * Removes sent records older than 24 hours.\n *\n * @returns the number of records deleted.\n */\nexport function pruneOld(): number {\n  const db = getDatabase();\n  const cutoff = Math.floor(Date.now() / MS_PER_SECOND) - SENT_PRUNE_AGE_SECONDS;\n\n  const info = db.prepare(\n    `DELETE FROM team_outbox\n     WHERE sent_at IS NOT NULL AND sent_at < ?`,\n  ).run(cutoff);\n\n  return info.changes;\n}\n\n/**\n * Count pending (unsent) outbox records.\n */\nexport function countPending(): number {\n  const db = getDatabase();\n\n  const row = db.prepare(\n    `SELECT COUNT(*) as count FROM team_outbox WHERE sent_at IS NULL`,\n  ).get() as { count: number };\n\n  return row.count;\n}\n\n// ---------------------------------------------------------------------------\n// Backfill\n// ---------------------------------------------------------------------------\n\n/** Tables to backfill (must have id, machine_id, synced_at columns). */\nconst BACKFILL_TABLES = [\n  'sessions',\n  'prompt_batches',\n  'spores',\n  'entities',\n  'graph_edges',\n  'resolution_events',\n  'plans',\n  'artifacts',\n  'digest_extracts',\n] as const;\n// entity_mentions excluded — no `id` column (composite key entity_id+note_id+note_type)\n\n/**\n * Enqueue all unsynced records across all synced tables into the outbox.\n *\n * Scans each table for rows where `synced_at IS NULL`, serializes the full\n * row as JSON, and inserts into the outbox. 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AND team_outbox.row_id = CAST(${table}.id AS TEXT)\n       )`,\n    ).all(table) as Record<string, unknown>[];\n\n    if (rows.length === 0) continue;\n\n    const insertBatch = db.transaction((batchRows: Record<string, unknown>[]) => {\n      const stmt = db.prepare(\n        `INSERT INTO team_outbox (table_name, row_id, operation, payload, machine_id, created_at)\n         VALUES (?, ?, 'upsert', ?, ?, ?)`,\n      );\n      for (const row of batchRows) {\n        stmt.run(table, String(row.id), JSON.stringify(row), machineId, now);\n      }\n    });\n\n    insertBatch(rows);\n    total += rows.length;\n  }\n\n  return total;\n}\n\n"],"mappings":";;;;;;;;;AAcA,IAAI,kBAAkB;AACtB,IAAI,gBAAgB;AASb,SAAS,gBAAgB,SAAkB,WAAyB;AACzE,oBAAkB;AAClB,kBAAgB;AAClB;AAOO,SAAS,oBAA6B;AAC3C,SAAO;AACT;AAKO,SAAS,mBAA2B;AACzC,SAAO;AACT;;;ACzBA,IAAM,mBAAmB;AAGzB,IAAM,yBAAyB;AAG/B,IAAM,gBAAgB;AAgCtB,IAAM,iBAAiB;AAAA,EACrB;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;AAEA,IAAM,iBAAiB,eAAe,KAAK,IAAI;AAO/C,SAAS,YAAY,KAAyC;AAC5D,SAAO;AAAA,IACL,IAAI,IAAI;AAAA,IACR,YAAY,IAAI;AAAA,IAChB,QAAQ,IAAI;AAAA,IACZ,WAAW,IAAI;AAAA,IACf,SAAS,IAAI;AAAA,IACb,YAAY,IAAI;AAAA,IAChB,YAAY,IAAI;AAAA,IAChB,SAAU,IAAI,WAAsB;AAAA,EACtC;AACF;AAYO,SAAS,QAAQ,WAAmB,KAAyD;AAClG,MAAI,CAAC,kBAAkB,EAAG;AAC1B,gBAAc;AAAA,IACZ,YAAY;AAAA,IACZ,QAAQ,OAAO,IAAI,EAAE;AAAA,IACrB,SAAS,KAAK,UAAU,GAAG;AAAA,IAC3B,YAAY,iBAAiB;AAAA,IAC7B,YAAY,IAAI,cAAc,KAAK,MAAM,KAAK,IAAI,IAAI,GAAI;AAAA,EAC5D,CAAC;AACH;AAWO,SAAS,cAAc,MAA+B;AAC3D,QAAM,KAAK,YAAY;AAEvB,QAAM,OAAO,GAAG;AAAA,IACd;AAAA;AAAA;AAAA,EAGF,EAAE;AAAA,IACA,KAAK;AAAA,IACL,KAAK;AAAA,IACL,KAAK,aAAa;AAAA,IAClB,KAAK;AAAA,IACL,KAAK;AAAA,IACL,KAAK;AAAA,EACP;AAEA,QAAM,KAAK,OAAO,KAAK,eAAe;AAEtC,SAAO;AAAA,IACL,GAAG,QAAQ,UAAU,cAAc,gCAAgC,EAAE,IAAI,EAAE;AAAA,EAC7E;AACF;AASO,SAAS,YAAY,OAA6B;AACvD,QAAM,KAAK,YAAY;AAEvB,QAAM,OAAO,GAAG;AAAA,IACd,UAAU,cAAc;AAAA;AAAA;AAAA;AAAA;AAAA,EAK1B,EAAE,IAAI,SAAS,gBAAgB;AAE/B,SAAO,KAAK,IAAI,WAAW;AAC7B;AAKO,SAAS,SAAS,KAAe,QAAsB;AAC5D,MAAI,IAAI,WAAW,EAAG;AAEtB,QAAM,KAAK,YAAY;AACvB,QAAM,eAAe,IAAI,IAAI,MAAM,GAAG,EAAE,KAAK,IAAI;AAEjD,KAAG;AAAA,IACD;AAAA;AAAA,oBAEgB,YAAY;AAAA,EAC9B,EAAE,IAAI,QAAQ,GAAG,GAAG;AACtB;AA2BO,SAAS,WAAmB;AACjC,QAAM,KAAK,YAAY;AACvB,QAAM,SAAS,KAAK,MAAM,KAAK,IAAI,IAAI,aAAa,IAAI;AAExD,QAAM,OAAO,GAAG;AAAA,IACd;AAAA;AAAA,EAEF,EAAE,IAAI,MAAM;AAEZ,SAAO,KAAK;AACd;AAKO,SAAS,eAAuB;AACrC,QAAM,KAAK,YAAY;AAEvB,QAAM,MAAM,GAAG;AAAA,IACb;AAAA,EACF,EAAE,IAAI;AAEN,SAAO,IAAI;AACb;AAOA,IAAM,kBAAkB;AAAA,EACtB;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;AAYO,SAAS,iBAAiB,WAA2B;AAC1D,QAAM,KAAK,YAAY;AACvB,MAAI,QAAQ;AAEZ,QAAM,MAAM,KAAK,MAAM,KAAK,IAAI,IAAI,aAAa;AAGjD,aAAW,SAAS,iBAAiB;AACnC,UAAM,OAAO,GAAG;AAAA,MACd,iBAAiB,KAAK;AAAA;AAAA;AAAA;AAAA,0EAI8C,KAAK;AAAA;AAAA,IAE3E,EAAE,IAAI,KAAK;AAEX,QAAI,KAAK,WAAW,EAAG;AAEvB,UAAM,cAAc,GAAG,YAAY,CAAC,cAAyC;AAC3E,YAAM,OAAO,GAAG;AAAA,QACd;AAAA;AAAA,MAEF;AACA,iBAAW,OAAO,WAAW;AAC3B,aAAK,IAAI,OAAO,OAAO,IAAI,EAAE,GAAG,KAAK,UAAU,GAAG,GAAG,WAAW,GAAG;AAAA,MACrE;AAAA,IACF,CAAC;AAED,gBAAY,IAAI;AAChB,aAAS,KAAK;AAAA,EAChB;AAEA,SAAO;AACT;","names":[]}
+{"version":3,"sources":["../src/daemon/team-context.ts","../src/db/queries/team-outbox.ts"],"sourcesContent":["/**\n * Module-level state for team sync.\n *\n * Initialized once by the daemon on startup. Query modules import\n * `isTeamSyncEnabled()` and `getTeamMachineId()` to decide whether\n * to enqueue outbox records on write.\n */\n\nimport { SYNC_PROTOCOL_VERSION, DEFAULT_MACHINE_ID } from '@myco/constants.js';\n\n// ---------------------------------------------------------------------------\n// Module state\n// ---------------------------------------------------------------------------\n\nlet teamSyncEnabled = false;\nlet teamMachineId = DEFAULT_MACHINE_ID;\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Initialize team context. Called once on daemon startup.\n */\nexport function initTeamContext(enabled: boolean, machineId: string): void {\n  teamSyncEnabled = enabled;\n  teamMachineId = machineId;\n}\n\n/**\n * Whether team sync is currently enabled.\n *\n * Query modules check this before enqueuing outbox records.\n */\nexport function isTeamSyncEnabled(): boolean {\n  return teamSyncEnabled;\n}\n\n/**\n * The machine ID for this instance.\n */\nexport function getTeamMachineId(): string {\n  return teamMachineId;\n}\n\n/**\n * The sync protocol version in use.\n */\nexport function getTeamSyncProtocolVersion(): number {\n  return SYNC_PROTOCOL_VERSION;\n}\n\n/**\n * Reset team context (for testing).\n */\nexport function resetTeamContext(): void {\n  teamSyncEnabled = false;\n  teamMachineId = DEFAULT_MACHINE_ID;\n}\n","/**\n * Team outbox CRUD query helpers.\n *\n * The outbox pattern: write paths enqueue records here when team sync is enabled.\n * The sync client flushes pending records in batches to the Cloudflare Worker.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport { isTeamSyncEnabled, getTeamMachineId } from '@myco/daemon/team-context.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Max records returned per listPending call. */\nconst BURST_BATCH_SIZE = 200;\n\n/** Age in seconds after which sent records are pruned (24 hours). */\nconst SENT_PRUNE_AGE_SECONDS = 86_400;\n\n/** Milliseconds-per-second multiplier for epoch math. */\nconst MS_PER_SECOND = 1000;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required when enqueuing an outbox record. */\nexport interface OutboxInsert {\n  table_name: string;\n  row_id: string;\n  operation?: string;\n  payload: string;\n  machine_id: string;\n  created_at: number;\n}\n\n/** Row shape returned from outbox queries. */\nexport interface OutboxRow {\n  id: number;\n  table_name: string;\n  row_id: string;\n  operation: string;\n  payload: string;\n  machine_id: string;\n  created_at: number;\n  sent_at: number | null;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst OUTBOX_COLUMNS = [\n  'id',\n  'table_name',\n  'row_id',\n  'operation',\n  'payload',\n  'machine_id',\n  'created_at',\n  'sent_at',\n] as const;\n\nconst SELECT_COLUMNS = OUTBOX_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed OutboxRow. */\nfunction toOutboxRow(row: Record<string, unknown>): OutboxRow {\n  return {\n    id: row.id as number,\n    table_name: row.table_name as string,\n    row_id: row.row_id as string,\n    operation: row.operation as string,\n    payload: row.payload as string,\n    machine_id: row.machine_id as string,\n    created_at: row.created_at as number,\n    sent_at: (row.sent_at as number) ?? null,\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Convenience helper — used by query modules\n// ---------------------------------------------------------------------------\n\n/**\n * Enqueue a row for team sync if sync is enabled.\n *\n * Centralizes the if-enabled / enqueue / serialize pattern that every\n * write-path query module previously duplicated inline.\n */\nexport function syncRow(tableName: string, row: { id: string | number; created_at?: number }): void {\n  if (!isTeamSyncEnabled()) return;\n  enqueueOutbox({\n    table_name: tableName,\n    row_id: String(row.id),\n    payload: JSON.stringify(row),\n    machine_id: getTeamMachineId(),\n    created_at: row.created_at ?? Math.floor(Date.now() / 1000),\n  });\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Enqueue a record into the team outbox for later sync.\n *\n * Inserted with `sent_at = NULL` (pending).\n */\nexport function enqueueOutbox(data: OutboxInsert): OutboxRow {\n  const db = getDatabase();\n\n  const info = db.prepare(\n    `INSERT INTO team_outbox (\n       table_name, row_id, operation, payload, machine_id, created_at\n     ) VALUES (?, ?, ?, ?, ?, ?)`,\n  ).run(\n    data.table_name,\n    data.row_id,\n    data.operation ?? 'upsert',\n    data.payload,\n    data.machine_id,\n    data.created_at,\n  );\n\n  const id = Number(info.lastInsertRowid);\n\n  return toOutboxRow(\n    db.prepare(`SELECT ${SELECT_COLUMNS} FROM team_outbox WHERE id = ?`).get(id) as Record<string, unknown>,\n  );\n}\n\n/**\n * List pending outbox records (oldest-first).\n *\n * Uses burst sizing: fetches BURST_BATCH_SIZE rows and returns them all.\n * If fewer than BURST_THRESHOLD rows come back, callers get a normal-size\n * batch; if more, the full burst. This avoids a separate COUNT query.\n */\nexport function listPending(limit?: number): OutboxRow[] {\n  const db = getDatabase();\n\n  const rows = db.prepare(\n    `SELECT ${SELECT_COLUMNS}\n     FROM team_outbox\n     WHERE sent_at IS NULL\n     ORDER BY created_at ASC\n     LIMIT ?`,\n  ).all(limit ?? BURST_BATCH_SIZE) as Record<string, unknown>[];\n\n  return rows.map(toOutboxRow);\n}\n\n/**\n * Mark outbox records as sent by setting sent_at.\n */\nexport function markSent(ids: number[], sentAt: number): void {\n  if (ids.length === 0) return;\n\n  const db = getDatabase();\n  const placeholders = ids.map(() => '?').join(', ');\n\n  db.prepare(\n    `UPDATE team_outbox\n     SET sent_at = ?\n     WHERE id IN (${placeholders})`,\n  ).run(sentAt, ...ids);\n}\n\n/**\n * Reset sent_at to NULL for records that need to be retried.\n *\n * This allows the sync client to re-enqueue specific records for retry.\n */\nexport function markForRetry(ids: number[]): void {\n  if (ids.length === 0) return;\n\n  const db = getDatabase();\n  const placeholders = ids.map(() => '?').join(', ');\n\n  db.prepare(\n    `UPDATE team_outbox\n     SET sent_at = NULL\n     WHERE id IN (${placeholders})`,\n  ).run(...ids);\n}\n\n/**\n * Prune old outbox records.\n *\n * Removes sent records older than 24 hours.\n *\n * @returns the number of records deleted.\n */\nexport function pruneOld(): number {\n  const db = getDatabase();\n  const cutoff = Math.floor(Date.now() / MS_PER_SECOND) - SENT_PRUNE_AGE_SECONDS;\n\n  const info = db.prepare(\n    `DELETE FROM team_outbox\n     WHERE sent_at IS NOT NULL AND sent_at < ?`,\n  ).run(cutoff);\n\n  return info.changes;\n}\n\n/**\n * Count pending (unsent) outbox records.\n */\nexport function countPending(): number {\n  const db = getDatabase();\n\n  const row = db.prepare(\n    `SELECT COUNT(*) as count FROM team_outbox WHERE sent_at IS NULL`,\n  ).get() as { count: number };\n\n  return row.count;\n}\n\n// ---------------------------------------------------------------------------\n// Source-row sync bookkeeping\n// ---------------------------------------------------------------------------\n\n/** Tables eligible for backfill/sync (must have id, machine_id, synced_at columns). */\nconst BACKFILL_TABLES = [\n  'sessions',\n  'prompt_batches',\n  'spores',\n  'entities',\n  'graph_edges',\n  'resolution_events',\n  'plans',\n  'artifacts',\n  'digest_extracts',\n  'skill_candidates',\n  'skill_records',\n] as const;\n// entity_mentions excluded — no `id` column (composite key entity_id+note_id+note_type)\n// skill_usage excluded — no `synced_at` column (syncs via syncRow on insert)\n\nconst BACKFILL_TABLE_SET = new Set<string>(BACKFILL_TABLES);\n\n/**\n * Mark source rows as synced after successful outbox flush.\n *\n * Groups outbox records by table_name, then sets `synced_at` on the\n * corresponding source rows. This closes the re-enqueue loop: once\n * synced_at is non-NULL, `backfillUnsynced` skips the row even after\n * the outbox entry is pruned.\n */\nexport function markSourceRowsSynced(records: OutboxRow[], syncedAt: number): void {\n  const db = getDatabase();\n\n  // Group row_ids by table\n  const byTable = new Map<string, string[]>();\n  for (const rec of records) {\n    if (!BACKFILL_TABLE_SET.has(rec.table_name)) continue;\n    const ids = byTable.get(rec.table_name) ?? [];\n    ids.push(rec.row_id);\n    byTable.set(rec.table_name, ids);\n  }\n\n  for (const [table, ids] of byTable) {\n    const placeholders = ids.map(() => '?').join(', ');\n    db.prepare(\n      `UPDATE ${table} SET synced_at = ? WHERE id IN (${placeholders}) AND synced_at IS NULL`,\n    ).run(syncedAt, ...ids);\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Backfill\n// ---------------------------------------------------------------------------\n\n/**\n * Enqueue all unsynced records across all synced tables into the outbox.\n *\n * Scans each table for rows where `synced_at IS NULL`, serializes the full\n * row as JSON, and inserts into the outbox. Idempotent — re-running only\n * picks up rows not yet in the outbox (checked via existing outbox entries).\n *\n * @returns the total number of records enqueued.\n */\nexport function backfillUnsynced(machineId: string): number {\n  const db = getDatabase();\n  let total = 0;\n\n  const now = Math.floor(Date.now() / MS_PER_SECOND);\n\n  // Process one table at a time in separate transactions to avoid long locks\n  for (const table of BACKFILL_TABLES) {\n    const rows = db.prepare(\n      `SELECT * FROM ${table}\n       WHERE synced_at IS NULL\n       AND NOT EXISTS (\n         SELECT 1 FROM team_outbox\n         WHERE team_outbox.table_name = ? AND team_outbox.row_id = CAST(${table}.id AS TEXT)\n       )`,\n    ).all(table) as Record<string, unknown>[];\n\n    if (rows.length === 0) continue;\n\n    const insertBatch = db.transaction((batchRows: Record<string, unknown>[]) => {\n      const stmt = db.prepare(\n        `INSERT INTO team_outbox (table_name, row_id, operation, payload, machine_id, created_at)\n         VALUES (?, ?, 'upsert', ?, ?, ?)`,\n      );\n      for (const row of batchRows) {\n        stmt.run(table, String(row.id), JSON.stringify(row), machineId, now);\n      }\n    });\n\n    insertBatch(rows);\n    total += rows.length;\n  }\n\n  return total;\n}\n\n"],"mappings":";;;;;;;;;AAcA,IAAI,kBAAkB;AACtB,IAAI,gBAAgB;AASb,SAAS,gBAAgB,SAAkB,WAAyB;AACzE,oBAAkB;AAClB,kBAAgB;AAClB;AAOO,SAAS,oBAA6B;AAC3C,SAAO;AACT;AAKO,SAAS,mBAA2B;AACzC,SAAO;AACT;;;ACzBA,IAAM,mBAAmB;AAGzB,IAAM,yBAAyB;AAG/B,IAAM,gBAAgB;AAgCtB,IAAM,iBAAiB;AAAA,EACrB;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;AAEA,IAAM,iBAAiB,eAAe,KAAK,IAAI;AAO/C,SAAS,YAAY,KAAyC;AAC5D,SAAO;AAAA,IACL,IAAI,IAAI;AAAA,IACR,YAAY,IAAI;AAAA,IAChB,QAAQ,IAAI;AAAA,IACZ,WAAW,IAAI;AAAA,IACf,SAAS,IAAI;AAAA,IACb,YAAY,IAAI;AAAA,IAChB,YAAY,IAAI;AAAA,IAChB,SAAU,IAAI,WAAsB;AAAA,EACtC;AACF;AAYO,SAAS,QAAQ,WAAmB,KAAyD;AAClG,MAAI,CAAC,kBAAkB,EAAG;AAC1B,gBAAc;AAAA,IACZ,YAAY;AAAA,IACZ,QAAQ,OAAO,IAAI,EAAE;AAAA,IACrB,SAAS,KAAK,UAAU,GAAG;AAAA,IAC3B,YAAY,iBAAiB;AAAA,IAC7B,YAAY,IAAI,cAAc,KAAK,MAAM,KAAK,IAAI,IAAI,GAAI;AAAA,EAC5D,CAAC;AACH;AAWO,SAAS,cAAc,MAA+B;AAC3D,QAAM,KAAK,YAAY;AAEvB,QAAM,OAAO,GAAG;AAAA,IACd;AAAA;AAAA;AAAA,EAGF,EAAE;AAAA,IACA,KAAK;AAAA,IACL,KAAK;AAAA,IACL,KAAK,aAAa;AAAA,IAClB,KAAK;AAAA,IACL,KAAK;AAAA,IACL,KAAK;AAAA,EACP;AAEA,QAAM,KAAK,OAAO,KAAK,eAAe;AAEtC,SAAO;AAAA,IACL,GAAG,QAAQ,UAAU,cAAc,gCAAgC,EAAE,IAAI,EAAE;AAAA,EAC7E;AACF;AASO,SAAS,YAAY,OAA6B;AACvD,QAAM,KAAK,YAAY;AAEvB,QAAM,OAAO,GAAG;AAAA,IACd,UAAU,cAAc;AAAA;AAAA;AAAA;AAAA;AAAA,EAK1B,EAAE,IAAI,SAAS,gBAAgB;AAE/B,SAAO,KAAK,IAAI,WAAW;AAC7B;AAKO,SAAS,SAAS,KAAe,QAAsB;AAC5D,MAAI,IAAI,WAAW,EAAG;AAEtB,QAAM,KAAK,YAAY;AACvB,QAAM,eAAe,IAAI,IAAI,MAAM,GAAG,EAAE,KAAK,IAAI;AAEjD,KAAG;AAAA,IACD;AAAA;AAAA,oBAEgB,YAAY;AAAA,EAC9B,EAAE,IAAI,QAAQ,GAAG,GAAG;AACtB;AA2BO,SAAS,WAAmB;AACjC,QAAM,KAAK,YAAY;AACvB,QAAM,SAAS,KAAK,MAAM,KAAK,IAAI,IAAI,aAAa,IAAI;AAExD,QAAM,OAAO,GAAG;AAAA,IACd;AAAA;AAAA,EAEF,EAAE,IAAI,MAAM;AAEZ,SAAO,KAAK;AACd;AAKO,SAAS,eAAuB;AACrC,QAAM,KAAK,YAAY;AAEvB,QAAM,MAAM,GAAG;AAAA,IACb;AAAA,EACF,EAAE,IAAI;AAEN,SAAO,IAAI;AACb;AAOA,IAAM,kBAAkB;AAAA,EACtB;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;AAIA,IAAM,qBAAqB,IAAI,IAAY,eAAe;AAUnD,SAAS,qBAAqB,SAAsB,UAAwB;AACjF,QAAM,KAAK,YAAY;AAGvB,QAAM,UAAU,oBAAI,IAAsB;AAC1C,aAAW,OAAO,SAAS;AACzB,QAAI,CAAC,mBAAmB,IAAI,IAAI,UAAU,EAAG;AAC7C,UAAM,MAAM,QAAQ,IAAI,IAAI,UAAU,KAAK,CAAC;AAC5C,QAAI,KAAK,IAAI,MAAM;AACnB,YAAQ,IAAI,IAAI,YAAY,GAAG;AAAA,EACjC;AAEA,aAAW,CAAC,OAAO,GAAG,KAAK,SAAS;AAClC,UAAM,eAAe,IAAI,IAAI,MAAM,GAAG,EAAE,KAAK,IAAI;AACjD,OAAG;AAAA,MACD,UAAU,KAAK,mCAAmC,YAAY;AAAA,IAChE,EAAE,IAAI,UAAU,GAAG,GAAG;AAAA,EACxB;AACF;AAeO,SAAS,iBAAiB,WAA2B;AAC1D,QAAM,KAAK,YAAY;AACvB,MAAI,QAAQ;AAEZ,QAAM,MAAM,KAAK,MAAM,KAAK,IAAI,IAAI,aAAa;AAGjD,aAAW,SAAS,iBAAiB;AACnC,UAAM,OAAO,GAAG;AAAA,MACd,iBAAiB,KAAK;AAAA;AAAA;AAAA;AAAA,0EAI8C,KAAK;AAAA;AAAA,IAE3E,EAAE,IAAI,KAAK;AAEX,QAAI,KAAK,WAAW,EAAG;AAEvB,UAAM,cAAc,GAAG,YAAY,CAAC,cAAyC;AAC3E,YAAM,OAAO,GAAG;AAAA,QACd;AAAA;AAAA,MAEF;AACA,iBAAW,OAAO,WAAW;AAC3B,aAAK,IAAI,OAAO,OAAO,IAAI,EAAE,GAAG,KAAK,UAAU,GAAG,GAAG,WAAW,GAAG;AAAA,MACrE;AAAA,IACF,CAAC;AAED,gBAAY,IAAI;AAChB,aAAS,KAAK;AAAA,EAChB;AAEA,SAAO;AACT;","names":[]}

package/dist/chunk-SBVDG5JP.js

@@ -0,0 +1,112 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  SymbiontInstaller
+} from "./chunk-TNCBMGWB.js";
+import {
+  LmStudioBackend,
+  OllamaBackend
+} from "./chunk-HHZ3RTEI.js";
+import {
+  closeDatabase,
+  initDatabase,
+  vaultDbPath
+} from "./chunk-MYX5NCRH.js";
+import {
+  DaemonClient
+} from "./chunk-UWXJCLCK.js";
+
+// src/cli/shared.ts
+import fs from "fs";
+import path from "path";
+import os from "os";
+function initVaultDb(vaultDir) {
+  initDatabase(vaultDbPath(vaultDir));
+  return closeDatabase;
+}
+async function connectToDaemon(vaultDir) {
+  const client = new DaemonClient(vaultDir);
+  const healthy = await client.ensureRunning();
+  if (!healthy) {
+    console.error("Failed to connect to daemon");
+    process.exit(1);
+  }
+  return client;
+}
+function loadEnv() {
+  const envPath = path.resolve(process.cwd(), ".env");
+  if (!fs.existsSync(envPath)) return;
+  for (const line of fs.readFileSync(envPath, "utf-8").split("\n")) {
+    const match = line.match(/^\s*([^#=]+?)\s*=\s*(.*?)\s*$/);
+    if (match && !process.env[match[1]]) {
+      process.env[match[1]] = match[2];
+    }
+  }
+}
+function isProcessAlive(pid) {
+  try {
+    process.kill(pid, 0);
+    return true;
+  } catch {
+    return false;
+  }
+}
+var PROVIDER_DEFAULTS = {
+  ollama: { base_url: OllamaBackend.DEFAULT_BASE_URL },
+  "lm-studio": { base_url: LmStudioBackend.DEFAULT_BASE_URL }
+};
+var VAULT_GITIGNORE = `# SQLite database
+myco.db*
+vectors.db*
+
+# Daemon state \u2014 per-machine, ephemeral
+daemon.json
+buffer/
+logs/
+
+# Secrets \u2014 API keys for cloud providers
+secrets.env
+
+# Machine ID
+machine_id
+
+# Binary attachments \u2014 screenshots captured from transcripts
+attachments/
+
+# Team worker deployment \u2014 patched wrangler.toml + source copy
+.team-worker/
+`;
+function registerSymbionts(manifests, projectRoot, packageRoot, verb) {
+  let count = 0;
+  for (const manifest of manifests) {
+    try {
+      const installer = new SymbiontInstaller(manifest, projectRoot, packageRoot);
+      const result = installer.install();
+      const installed = [
+        result.hooks && "hooks",
+        result.mcp && "MCP server",
+        result.skills && "skills",
+        result.settings && "settings",
+        result.instructions && "instructions"
+      ].filter(Boolean);
+      if (installed.length > 0) {
+        console.log(`  \u2713 ${verb} ${manifest.displayName}: ${installed.join(", ")}`);
+        count++;
+      } else {
+        console.log(`  \u2013 ${manifest.displayName}: no registration targets configured`);
+      }
+    } catch (err) {
+      console.error(`  \u2717 Failed to register ${manifest.displayName}: ${err.message}`);
+    }
+  }
+  return count;
+}
+
+export {
+  initVaultDb,
+  connectToDaemon,
+  loadEnv,
+  isProcessAlive,
+  VAULT_GITIGNORE,
+  registerSymbionts
+};
+//# sourceMappingURL=chunk-SBVDG5JP.js.map

package/dist/chunk-SBVDG5JP.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/shared.ts"],"sourcesContent":["import fs from 'node:fs';\nimport path from 'node:path';\nimport os from 'node:os';\nimport { OllamaBackend } from '../intelligence/ollama.js';\nimport { LmStudioBackend } from '../intelligence/lm-studio.js';\n\nimport { DaemonClient } from '../hooks/client.js';\nimport { initDatabase, closeDatabase, vaultDbPath } from '../db/client.js';\nimport { SymbiontInstaller } from '../symbionts/installer.js';\nimport type { SymbiontManifest } from '../symbionts/manifest-schema.js';\n\nexport { parseStringFlag, parseIntFlag } from '../logs/format.js';\n\n/**\n * Initialize the singleton database for direct CLI reads.\n * Used by CLI commands that only need reads (stats, search, session).\n * Does NOT require the daemon to be running — WAL mode allows concurrent reads.\n *\n * @returns a cleanup function that closes the database.\n */\nexport function initVaultDb(vaultDir: string): () => void {\n  initDatabase(vaultDbPath(vaultDir));\n  return closeDatabase;\n}\n\n/** Connect to the daemon, ensuring it's running. Exits on failure. */\nexport async function connectToDaemon(vaultDir: string): Promise<DaemonClient> {\n  const client = new DaemonClient(vaultDir);\n  const healthy = await client.ensureRunning();\n  if (!healthy) {\n    console.error('Failed to connect to daemon');\n    process.exit(1);\n  }\n  return client;\n}\n\n/** Load .env from cwd (not script location — that's the plugin install dir). */\nexport function loadEnv(): void {\n  const envPath = path.resolve(process.cwd(), '.env');\n  if (!fs.existsSync(envPath)) return;\n  for (const line of fs.readFileSync(envPath, 'utf-8').split('\\n')) {\n    const match = line.match(/^\\s*([^#=]+?)\\s*=\\s*(.*?)\\s*$/);\n    if (match && !process.env[match[1]]) {\n      process.env[match[1]] = match[2];\n    }\n  }\n}\n\nexport function isProcessAlive(pid: number): boolean {\n  try { process.kill(pid, 0); return true; } catch { return false; }\n}\n\n// --- Provider defaults (sourced from backend classes) ---\nexport const PROVIDER_DEFAULTS: Record<string, { base_url: string }> = {\n  ollama: { base_url: OllamaBackend.DEFAULT_BASE_URL },\n  'lm-studio': { base_url: LmStudioBackend.DEFAULT_BASE_URL },\n};\n\n\nexport const VAULT_GITIGNORE = `# SQLite database\nmyco.db*\nvectors.db*\n\n# Daemon state — per-machine, ephemeral\ndaemon.json\nbuffer/\nlogs/\n\n# Secrets — API keys for cloud providers\nsecrets.env\n\n# Machine ID\nmachine_id\n\n# Binary attachments — screenshots captured from transcripts\nattachments/\n\n# Team worker deployment — patched wrangler.toml + source copy\n.team-worker/\n`;\n\n/** Collapse an absolute home-dir path to its `~/` form for portable config storage. */\nexport function collapseHomePath(absPath: string): string {\n  const home = os.homedir();\n  if (absPath.startsWith(home + path.sep) || absPath === home) {\n    return '~' + absPath.slice(home.length);\n  }\n  return absPath;\n}\n\n/**\n * Run the SymbiontInstaller for each symbiont manifest and log results.\n * Shared between myco init and myco update.\n */\nexport function registerSymbionts(\n  manifests: SymbiontManifest[],\n  projectRoot: string,\n  packageRoot: string,\n  verb: 'Registered' | 'Updated',\n): number {\n  let count = 0;\n  for (const manifest of manifests) {\n    try {\n      const installer = new SymbiontInstaller(manifest, projectRoot, packageRoot);\n      const result = installer.install();\n\n      const installed = [\n        result.hooks && 'hooks',\n        result.mcp && 'MCP server',\n        result.skills && 'skills',\n        result.settings && 'settings',\n        result.instructions && 'instructions',\n      ].filter(Boolean);\n\n      if (installed.length > 0) {\n        console.log(`  \\u2713 ${verb} ${manifest.displayName}: ${installed.join(', ')}`);\n        count++;\n      } else {\n        console.log(`  \\u2013 ${manifest.displayName}: no registration targets configured`);\n      }\n    } catch (err) {\n      console.error(`  \\u2717 Failed to register ${manifest.displayName}: ${(err as Error).message}`);\n    }\n  }\n  return count;\n}\n\n"],"mappings":";;;;;;;;;;;;;;;;;;AAAA,OAAO,QAAQ;AACf,OAAO,UAAU;AACjB,OAAO,QAAQ;AAkBR,SAAS,YAAY,UAA8B;AACxD,eAAa,YAAY,QAAQ,CAAC;AAClC,SAAO;AACT;AAGA,eAAsB,gBAAgB,UAAyC;AAC7E,QAAM,SAAS,IAAI,aAAa,QAAQ;AACxC,QAAM,UAAU,MAAM,OAAO,cAAc;AAC3C,MAAI,CAAC,SAAS;AACZ,YAAQ,MAAM,6BAA6B;AAC3C,YAAQ,KAAK,CAAC;AAAA,EAChB;AACA,SAAO;AACT;AAGO,SAAS,UAAgB;AAC9B,QAAM,UAAU,KAAK,QAAQ,QAAQ,IAAI,GAAG,MAAM;AAClD,MAAI,CAAC,GAAG,WAAW,OAAO,EAAG;AAC7B,aAAW,QAAQ,GAAG,aAAa,SAAS,OAAO,EAAE,MAAM,IAAI,GAAG;AAChE,UAAM,QAAQ,KAAK,MAAM,+BAA+B;AACxD,QAAI,SAAS,CAAC,QAAQ,IAAI,MAAM,CAAC,CAAC,GAAG;AACnC,cAAQ,IAAI,MAAM,CAAC,CAAC,IAAI,MAAM,CAAC;AAAA,IACjC;AAAA,EACF;AACF;AAEO,SAAS,eAAe,KAAsB;AACnD,MAAI;AAAE,YAAQ,KAAK,KAAK,CAAC;AAAG,WAAO;AAAA,EAAM,QAAQ;AAAE,WAAO;AAAA,EAAO;AACnE;AAGO,IAAM,oBAA0D;AAAA,EACrE,QAAQ,EAAE,UAAU,cAAc,iBAAiB;AAAA,EACnD,aAAa,EAAE,UAAU,gBAAgB,iBAAiB;AAC5D;AAGO,IAAM,kBAAkB;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAmCxB,SAAS,kBACd,WACA,aACA,aACA,MACQ;AACR,MAAI,QAAQ;AACZ,aAAW,YAAY,WAAW;AAChC,QAAI;AACF,YAAM,YAAY,IAAI,kBAAkB,UAAU,aAAa,WAAW;AAC1E,YAAM,SAAS,UAAU,QAAQ;AAEjC,YAAM,YAAY;AAAA,QAChB,OAAO,SAAS;AAAA,QAChB,OAAO,OAAO;AAAA,QACd,OAAO,UAAU;AAAA,QACjB,OAAO,YAAY;AAAA,QACnB,OAAO,gBAAgB;AAAA,MACzB,EAAE,OAAO,OAAO;AAEhB,UAAI,UAAU,SAAS,GAAG;AACxB,gBAAQ,IAAI,YAAY,IAAI,IAAI,SAAS,WAAW,KAAK,UAAU,KAAK,IAAI,CAAC,EAAE;AAC/E;AAAA,MACF,OAAO;AACL,gBAAQ,IAAI,YAAY,SAAS,WAAW,sCAAsC;AAAA,MACpF;AAAA,IACF,SAAS,KAAK;AACZ,cAAQ,MAAM,+BAA+B,SAAS,WAAW,KAAM,IAAc,OAAO,EAAE;AAAA,IAChG;AAAA,EACF;AACA,SAAO;AACT;","names":[]}

package/dist/{chunk-M5XWW7UI.js → chunk-SODRR3HE.js}

@@ -37,6 +37,13 @@ function withTaskConfig(config, taskId, update) {
     if (update.timeoutSeconds === null) delete entry.timeoutSeconds;
     else if (update.timeoutSeconds !== void 0) entry.timeoutSeconds = update.timeoutSeconds;
   }
+  if ("schedule" in update) {
+    if (update.schedule === null) {
+      delete entry.schedule;
+    } else if (update.schedule !== void 0) {
+      entry.schedule = { ...entry.schedule, ...update.schedule };
+    }
+  }
   if ("phases" in update) {
     if (update.phases === null) {
       delete entry.phases;
@@ -94,4 +101,4 @@ export {
   withTaskConfig,
   withEmbedding
 };
-//# sourceMappingURL=chunk-M5XWW7UI.js.map
+//# sourceMappingURL=chunk-SODRR3HE.js.map

package/dist/chunk-SODRR3HE.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/config/updates.ts"],"sourcesContent":["import type { MycoConfig, EmbeddingProviderConfig, ContextConfig, TaskProviderOverride, PhaseOverride } from './schema.js';\n\n/**\n * Set a value at a dot-separated path, returning a new config object.\n * Creates intermediate objects along the path as needed.\n */\nexport function withValue(config: MycoConfig, dotPath: string, value: unknown): MycoConfig {\n  const clone = structuredClone(config) as MycoConfig & Record<string, unknown>;\n  const segments = dotPath.split('.');\n  let current: Record<string, unknown> = clone;\n\n  for (let i = 0; i < segments.length - 1; i++) {\n    const segment = segments[i];\n    if (current[segment] === undefined || current[segment] === null || typeof current[segment] !== 'object') {\n      current[segment] = {};\n    }\n    current = current[segment] as Record<string, unknown>;\n  }\n\n  current[segments[segments.length - 1]] = value;\n\n  return clone as MycoConfig;\n}\n\n/** Provider override shape used in task config updates. Null means delete. */\ninterface ProviderInput {\n  type: 'cloud' | 'ollama' | 'lmstudio';\n  model?: string;\n  base_url?: string;\n  context_length?: number;\n}\n\n/** Phase override input. Null fields mean delete. */\ninterface PhaseInput {\n  provider?: ProviderInput | null;\n  model?: string | null;\n  maxTurns?: number | null;\n}\n\n/** Input shape for task config updates. Null values mean \"delete this field\". */\nexport interface TaskConfigUpdate {\n  provider?: ProviderInput | null;\n  model?: string | null;\n  maxTurns?: number | null;\n  timeoutSeconds?: number | null;\n  phases?: Record<string, PhaseInput | null> | null;\n  schedule?: { enabled?: boolean; intervalSeconds?: number; runIn?: ('active' | 'idle' | 'sleep')[] } | null;\n}\n\n/**\n * Apply partial task config updates, returning a new config object.\n * Null values delete fields. Empty task entries and phase maps are cleaned up.\n */\nexport function withTaskConfig(\n  config: MycoConfig,\n  taskId: string,\n  update: TaskConfigUpdate,\n): MycoConfig {\n  const tasks = { ...(config.agent.tasks ?? {}) };\n  const entry: TaskProviderOverride = { ...(tasks[taskId] ?? {}) };\n\n  // Apply top-level fields\n  if ('provider' in update) {\n    if (update.provider === null) {\n      delete entry.provider;\n    } else if (update.provider !== undefined) {\n      entry.provider = { ...update.provider };\n    }\n  }\n\n  if ('model' in update) {\n    if (update.model === null) delete entry.model;\n    else if (update.model !== undefined) entry.model = update.model;\n  }\n\n  if ('maxTurns' in update) {\n    if (update.maxTurns === null) delete entry.maxTurns;\n    else if (update.maxTurns !== undefined) entry.maxTurns = update.maxTurns;\n  }\n\n  if ('timeoutSeconds' in update) {\n    if (update.timeoutSeconds === null) delete entry.timeoutSeconds;\n    else if (update.timeoutSeconds !== undefined) entry.timeoutSeconds = update.timeoutSeconds;\n  }\n\n  // Handle schedule\n  if ('schedule' in update) {\n    if (update.schedule === null) {\n      delete entry.schedule;\n    } else if (update.schedule !== undefined) {\n      entry.schedule = { ...entry.schedule, ...update.schedule };\n    }\n  }\n\n  // Apply phase overrides\n  if ('phases' in update) {\n    if (update.phases === null) {\n      delete entry.phases;\n    } else if (update.phases !== undefined) {\n      const phases: Record<string, PhaseOverride> = { ...(entry.phases ?? {}) };\n\n      for (const [phaseName, phaseValue] of Object.entries(update.phases)) {\n        if (phaseValue === null) {\n          delete phases[phaseName];\n        } else {\n          const pe: PhaseOverride = { ...(phases[phaseName] ?? {}) };\n          if ('provider' in phaseValue) {\n            if (phaseValue.provider === null) delete pe.provider;\n            else if (phaseValue.provider !== undefined) pe.provider = { ...phaseValue.provider };\n          }\n          if ('model' in phaseValue) {\n            if (phaseValue.model === null) delete pe.model;\n            else if (phaseValue.model !== undefined) pe.model = phaseValue.model;\n          }\n          if ('maxTurns' in phaseValue) {\n            if (phaseValue.maxTurns === null) delete pe.maxTurns;\n            else if (phaseValue.maxTurns !== undefined) pe.maxTurns = phaseValue.maxTurns;\n          }\n          phases[phaseName] = pe;\n        }\n      }\n\n      // Clean up empty phases map\n      if (Object.keys(phases).length === 0) {\n        delete entry.phases;\n      } else {\n        entry.phases = phases;\n      }\n    }\n  }\n\n  // Clean up empty task entry\n  if (Object.keys(entry).length === 0) {\n    delete tasks[taskId];\n  } else {\n    tasks[taskId] = entry;\n  }\n\n  return {\n    ...config,\n    agent: {\n      ...config.agent,\n      tasks: Object.keys(tasks).length > 0 ? tasks : undefined,\n    },\n  };\n}\n\n/**\n * Merge partial embedding updates into config, returning a new config object.\n */\nexport function withEmbedding(\n  config: MycoConfig,\n  updates: Partial<EmbeddingProviderConfig>,\n): MycoConfig {\n  return {\n    ...config,\n    embedding: { ...config.embedding, ...updates },\n  };\n}\n\n/**\n * Merge partial context injection updates into config, returning a new config object.\n */\nexport function withContext(\n  config: MycoConfig,\n  updates: Partial<ContextConfig>,\n): MycoConfig {\n  return {\n    ...config,\n    context: { ...config.context, ...updates },\n  };\n}\n"],"mappings":";;;AAMO,SAAS,UAAU,QAAoB,SAAiB,OAA4B;AACzF,QAAM,QAAQ,gBAAgB,MAAM;AACpC,QAAM,WAAW,QAAQ,MAAM,GAAG;AAClC,MAAI,UAAmC;AAEvC,WAAS,IAAI,GAAG,IAAI,SAAS,SAAS,GAAG,KAAK;AAC5C,UAAM,UAAU,SAAS,CAAC;AAC1B,QAAI,QAAQ,OAAO,MAAM,UAAa,QAAQ,OAAO,MAAM,QAAQ,OAAO,QAAQ,OAAO,MAAM,UAAU;AACvG,cAAQ,OAAO,IAAI,CAAC;AAAA,IACtB;AACA,cAAU,QAAQ,OAAO;AAAA,EAC3B;AAEA,UAAQ,SAAS,SAAS,SAAS,CAAC,CAAC,IAAI;AAEzC,SAAO;AACT;AA+BO,SAAS,eACd,QACA,QACA,QACY;AACZ,QAAM,QAAQ,EAAE,GAAI,OAAO,MAAM,SAAS,CAAC,EAAG;AAC9C,QAAM,QAA8B,EAAE,GAAI,MAAM,MAAM,KAAK,CAAC,EAAG;AAG/D,MAAI,cAAc,QAAQ;AACxB,QAAI,OAAO,aAAa,MAAM;AAC5B,aAAO,MAAM;AAAA,IACf,WAAW,OAAO,aAAa,QAAW;AACxC,YAAM,WAAW,EAAE,GAAG,OAAO,SAAS;AAAA,IACxC;AAAA,EACF;AAEA,MAAI,WAAW,QAAQ;AACrB,QAAI,OAAO,UAAU,KAAM,QAAO,MAAM;AAAA,aAC/B,OAAO,UAAU,OAAW,OAAM,QAAQ,OAAO;AAAA,EAC5D;AAEA,MAAI,cAAc,QAAQ;AACxB,QAAI,OAAO,aAAa,KAAM,QAAO,MAAM;AAAA,aAClC,OAAO,aAAa,OAAW,OAAM,WAAW,OAAO;AAAA,EAClE;AAEA,MAAI,oBAAoB,QAAQ;AAC9B,QAAI,OAAO,mBAAmB,KAAM,QAAO,MAAM;AAAA,aACxC,OAAO,mBAAmB,OAAW,OAAM,iBAAiB,OAAO;AAAA,EAC9E;AAGA,MAAI,cAAc,QAAQ;AACxB,QAAI,OAAO,aAAa,MAAM;AAC5B,aAAO,MAAM;AAAA,IACf,WAAW,OAAO,aAAa,QAAW;AACxC,YAAM,WAAW,EAAE,GAAG,MAAM,UAAU,GAAG,OAAO,SAAS;AAAA,IAC3D;AAAA,EACF;AAGA,MAAI,YAAY,QAAQ;AACtB,QAAI,OAAO,WAAW,MAAM;AAC1B,aAAO,MAAM;AAAA,IACf,WAAW,OAAO,WAAW,QAAW;AACtC,YAAM,SAAwC,EAAE,GAAI,MAAM,UAAU,CAAC,EAAG;AAExE,iBAAW,CAAC,WAAW,UAAU,KAAK,OAAO,QAAQ,OAAO,MAAM,GAAG;AACnE,YAAI,eAAe,MAAM;AACvB,iBAAO,OAAO,SAAS;AAAA,QACzB,OAAO;AACL,gBAAM,KAAoB,EAAE,GAAI,OAAO,SAAS,KAAK,CAAC,EAAG;AACzD,cAAI,cAAc,YAAY;AAC5B,gBAAI,WAAW,aAAa,KAAM,QAAO,GAAG;AAAA,qBACnC,WAAW,aAAa,OAAW,IAAG,WAAW,EAAE,GAAG,WAAW,SAAS;AAAA,UACrF;AACA,cAAI,WAAW,YAAY;AACzB,gBAAI,WAAW,UAAU,KAAM,QAAO,GAAG;AAAA,qBAChC,WAAW,UAAU,OAAW,IAAG,QAAQ,WAAW;AAAA,UACjE;AACA,cAAI,cAAc,YAAY;AAC5B,gBAAI,WAAW,aAAa,KAAM,QAAO,GAAG;AAAA,qBACnC,WAAW,aAAa,OAAW,IAAG,WAAW,WAAW;AAAA,UACvE;AACA,iBAAO,SAAS,IAAI;AAAA,QACtB;AAAA,MACF;AAGA,UAAI,OAAO,KAAK,MAAM,EAAE,WAAW,GAAG;AACpC,eAAO,MAAM;AAAA,MACf,OAAO;AACL,cAAM,SAAS;AAAA,MACjB;AAAA,IACF;AAAA,EACF;AAGA,MAAI,OAAO,KAAK,KAAK,EAAE,WAAW,GAAG;AACnC,WAAO,MAAM,MAAM;AAAA,EACrB,OAAO;AACL,UAAM,MAAM,IAAI;AAAA,EAClB;AAEA,SAAO;AAAA,IACL,GAAG;AAAA,IACH,OAAO;AAAA,MACL,GAAG,OAAO;AAAA,MACV,OAAO,OAAO,KAAK,KAAK,EAAE,SAAS,IAAI,QAAQ;AAAA,IACjD;AAAA,EACF;AACF;AAKO,SAAS,cACd,QACA,SACY;AACZ,SAAO;AAAA,IACL,GAAG;AAAA,IACH,WAAW,EAAE,GAAG,OAAO,WAAW,GAAG,QAAQ;AAAA,EAC/C;AACF;","names":[]}

package/dist/{chunk-SFC4GXEN.js → chunk-TNCBMGWB.js}

@@ -1,16 +1,4 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
-import {
-  LmStudioBackend,
-  OllamaBackend
-} from "./chunk-LUQBT2Y4.js";
-import {
-  closeDatabase,
-  initDatabase,
-  vaultDbPath
-} from "./chunk-MYX5NCRH.js";
-import {
-  DaemonClient
-} from "./chunk-SVQAPEYH.js";
 
 // src/symbionts/installer.ts
 import fs from "fs";
@@ -25,7 +13,9 @@ function isMycoHookGroup(group) {
   if (typeof group.command === "string" && isMycoHookCommand(group.command)) return true;
   return false;
 }
-var GITIGNORE_SKILLS_COMMENT = "# Myco skill symlinks (machine-specific)";
+var GITIGNORE_COMMENT = "# Myco managed (machine-specific)";
+var GITIGNORE_SKILLS_COMMENT_LEGACY = "# Myco skill symlinks (machine-specific)";
+var WRANGLER_CACHE_DIR = ".wrangler/";
 var TEMPLATES_SUBDIR = "src/symbionts/templates";
 var HOOK_GUARD_TEMPLATE_FILENAME = "hook-guard.cjs";
 var HOOK_GUARD_INSTALLED_FILENAME = "myco-hook.cjs";
@@ -329,7 +319,8 @@ var SymbiontInstaller = class {
     const skillNames = this.listSkillDirs();
     const desired = [
       ...skillNames.map((name) => `${CANONICAL_SKILLS_DIR}/${name}`),
-      ...reg.skillsTarget !== CANONICAL_SKILLS_DIR ? skillNames.map((name) => `${reg.skillsTarget}/${name}`) : []
+      ...reg.skillsTarget !== CANONICAL_SKILLS_DIR ? skillNames.map((name) => `${reg.skillsTarget}/${name}`) : [],
+      WRANGLER_CACHE_DIR
     ];
     const gitignorePath = path.join(this.projectRoot, ".gitignore");
     let content = "";
@@ -338,7 +329,7 @@ var SymbiontInstaller = class {
     } catch {
     }
     const stripped = this.stripMycoGitignoreBlock(content, skillNames);
-    const desiredBlock = desired.length > 0 ? `${GITIGNORE_SKILLS_COMMENT}
+    const desiredBlock = desired.length > 0 ? `${GITIGNORE_COMMENT}
 ${desired.join("\n")}
 ` : "";
     if (stripped === content && desiredBlock === "") return;
@@ -356,9 +347,11 @@ ${desired.join("\n")}
   stripMycoGitignoreBlock(content, skillNames) {
     const reg = this.manifest.registration;
     const ownedLines = /* @__PURE__ */ new Set([
-      GITIGNORE_SKILLS_COMMENT,
-      `${CANONICAL_SKILLS_DIR}/`
+      GITIGNORE_COMMENT,
+      GITIGNORE_SKILLS_COMMENT_LEGACY,
+      `${CANONICAL_SKILLS_DIR}/`,
       // legacy blanket entry
+      WRANGLER_CACHE_DIR
     ]);
     for (const name of skillNames) {
       ownedLines.add(`${CANONICAL_SKILLS_DIR}/${name}`);
@@ -786,101 +779,43 @@ function ensureSymlink(linkPath, target) {
   }
   fs.symlinkSync(target, linkPath);
 }
-
-// src/cli/shared.ts
-import fs2 from "fs";
-import path2 from "path";
-import os from "os";
-function initVaultDb(vaultDir) {
-  initDatabase(vaultDbPath(vaultDir));
-  return closeDatabase;
-}
-async function connectToDaemon(vaultDir) {
-  const client = new DaemonClient(vaultDir);
-  const healthy = await client.ensureRunning();
-  if (!healthy) {
-    console.error("Failed to connect to daemon");
-    process.exit(1);
-  }
-  return client;
-}
-function loadEnv() {
-  const envPath = path2.resolve(process.cwd(), ".env");
-  if (!fs2.existsSync(envPath)) return;
-  for (const line of fs2.readFileSync(envPath, "utf-8").split("\n")) {
-    const match = line.match(/^\s*([^#=]+?)\s*=\s*(.*?)\s*$/);
-    if (match && !process.env[match[1]]) {
-      process.env[match[1]] = match[2];
+function syncSkillSymlinks(projectRoot, skillName, opts) {
+  const manifestDir = path.join(path.dirname(new URL(import.meta.url).pathname), "manifests");
+  if (!fs.existsSync(manifestDir)) return;
+  const targets = /* @__PURE__ */ new Set();
+  for (const file of fs.readdirSync(manifestDir).filter((f) => f.endsWith(".yaml"))) {
+    try {
+      const content = fs.readFileSync(path.join(manifestDir, file), "utf-8");
+      const match = content.match(/skillsTarget:\s*(.+)/);
+      if (match) targets.add(match[1].trim());
+    } catch {
     }
   }
-}
-function isProcessAlive(pid) {
-  try {
-    process.kill(pid, 0);
-    return true;
-  } catch {
-    return false;
-  }
-}
-var PROVIDER_DEFAULTS = {
-  ollama: { base_url: OllamaBackend.DEFAULT_BASE_URL },
-  "lm-studio": { base_url: LmStudioBackend.DEFAULT_BASE_URL }
-};
-var VAULT_GITIGNORE = `# SQLite database
-myco.db*
-vectors.db*
-
-# Daemon state \u2014 per-machine, ephemeral
-daemon.json
-buffer/
-logs/
-
-# Secrets \u2014 API keys for cloud providers
-secrets.env
-
-# Machine ID
-machine_id
-
-# Binary attachments \u2014 screenshots captured from transcripts
-attachments/
-
-# Team worker deployment \u2014 patched wrangler.toml + source copy
-.team-worker/
-`;
-function registerSymbionts(manifests, projectRoot, packageRoot, verb) {
-  let count = 0;
-  for (const manifest of manifests) {
-    try {
-      const installer = new SymbiontInstaller(manifest, projectRoot, packageRoot);
-      const result = installer.install();
-      const installed = [
-        result.hooks && "hooks",
-        result.mcp && "MCP server",
-        result.skills && "skills",
-        result.settings && "settings",
-        result.instructions && "instructions"
-      ].filter(Boolean);
-      if (installed.length > 0) {
-        console.log(`  \u2713 ${verb} ${manifest.displayName}: ${installed.join(", ")}`);
-        count++;
-      } else {
-        console.log(`  \u2013 ${manifest.displayName}: no registration targets configured`);
+  for (const target of targets) {
+    if (target === CANONICAL_SKILLS_DIR) continue;
+    const agentSkillsDir = path.join(projectRoot, target);
+    const linkPath = path.join(agentSkillsDir, skillName);
+    if (opts?.remove) {
+      try {
+        fs.unlinkSync(linkPath);
+      } catch {
+      }
+      try {
+        fs.rmdirSync(agentSkillsDir);
+      } catch {
       }
-    } catch (err) {
-      console.error(`  \u2717 Failed to register ${manifest.displayName}: ${err.message}`);
+    } else {
+      fs.mkdirSync(agentSkillsDir, { recursive: true });
+      const canonicalDir = path.join(projectRoot, CANONICAL_SKILLS_DIR);
+      const relTarget = path.join(path.relative(agentSkillsDir, canonicalDir), skillName);
+      ensureSymlink(linkPath, relTarget);
     }
   }
-  return count;
 }
 
 export {
   MYCO_MCP_SERVER_NAME,
   SymbiontInstaller,
-  initVaultDb,
-  connectToDaemon,
-  loadEnv,
-  isProcessAlive,
-  VAULT_GITIGNORE,
-  registerSymbionts
+  syncSkillSymlinks
 };
-//# sourceMappingURL=chunk-SFC4GXEN.js.map
+//# sourceMappingURL=chunk-TNCBMGWB.js.map

package/dist/chunk-TNCBMGWB.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/symbionts/installer.ts"],"sourcesContent":["import type { SymbiontManifest } from './manifest-schema.js';\nimport fs from 'node:fs';\nimport path from 'node:path';\n\n/** Prefix used to identify Myco-owned hooks in settings files. */\nconst MYCO_HOOK_COMMAND_PREFIX = 'myco-run';\nconst MYCO_HOOK_GUARD_PREFIX = 'node .agents/myco-hook.cjs';\n\n/** Check if a command string belongs to Myco (old or new guard format). */\nfunction isMycoHookCommand(command: string): boolean {\n  return command.startsWith(MYCO_HOOK_COMMAND_PREFIX) || command.startsWith(MYCO_HOOK_GUARD_PREFIX);\n}\n\n/**\n * Check if a hook group is Myco-owned.\n * Handles both nested format (Claude Code, Codex, etc.) and flat format (Windsurf).\n *\n * Nested: { hooks: [{ command: \"node .agents/myco-hook.cjs ...\" }] }\n * Flat:   { command: \"node .agents/myco-hook.cjs ...\" }\n */\nfunction isMycoHookGroup(group: Record<string, unknown>): boolean {\n  // Nested format: { hooks: [{ command: \"...\" }] }\n  if (Array.isArray(group.hooks) && group.hooks.some((h: { command?: string }) => h.command && isMycoHookCommand(h.command))) return true;\n  // Flat format: { command: \"...\" }\n  if (typeof group.command === 'string' && isMycoHookCommand(group.command)) return true;\n  return false;\n}\n\n/** Current comment header for Myco-managed .gitignore block. */\nconst GITIGNORE_COMMENT = '# Myco managed (machine-specific)';\n\n/** Legacy comment header — recognized for cleanup during reconciliation. */\nconst GITIGNORE_SKILLS_COMMENT_LEGACY = '# Myco skill symlinks (machine-specific)';\n\n/** Wrangler cache directory created by team sync operations. */\nconst WRANGLER_CACHE_DIR = '.wrangler/';\n\n/** Subdirectory within the package where symbiont templates live. */\nconst TEMPLATES_SUBDIR = 'src/symbionts/templates';\n\n/** Filename of the hook guard template in the templates directory. */\nconst HOOK_GUARD_TEMPLATE_FILENAME = 'hook-guard.cjs';\n\n/** Filename when installed into the project .agents/ directory. */\nconst HOOK_GUARD_INSTALLED_FILENAME = 'myco-hook.cjs';\n\n/** Project-relative path where the hook guard is installed. */\nconst HOOK_GUARD_PROJECT_PATH = `.agents/${HOOK_GUARD_INSTALLED_FILENAME}`;\n\n/** Subdirectory within the package where skills live. */\nconst SKILLS_SUBDIR = 'skills';\n\n/** Canonical cross-agent skills directory. */\nconst CANONICAL_SKILLS_DIR = '.agents/skills';\n\n/** MCP server name used by Myco in all symbiont configurations. */\nexport const MYCO_MCP_SERVER_NAME = 'myco';\n\n/** Marker text used to identify unmodified instruction stubs. */\nconst INSTRUCTIONS_STUB_MARKER = 'Edit AGENTS.md, not this file';\n\n/** Start/end markers for the reference block prepended to existing instruction files. */\nconst INSTRUCTIONS_REF_START = '<!-- myco:agents-ref:start -->';\nconst INSTRUCTIONS_REF_END = '<!-- myco:agents-ref:end -->';\n\n/** Reference block prepended to existing instruction files. */\nconst INSTRUCTIONS_REF_BLOCK = `${INSTRUCTIONS_REF_START}\n> **Project intelligence:** This project uses [Myco](https://myco.sh). The canonical project rules are in [\\`AGENTS.md\\`](AGENTS.md) — read and follow it alongside this file.\n${INSTRUCTIONS_REF_END}\n\n`;\n\nexport interface InstallResult {\n  hooks: boolean;\n  mcp: boolean;\n  skills: boolean;\n  settings: boolean;\n  instructions: boolean;\n}\n\nexport class SymbiontInstaller {\n  constructor(\n    private manifest: SymbiontManifest,\n    private projectRoot: string,\n    private packageRoot: string,\n  ) {}\n\n  /**\n   * Copy the hook-guard script into .agents/myco-hook.cjs.\n   * Returns true if the file was written (or updated); false if skipped or N/A.\n   */\n  installHookGuard(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.hooksTarget) return false;\n\n    const guardTemplate = this.loadHookGuardTemplate();\n    if (!guardTemplate) return false;\n\n    const targetPath = path.join(this.projectRoot, HOOK_GUARD_PROJECT_PATH);\n\n    // Skip if already current\n    try {\n      if (fs.readFileSync(targetPath, 'utf-8') === guardTemplate) return false;\n    } catch { /* doesn't exist — proceed */ }\n\n    fs.mkdirSync(path.dirname(targetPath), { recursive: true });\n    fs.writeFileSync(targetPath, guardTemplate, 'utf-8');\n    return true;\n  }\n\n  /**\n   * Remove the hook-guard script from .agents/myco-hook.cjs.\n   * Returns true if the file was removed; false otherwise.\n   */\n  uninstallHookGuard(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.hooksTarget) return false;\n\n    const targetPath = path.join(this.projectRoot, HOOK_GUARD_PROJECT_PATH);\n    try {\n      fs.unlinkSync(targetPath);\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  /** Load the hook-guard template from package root. */\n  private loadHookGuardTemplate(): string | null {\n    const candidates = [\n      path.join(this.packageRoot, TEMPLATES_SUBDIR, HOOK_GUARD_TEMPLATE_FILENAME),\n      path.join(this.packageRoot, 'dist', TEMPLATES_SUBDIR, HOOK_GUARD_TEMPLATE_FILENAME),\n    ];\n    for (const p of candidates) {\n      try { return fs.readFileSync(p, 'utf-8'); } catch { /* try next */ }\n    }\n    return null;\n  }\n\n  /** Load a JSON template file for this symbiont. Returns null if not found. */\n  loadTemplate(name: string): Record<string, unknown> | null {\n    // Check both source layout and dist layout\n    const candidates = [\n      path.join(this.packageRoot, TEMPLATES_SUBDIR, this.manifest.name, `${name}.json`),\n      // tsup preserves the src/ prefix under dist/, so the same subdir works in both layouts\n      path.join(this.packageRoot, 'dist', TEMPLATES_SUBDIR, this.manifest.name, `${name}.json`),\n    ];\n    for (const filePath of candidates) {\n      try {\n        return JSON.parse(fs.readFileSync(filePath, 'utf-8'));\n      } catch { /* not found or malformed — try next */ }\n    }\n    return null;\n  }\n\n  /** Run all registration steps. */\n  install(): InstallResult {\n    const reg = this.manifest.registration;\n    // Install hook guard before hooks so the guard script is in place when hooks reference it\n    this.installHookGuard();\n    const result = this.shouldBatchJsonTargets(reg)\n      ? this.installBatchedJson(reg!)\n      : {\n          hooks: this.installHooks(),\n          mcp: this.installMcp(),\n          skills: this.installSkills(),\n          settings: this.installSettings(),\n          instructions: this.installInstructions(),\n        };\n    this.updateGitignore();\n    return result;\n  }\n\n  /**\n   * Check if ALL non-null JSON targets share the same file (e.g., Gemini).\n   * Only batches when every target resolves to one path — partial overlaps\n   * (e.g., Claude Code: hooks+settings share but MCP is separate) use normal path.\n   */\n  private shouldBatchJsonTargets(reg: typeof this.manifest.registration): boolean {\n    if (!reg) return false;\n    const mcpFormat = reg.mcpFormat ?? 'json';\n    if (mcpFormat !== 'json') return false;\n    const targets = [reg.hooksTarget, reg.mcpTarget, reg.settingsTarget].filter(Boolean);\n    return targets.length > 1 && new Set(targets).size === 1;\n  }\n\n  /**\n   * Batched install for agents where hooks, MCP, and settings share one JSON file.\n   * Single read → apply all transforms in memory → single write.\n   */\n  private installBatchedJson(reg: NonNullable<typeof this.manifest.registration>): InstallResult {\n    const targetPath = path.join(this.projectRoot, reg.hooksTarget ?? reg.mcpTarget ?? reg.settingsTarget!);\n    let data = readJsonFile(targetPath);\n    let hooks = false, mcp = false, settings = false;\n\n    // Apply hooks transform\n    const hooksTemplate = reg.hooksTarget ? this.loadTemplate('hooks') : null;\n    if (hooksTemplate) {\n      const existingHooks = (data.hooks ?? {}) as Record<string, unknown[]>;\n      const mergedHooks: Record<string, unknown[]> = {};\n      for (const [event, groups] of Object.entries(existingHooks)) {\n        const nonMyco = (groups as Array<Record<string, unknown>>).filter((g) => !isMycoHookGroup(g));\n        if (nonMyco.length > 0) mergedHooks[event] = nonMyco;\n      }\n      for (const [event, groups] of Object.entries(hooksTemplate)) {\n        mergedHooks[event] = [...(mergedHooks[event] ?? []), ...(groups as unknown[])];\n      }\n      data.hooks = mergedHooks;\n      hooks = true;\n    }\n\n    // Apply MCP transform\n    const mcpTemplate = reg.mcpTarget ? this.loadTemplate('mcp') : null;\n    if (mcpTemplate) {\n      const servers = (data.mcpServers ?? {}) as Record<string, unknown>;\n      for (const [name, def] of Object.entries(mcpTemplate)) {\n        servers[name] = def;\n      }\n      data.mcpServers = servers;\n      mcp = true;\n    }\n\n    // Apply settings transform\n    const settingsTemplate = reg.settingsTarget ? this.loadTemplate('settings') : null;\n    if (settingsTemplate) {\n      data = deepMergeSettings(data, settingsTemplate);\n      settings = true;\n    }\n\n    writeJsonFile(targetPath, data);\n\n    return {\n      hooks,\n      mcp,\n      skills: this.installSkills(),\n      settings,\n      instructions: this.installInstructions(),\n    };\n  }\n\n  /** Remove all Myco registration from this symbiont's project files. */\n  uninstall(): InstallResult {\n    const reg = this.manifest.registration;\n    const result = this.shouldBatchJsonTargets(reg)\n      ? this.uninstallBatchedJson(reg!)\n      : {\n          hooks: this.uninstallHooks(),\n          mcp: this.uninstallMcp(),\n          skills: this.uninstallSkills(),\n          settings: this.uninstallSettings(),\n          instructions: this.uninstallInstructions(),\n        };\n    // Remove hook guard after hooks/settings so the file is cleaned up last\n    this.uninstallHookGuard();\n    this.cleanGitignore();\n    return result;\n  }\n\n  /**\n   * Batched uninstall for agents where hooks, MCP, and settings share one JSON file.\n   */\n  private uninstallBatchedJson(reg: NonNullable<typeof this.manifest.registration>): InstallResult {\n    const targetPath = path.join(this.projectRoot, reg.hooksTarget ?? reg.mcpTarget ?? reg.settingsTarget!);\n    const data = readJsonFile(targetPath);\n    if (Object.keys(data).length === 0) {\n      return { hooks: false, mcp: false, skills: this.uninstallSkills(), settings: false, instructions: this.uninstallInstructions() };\n    }\n\n    let hooks = false, mcp = false, settings = false;\n\n    // Remove hooks\n    if (reg.hooksTarget) {\n      const existingHooks = (data.hooks ?? {}) as Record<string, unknown[]>;\n      if (Object.keys(existingHooks).length > 0) {\n        const cleaned: Record<string, unknown[]> = {};\n        for (const [event, groups] of Object.entries(existingHooks)) {\n          const nonMyco = (groups as Array<Record<string, unknown>>).filter((g) => !isMycoHookGroup(g));\n          if (nonMyco.length > 0) cleaned[event] = nonMyco;\n        }\n        if (Object.keys(cleaned).length === 0) {\n          delete data.hooks;\n        } else {\n          data.hooks = cleaned;\n        }\n        hooks = true;\n      }\n    }\n\n    // Remove MCP\n    if (reg.mcpTarget) {\n      const servers = (data.mcpServers ?? {}) as Record<string, unknown>;\n      if (servers[MYCO_MCP_SERVER_NAME]) {\n        delete servers[MYCO_MCP_SERVER_NAME];\n        if (Object.keys(servers).length === 0) delete data.mcpServers;\n        else data.mcpServers = servers;\n        mcp = true;\n      }\n    }\n\n    // Remove settings\n    const settingsTemplate = reg.settingsTarget ? this.loadTemplate('settings') : null;\n    if (settingsTemplate) {\n      settings = deepRemoveSettings(data, settingsTemplate);\n    }\n\n    writeOrDeleteJsonFile(targetPath, data);\n\n    return { hooks, mcp, skills: this.uninstallSkills(), settings, instructions: this.uninstallInstructions() };\n  }\n\n  /**\n   * Ensure the instruction file references AGENTS.md.\n   * - File doesn't exist: write the full stub template.\n   * - File exists without reference: prepend a reference block.\n   * - File already has reference: skip (idempotent).\n   *\n   * Also ensures AGENTS.md exists — creates a starter if missing.\n   */\n  installInstructions(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.instructionsFile) return false;\n\n    // Ensure AGENTS.md exists before creating stubs that reference it\n    ensureAgentsMd(this.projectRoot, this.packageRoot);\n\n    const targetPath = path.join(this.projectRoot, reg.instructionsFile);\n\n    // Check if file already exists\n    let existing: string | null = null;\n    try { existing = fs.readFileSync(targetPath, 'utf-8'); } catch { /* doesn't exist */ }\n\n    if (existing !== null) {\n      // File exists — check if it already has our reference\n      if (existing.includes(INSTRUCTIONS_REF_START) || existing.includes(INSTRUCTIONS_STUB_MARKER)) {\n        return false; // Already has reference — idempotent\n      }\n      // Prepend reference block to existing content\n      fs.writeFileSync(targetPath, INSTRUCTIONS_REF_BLOCK + existing, 'utf-8');\n      return true;\n    }\n\n    // File doesn't exist — write the full stub template\n    const templateCandidates = [\n      path.join(this.packageRoot, 'src/symbionts/templates/instructions-stub.md'),\n      path.join(this.packageRoot, 'dist/src/symbionts/templates/instructions-stub.md'),\n    ];\n    let stub: string | null = null;\n    for (const p of templateCandidates) {\n      try { stub = fs.readFileSync(p, 'utf-8'); break; } catch { /* try next */ }\n    }\n    if (!stub) return false;\n\n    stub = stub.replace('{agentDisplayName}', this.manifest.displayName);\n    fs.mkdirSync(path.dirname(targetPath), { recursive: true });\n    fs.writeFileSync(targetPath, stub, 'utf-8');\n    return true;\n  }\n\n  /**\n   * Remove Myco's instruction file reference.\n   * - If file is the full stub (only Myco content): delete it.\n   * - If file has user content + prepended reference: remove just the reference block.\n   */\n  uninstallInstructions(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.instructionsFile) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.instructionsFile);\n    let content: string;\n    try { content = fs.readFileSync(targetPath, 'utf-8'); } catch { return false; }\n\n    // Case 1: Full stub — delete the file entirely\n    if (content.includes(INSTRUCTIONS_STUB_MARKER)) {\n      fs.unlinkSync(targetPath);\n      return true;\n    }\n\n    // Case 2: Prepended reference block — remove just the block\n    if (content.includes(INSTRUCTIONS_REF_START)) {\n      const startIdx = content.indexOf(INSTRUCTIONS_REF_START);\n      const endIdx = content.indexOf(INSTRUCTIONS_REF_END);\n      if (endIdx > startIdx) {\n        // Remove from start marker through end marker + trailing whitespace\n        const afterEnd = endIdx + INSTRUCTIONS_REF_END.length;\n        const cleaned = (content.slice(0, startIdx) + content.slice(afterEnd)).replace(/^\\n+/, '');\n        fs.writeFileSync(targetPath, cleaned, 'utf-8');\n        return true;\n      }\n    }\n\n    return false;\n  }\n\n  /** List skill directory names from the package root. Returns empty array if not found. */\n  private listSkillDirs(): string[] {\n    try {\n      return fs.readdirSync(path.join(this.packageRoot, SKILLS_SUBDIR), { withFileTypes: true })\n        .filter((d) => d.isDirectory())\n        .map((d) => d.name);\n    } catch { return []; }\n  }\n\n  /**\n   * Reconcile Myco-owned skill entries in project .gitignore.\n   * Computes the desired entry set, strips any existing Myco block\n   * (and legacy entries), then writes the current block if changed.\n   */\n  private updateGitignore(): void {\n    const reg = this.manifest.registration;\n    if (!reg?.skillsTarget) return;\n\n    const skillNames = this.listSkillDirs();\n\n    // Desired state: per-skill entries + infrastructure artifacts\n    const desired = [\n      ...skillNames.map((name) => `${CANONICAL_SKILLS_DIR}/${name}`),\n      ...(reg.skillsTarget !== CANONICAL_SKILLS_DIR\n        ? skillNames.map((name) => `${reg.skillsTarget}/${name}`)\n        : []\n      ),\n      WRANGLER_CACHE_DIR,\n    ];\n\n    const gitignorePath = path.join(this.projectRoot, '.gitignore');\n    let content = '';\n    try { content = fs.readFileSync(gitignorePath, 'utf-8'); } catch { /* doesn't exist yet */ }\n\n    // Strip existing Myco block and any legacy entries\n    const stripped = this.stripMycoGitignoreBlock(content, skillNames);\n\n    // Build the new block\n    const desiredBlock = desired.length > 0\n      ? `${GITIGNORE_COMMENT}\\n${desired.join('\\n')}\\n`\n      : '';\n\n    // Check if anything changed\n    if (stripped === content && desiredBlock === '') return;\n    const separator = stripped.length > 0 && !stripped.endsWith('\\n') ? '\\n' : '';\n    const spacer = stripped.length > 0 && desiredBlock.length > 0 ? '\\n' : '';\n    const result = stripped + separator + spacer + desiredBlock;\n    if (result === content) return;\n\n    fs.writeFileSync(gitignorePath, result, 'utf-8');\n  }\n\n  /**\n   * Remove all Myco-owned gitignore entries: the comment header, per-skill\n   * entries for both canonical and agent-specific paths, and legacy blanket\n   * directory entries. Returns the cleaned content.\n   */\n  private stripMycoGitignoreBlock(content: string, skillNames: string[]): string {\n    const reg = this.manifest.registration;\n    const ownedLines = new Set<string>([\n      GITIGNORE_COMMENT,\n      GITIGNORE_SKILLS_COMMENT_LEGACY,\n      `${CANONICAL_SKILLS_DIR}/`, // legacy blanket entry\n      WRANGLER_CACHE_DIR,\n    ]);\n    for (const name of skillNames) {\n      ownedLines.add(`${CANONICAL_SKILLS_DIR}/${name}`);\n      if (reg?.skillsTarget && reg.skillsTarget !== CANONICAL_SKILLS_DIR) {\n        ownedLines.add(`${reg.skillsTarget}/${name}`);\n      }\n    }\n\n    const lines = content.split('\\n');\n    const filtered = lines.filter((line) => !ownedLines.has(line));\n    return filtered.join('\\n').replace(/\\n{3,}/g, '\\n\\n').trimEnd() + (filtered.length > 0 ? '\\n' : '');\n  }\n\n  /**\n   * Merge hooks template into the target settings file.\n   * Replaces all Myco-owned hook groups; preserves non-Myco hooks.\n   */\n  installHooks(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.hooksTarget) return false;\n\n    const template = this.loadTemplate('hooks');\n    if (!template) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.hooksTarget);\n    const settings = readJsonFile(targetPath);\n    const existingHooks = (settings.hooks ?? {}) as Record<string, unknown[]>;\n\n    // Build merged hooks: for each event, keep non-Myco groups + add template groups\n    const mergedHooks: Record<string, unknown[]> = {};\n\n    // Preserve non-Myco hooks from existing config\n    for (const [event, groups] of Object.entries(existingHooks)) {\n      const nonMycoGroups = (groups as Array<Record<string, unknown>>).filter(\n        (group) => !isMycoHookGroup(group),\n      );\n      if (nonMycoGroups.length > 0) {\n        mergedHooks[event] = nonMycoGroups;\n      }\n    }\n\n    // Add template hooks\n    for (const [event, groups] of Object.entries(template)) {\n      mergedHooks[event] = [...(mergedHooks[event] ?? []), ...(groups as unknown[])];\n    }\n\n    settings.hooks = mergedHooks;\n    writeJsonFile(targetPath, settings);\n    return true;\n  }\n\n  /**\n   * Merge MCP server template into the target config file.\n   * Replaces the `myco` server entry; preserves other servers.\n   */\n  installMcp(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.mcpTarget) return false;\n\n    const template = this.loadTemplate('mcp');\n    if (!template) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.mcpTarget);\n    const mcpFormat = reg.mcpFormat ?? 'json';\n\n    if (mcpFormat === 'toml') {\n      return this.installMcpToml(targetPath, template);\n    }\n    return this.installMcpJson(targetPath, template);\n  }\n\n  /** Write MCP servers to a JSON config file. */\n  private installMcpJson(targetPath: string, template: Record<string, unknown>): boolean {\n    const config = readJsonFile(targetPath);\n    const servers = (config.mcpServers ?? {}) as Record<string, unknown>;\n\n    for (const [name, def] of Object.entries(template)) {\n      servers[name] = def;\n    }\n\n    config.mcpServers = servers;\n    writeJsonFile(targetPath, config);\n    return true;\n  }\n\n  /** Write MCP servers to a TOML config file. */\n  private installMcpToml(targetPath: string, template: Record<string, unknown>): boolean {\n    let raw = '';\n    try { raw = fs.readFileSync(targetPath, 'utf-8'); } catch { /* doesn't exist */ }\n\n    for (const [name, def] of Object.entries(template)) {\n      raw = buildTomlMcpSection(raw, name, def as Record<string, unknown>);\n    }\n\n    fs.mkdirSync(path.dirname(targetPath), { recursive: true });\n    fs.writeFileSync(targetPath, raw, 'utf-8');\n    return true;\n  }\n\n  /**\n   * Create symlinks for skills through .agents/skills/ canonical layer.\n   * Canonical: .agents/skills/<name> -> <packageRoot>/skills/<name>\n   * Agent-specific: <skillsTarget>/<name> -> ../../.agents/skills/<name>\n   */\n  installSkills(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.skillsTarget) return false;\n\n    const skillNames = this.listSkillDirs();\n    if (skillNames.length === 0) return false;\n\n    const skillsSrc = path.join(this.packageRoot, SKILLS_SUBDIR);\n\n    // Create canonical symlinks: .agents/skills/<name> -> package skills\n    const canonicalDir = path.join(this.projectRoot, CANONICAL_SKILLS_DIR);\n    fs.mkdirSync(canonicalDir, { recursive: true });\n\n    for (const name of skillNames) {\n      const canonicalLink = path.join(canonicalDir, name);\n      const target = path.join(skillsSrc, name);\n      ensureSymlink(canonicalLink, target);\n    }\n\n    // Create agent-specific symlinks if skillsTarget differs from canonical\n    const agentSkillsDir = path.join(this.projectRoot, reg.skillsTarget);\n    const canonicalRel = path.relative(agentSkillsDir, canonicalDir);\n\n    if (reg.skillsTarget !== CANONICAL_SKILLS_DIR) {\n      fs.mkdirSync(agentSkillsDir, { recursive: true });\n      for (const name of skillNames) {\n        const agentLink = path.join(agentSkillsDir, name);\n        const relTarget = path.join(canonicalRel, name);\n        ensureSymlink(agentLink, relTarget);\n      }\n    }\n\n    return true;\n  }\n\n  /**\n   * Merge settings template into the target settings file.\n   * Deep merges objects and deduplicates arrays.\n   */\n  installSettings(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.settingsTarget) return false;\n\n    const template = this.loadTemplate('settings');\n    if (!template) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.settingsTarget);\n    const existing = readJsonFile(targetPath);\n    const merged = deepMergeSettings(existing, template);\n    writeJsonFile(targetPath, merged);\n    return true;\n  }\n\n  /**\n   * Remove Myco entries from the target settings file.\n   * Template-driven: loads the settings template and removes matching values.\n   * Arrays: filter out values present in the template.\n   * Objects: delete keys present in the template.\n   */\n  uninstallSettings(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.settingsTarget) return false;\n\n    const template = this.loadTemplate('settings');\n    if (!template) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.settingsTarget);\n    const settings = readJsonFile(targetPath);\n    if (Object.keys(settings).length === 0) return false;\n\n    const changed = deepRemoveSettings(settings, template);\n    if (!changed) return false;\n\n    writeOrDeleteJsonFile(targetPath, settings);\n    return true;\n  }\n\n  /** Remove Myco hook groups from the target settings file. */\n  uninstallHooks(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.hooksTarget) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.hooksTarget);\n    const settings = readJsonFile(targetPath);\n    const existingHooks = (settings.hooks ?? {}) as Record<string, unknown[]>;\n    if (Object.keys(existingHooks).length === 0) return false;\n\n    const cleaned: Record<string, unknown[]> = {};\n    for (const [event, groups] of Object.entries(existingHooks)) {\n      const nonMyco = (groups as Array<Record<string, unknown>>).filter(\n        (group) => !isMycoHookGroup(group),\n      );\n      if (nonMyco.length > 0) {\n        cleaned[event] = nonMyco;\n      }\n    }\n\n    if (Object.keys(cleaned).length === 0) {\n      delete settings.hooks;\n    } else {\n      settings.hooks = cleaned;\n    }\n\n    writeOrDeleteJsonFile(targetPath, settings);\n    return true;\n  }\n\n  /** Remove Myco MCP server entry from the target config file. */\n  uninstallMcp(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.mcpTarget) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.mcpTarget);\n    const mcpFormat = reg.mcpFormat ?? 'json';\n\n    if (mcpFormat === 'toml') {\n      return this.uninstallMcpToml(targetPath);\n    }\n    return this.uninstallMcpJson(targetPath);\n  }\n\n  private uninstallMcpJson(targetPath: string): boolean {\n    const config = readJsonFile(targetPath);\n    const servers = (config.mcpServers ?? {}) as Record<string, unknown>;\n    if (!servers[MYCO_MCP_SERVER_NAME]) return false;\n\n    delete servers[MYCO_MCP_SERVER_NAME];\n\n    if (Object.keys(servers).length === 0) {\n      delete config.mcpServers;\n    } else {\n      config.mcpServers = servers;\n    }\n\n    writeOrDeleteJsonFile(targetPath, config);\n    return true;\n  }\n\n  private uninstallMcpToml(targetPath: string): boolean {\n    let raw = '';\n    try { raw = fs.readFileSync(targetPath, 'utf-8'); } catch { return false; }\n\n    const sectionHeader = `[mcp_servers.${MYCO_MCP_SERVER_NAME}]`;\n    if (!raw.includes(sectionHeader)) return false;\n\n    const startIdx = raw.indexOf(sectionHeader);\n    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, MYCO_MCP_SERVER_NAME);\n    const before = raw.slice(0, startIdx).trimEnd();\n    const after = raw.slice(endIdx).trimStart();\n    const updated = (before + (before && after ? 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