@goondocks/myco 0.15.1 → 0.16.1

package/dist/{chunk-23FJUKCN.js.map → chunk-SGYYOTNM.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/db/queries/sessions.ts"],"sourcesContent":["/**\n * Session CRUD query helpers.\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 { getTeamMachineId } from '@myco/daemon/team-context.js';\nimport { syncRow } from '@myco/db/queries/team-outbox.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of sessions returned by listSessions when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n/** Session status value when a session is closed normally. */\nconst STATUS_COMPLETED = 'completed';\n\n/** Default session status for new sessions. */\nconst DEFAULT_STATUS = 'active';\n\n/** Default prompt count for new sessions. */\nconst DEFAULT_PROMPT_COUNT = 0;\n\n/** Default tool count for new sessions. */\nconst DEFAULT_TOOL_COUNT = 0;\n\n/** Default processed flag for new sessions. */\nconst DEFAULT_PROCESSED = 0;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting/upserting a session. */\nexport interface SessionInsert {\n  id: string;\n  agent: string;\n  started_at: number;\n  created_at: number;\n  user?: string | null;\n  project_root?: string | null;\n  branch?: string | null;\n  ended_at?: number | null;\n  status?: string;\n  prompt_count?: number;\n  tool_count?: number;\n  title?: string | null;\n  summary?: string | null;\n  transcript_path?: string | null;\n  parent_session_id?: string | null;\n  parent_session_reason?: string | null;\n  processed?: number;\n  content_hash?: string | null;\n  machine_id?: string;\n}\n\n/** Row shape returned from session queries (all columns). */\nexport interface SessionRow {\n  id: string;\n  agent: string;\n  user: string | null;\n  project_root: string | null;\n  branch: string | null;\n  started_at: number;\n  ended_at: number | null;\n  status: string;\n  prompt_count: number;\n  tool_count: number;\n  title: string | null;\n  summary: string | null;\n  transcript_path: string | null;\n  parent_session_id: string | null;\n  parent_session_reason: string | null;\n  processed: number;\n  content_hash: string | null;\n  embedded: number;\n  created_at: number;\n  machine_id: string;\n  synced_at: number | null;\n}\n\n/** Updatable fields for `updateSession`. */\nexport interface SessionUpdate {\n  agent?: string;\n  user?: string | null;\n  project_root?: string | null;\n  branch?: string | null;\n  ended_at?: number | null;\n  status?: string;\n  prompt_count?: number;\n  tool_count?: number;\n  title?: string | null;\n  summary?: string | null;\n  transcript_path?: string | null;\n  parent_session_id?: string | null;\n  parent_session_reason?: string | null;\n  processed?: number;\n  content_hash?: string | null;\n}\n\n/** Filter options for `listSessions`. */\nexport interface ListSessionsOptions {\n  limit?: number;\n  offset?: number;\n  status?: string;\n  agent?: string;\n  search?: string;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst SESSION_COLUMNS = [\n  'id',\n  'agent',\n  '\"user\"',\n  'project_root',\n  'branch',\n  'started_at',\n  'ended_at',\n  'status',\n  'prompt_count',\n  'tool_count',\n  'title',\n  'summary',\n  'transcript_path',\n  'parent_session_id',\n  'parent_session_reason',\n  'processed',\n  'content_hash',\n  'embedded',\n  'created_at',\n  'machine_id',\n  'synced_at',\n] as const;\n\nconst SELECT_COLUMNS = SESSION_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/**\n * Normalize a SQLite result row into a typed SessionRow.\n *\n * The quoted \"user\" column comes back as `user` in the result object.\n */\nfunction toSessionRow(row: Record<string, unknown>): SessionRow {\n  return {\n    id: row.id as string,\n    agent: row.agent as string,\n    user: (row.user as string) ?? null,\n    project_root: (row.project_root as string) ?? null,\n    branch: (row.branch as string) ?? null,\n    started_at: row.started_at as number,\n    ended_at: (row.ended_at as number) ?? null,\n    status: row.status as string,\n    prompt_count: row.prompt_count as number,\n    tool_count: row.tool_count as number,\n    title: (row.title as string) ?? null,\n    summary: (row.summary as string) ?? null,\n    transcript_path: (row.transcript_path as string) ?? null,\n    parent_session_id: (row.parent_session_id as string) ?? null,\n    parent_session_reason: (row.parent_session_reason as string) ?? null,\n    processed: row.processed as number,\n    content_hash: (row.content_hash as string) ?? null,\n    embedded: (row.embedded as number) ?? 0,\n    created_at: row.created_at as number,\n    machine_id: (row.machine_id as string) ?? 'local',\n    synced_at: (row.synced_at as number) ?? null,\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a session or update it if the id already exists.\n *\n * On conflict the row is updated with the values from `data`, preserving\n * any columns not supplied via COALESCE with EXCLUDED values.\n */\nexport function upsertSession(data: SessionInsert): SessionRow {\n  const db = getDatabase();\n\n  db.prepare(\n    `INSERT INTO sessions (\n       id, agent, \"user\", project_root, branch,\n       started_at, ended_at, status, prompt_count, tool_count,\n       title, summary, transcript_path,\n       parent_session_id, parent_session_reason,\n       processed, content_hash, created_at, machine_id\n     ) VALUES (\n       ?, ?, ?, ?, ?,\n       ?, ?, ?, ?, ?,\n       ?, ?, ?,\n       ?, ?,\n       ?, ?, ?, ?\n     )\n     ON CONFLICT (id) DO UPDATE SET\n       agent                 = EXCLUDED.agent,\n       \"user\"                = EXCLUDED.\"user\",\n       project_root          = EXCLUDED.project_root,\n       branch                = EXCLUDED.branch,\n       started_at            = EXCLUDED.started_at,\n       ended_at              = COALESCE(EXCLUDED.ended_at, sessions.ended_at),\n       status                = COALESCE(EXCLUDED.status, sessions.status),\n       prompt_count          = CASE WHEN ? THEN EXCLUDED.prompt_count ELSE sessions.prompt_count END,\n       tool_count            = CASE WHEN ? THEN EXCLUDED.tool_count ELSE sessions.tool_count END,\n       title                 = COALESCE(EXCLUDED.title, sessions.title),\n       summary               = COALESCE(EXCLUDED.summary, sessions.summary),\n       transcript_path       = COALESCE(EXCLUDED.transcript_path, sessions.transcript_path),\n       parent_session_id     = EXCLUDED.parent_session_id,\n       parent_session_reason = EXCLUDED.parent_session_reason,\n       processed             = COALESCE(EXCLUDED.processed, sessions.processed),\n       content_hash          = EXCLUDED.content_hash`,\n  ).run(\n    data.id,\n    data.agent,\n    data.user ?? null,\n    data.project_root ?? null,\n    data.branch ?? null,\n    data.started_at,\n    data.ended_at ?? null,\n    data.status ?? DEFAULT_STATUS,\n    data.prompt_count ?? DEFAULT_PROMPT_COUNT,\n    data.tool_count ?? DEFAULT_TOOL_COUNT,\n    data.title ?? null,\n    data.summary ?? null,\n    data.transcript_path ?? null,\n    data.parent_session_id ?? null,\n    data.parent_session_reason ?? null,\n    data.processed ?? DEFAULT_PROCESSED,\n    data.content_hash ?? null,\n    data.created_at,\n    data.machine_id ?? getTeamMachineId(),\n    data.prompt_count !== undefined ? 1 : 0,\n    data.tool_count !== undefined ? 1 : 0,\n  );\n\n  const row = toSessionRow(\n    db.prepare(`SELECT ${SELECT_COLUMNS} FROM sessions WHERE id = ?`).get(data.id) as Record<string, unknown>,\n  );\n\n  syncRow('sessions', row);\n\n  return row;\n}\n\n/**\n * Retrieve a single session by id.\n *\n * @returns the session row, or null if not found.\n */\nexport function getSession(id: string): SessionRow | null {\n  const db = getDatabase();\n\n  const row = db.prepare(\n    `SELECT ${SELECT_COLUMNS} FROM sessions WHERE id = ?`,\n  ).get(id) as Record<string, unknown> | undefined;\n\n  if (!row) return null;\n  return toSessionRow(row);\n}\n\n/** Build WHERE clause and bound params from session filter options. */\nfunction buildSessionsWhere(\n  options: Omit<ListSessionsOptions, 'limit' | 'offset'>,\n): { where: string; params: unknown[] } {\n  const conditions: string[] = [];\n  const params: unknown[] = [];\n\n  if (options.status !== undefined) {\n    conditions.push(`status = ?`);\n    params.push(options.status);\n  }\n\n  if (options.agent !== undefined) {\n    conditions.push(`agent = ?`);\n    params.push(options.agent);\n  }\n\n  if (options.search !== undefined && options.search.length > 0) {\n    conditions.push(`(title LIKE ? OR id LIKE ?)`);\n    const pattern = `%${options.search}%`;\n    params.push(pattern, pattern);\n  }\n\n  return {\n    where: conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '',\n    params,\n  };\n}\n\n/**\n * List sessions with optional filters, ordered by created_at DESC.\n */\nexport function listSessions(\n  options: ListSessionsOptions = {},\n): SessionRow[] {\n  const db = getDatabase();\n  const { where, params } = buildSessionsWhere(options);\n  const limit = options.limit ?? DEFAULT_LIST_LIMIT;\n  const offset = options.offset ?? 0;\n\n  const rows = db.prepare(\n    `SELECT ${SELECT_COLUMNS}\n     FROM sessions\n     ${where}\n     ORDER BY created_at DESC\n     LIMIT ?\n     OFFSET ?`,\n  ).all(...params, limit, offset) as Record<string, unknown>[];\n\n  return rows.map(toSessionRow);\n}\n\n/**\n * Count sessions matching optional filters (for pagination totals).\n */\nexport function countSessions(\n  options: Omit<ListSessionsOptions, 'limit' | 'offset'> = {},\n): number {\n  const db = getDatabase();\n  const { where, params } = buildSessionsWhere(options);\n\n  const row = db.prepare(\n    `SELECT COUNT(*) as count FROM sessions ${where}`,\n  ).get(...params) as { count: number };\n\n  return row.count;\n}\n\n/**\n * Update specific fields on an existing session.\n *\n * @returns the updated row, or null if the session does not exist.\n */\nexport function updateSession(\n  id: string,\n  updates: SessionUpdate,\n): SessionRow | null {\n  const db = getDatabase();\n\n  const setClauses: string[] = [];\n  const params: unknown[] = [];\n\n  const fieldMap: Record<string, string> = {\n    agent: 'agent',\n    user: '\"user\"',\n    project_root: 'project_root',\n    branch: 'branch',\n    ended_at: 'ended_at',\n    status: 'status',\n    prompt_count: 'prompt_count',\n    tool_count: 'tool_count',\n    title: 'title',\n    summary: 'summary',\n    transcript_path: 'transcript_path',\n    parent_session_id: 'parent_session_id',\n    parent_session_reason: 'parent_session_reason',\n    processed: 'processed',\n    content_hash: 'content_hash',\n  };\n\n  for (const [key, column] of Object.entries(fieldMap)) {\n    if (key in updates) {\n      setClauses.push(`${column} = ?`);\n      params.push((updates as Record<string, unknown>)[key] ?? null);\n    }\n  }\n\n  if (setClauses.length === 0) return getSession(id);\n\n  params.push(id);\n\n  db.prepare(\n    `UPDATE sessions\n     SET ${setClauses.join(', ')}\n     WHERE id = ?`,\n  ).run(...params);\n\n  const updated = getSession(id);\n\n  if (updated) syncRow('sessions', updated);\n\n  return updated;\n}\n\n/**\n * Atomically increment tool_count for a session.\n *\n * Uses SQL `tool_count + 1` to avoid read-modify-write races.\n */\nexport function incrementSessionToolCount(id: string): void {\n  const db = getDatabase();\n  db.prepare(\n    `UPDATE sessions SET tool_count = COALESCE(tool_count, 0) + 1 WHERE id = ?`,\n  ).run(id);\n}\n\n/**\n * Close a session — set status to 'completed' and record the end time.\n *\n * @returns the updated row, or null if the session does not exist.\n */\nexport function closeSession(\n  id: string,\n  endedAt: number,\n): SessionRow | null {\n  const db = getDatabase();\n\n  db.prepare(\n    `UPDATE sessions\n     SET status = ?, ended_at = ?\n     WHERE id = ?`,\n  ).run(STATUS_COMPLETED, endedAt, id);\n\n  const closed = getSession(id);\n\n  if (closed) syncRow('sessions', closed);\n\n  return closed;\n}\n\n/**\n * Delete a session and all its child rows (batches, activities, attachments).\n *\n * No ON DELETE CASCADE in the schema, so we delete children first.\n * Returns true if the session existed and was deleted.\n */\nexport function deleteSession(id: string): boolean {\n  const db = getDatabase();\n\n  db.prepare(`DELETE FROM activities WHERE session_id = ?`).run(id);\n  db.prepare(`DELETE FROM attachments WHERE session_id = ?`).run(id);\n  db.prepare(`DELETE FROM prompt_batches WHERE session_id = ?`).run(id);\n  const info = db.prepare(`DELETE FROM sessions WHERE id = ?`).run(id);\n\n  return info.changes > 0;\n}\n\n// ---------------------------------------------------------------------------\n// Cascade delete + impact query\n// ---------------------------------------------------------------------------\n\n/** Counts of related data that would be affected by a session delete. */\nexport interface SessionImpact {\n  promptCount: number;\n  sporeCount: number;\n  attachmentCount: number;\n  graphEdgeCount: number;\n}\n\n/** Result of a cascade delete operation. */\nexport interface DeleteCascadeResult {\n  deleted: boolean;\n  counts: {\n    prompts: number;\n    spores: number;\n    attachments: number;\n    graphEdges: number;\n    resolutionEvents: number;\n  };\n  /** Spore IDs that were deleted (needed for vault file + vector cleanup). */\n  deletedSporeIds: string[];\n  /** Attachment file paths that were deleted from DB (needed for disk cleanup). */\n  deletedAttachmentPaths: string[];\n}\n\n/**\n * Get counts of all data related to a session, for pre-delete impact display.\n */\nexport function getSessionImpact(sessionId: string): SessionImpact {\n  const db = getDatabase();\n\n  const row = db.prepare(\n    `SELECT\n       (SELECT COUNT(*) FROM prompt_batches WHERE session_id = ?) AS promptCount,\n       (SELECT COUNT(*) FROM spores WHERE session_id = ?) AS sporeCount,\n       (SELECT COUNT(*) FROM attachments WHERE session_id = ?) AS attachmentCount,\n       (SELECT COUNT(*) FROM graph_edges WHERE session_id = ?) AS graphEdgeCount`,\n  ).get(sessionId, sessionId, sessionId, sessionId) as SessionImpact;\n\n  return row;\n}\n\n/**\n * Delete a session and ALL related data in a single transaction.\n *\n * Returns counts of deleted rows and IDs needed for post-transaction\n * cleanup (vault files, embedding vectors).\n */\nexport function deleteSessionCascade(sessionId: string): DeleteCascadeResult {\n  const db = getDatabase();\n\n  const zeroCounts: DeleteCascadeResult = {\n    deleted: false,\n    counts: { prompts: 0, spores: 0, attachments: 0, graphEdges: 0, resolutionEvents: 0 },\n    deletedSporeIds: [],\n    deletedAttachmentPaths: [],\n  };\n\n  // Check session exists first\n  const exists = db.prepare(`SELECT id FROM sessions WHERE id = ?`).get(sessionId);\n  if (!exists) return zeroCounts;\n\n  // Collect IDs/paths needed for post-transaction cleanup before deleting\n  const sporeIds = (db.prepare(\n    `SELECT id FROM spores WHERE session_id = ?`,\n  ).all(sessionId) as { id: string }[]).map((r) => r.id);\n\n  const attachmentPaths = (db.prepare(\n    `SELECT file_path FROM attachments WHERE session_id = ?`,\n  ).all(sessionId) as { file_path: string }[]).map((r) => r.file_path);\n\n  // Run all deletes in a single transaction\n  const result = db.transaction(() => {\n    db.prepare(`DELETE FROM activities WHERE session_id = ?`).run(sessionId);\n    const attachments = db.prepare(`DELETE FROM attachments WHERE session_id = ?`).run(sessionId);\n    const prompts = db.prepare(`DELETE FROM prompt_batches WHERE session_id = ?`).run(sessionId);\n    const resEvents = db.prepare(`DELETE FROM resolution_events WHERE session_id = ?`).run(sessionId);\n    const edges = db.prepare(`DELETE FROM graph_edges WHERE session_id = ?`).run(sessionId);\n    const spores = db.prepare(`DELETE FROM spores WHERE session_id = ?`).run(sessionId);\n    const session = db.prepare(`DELETE FROM sessions WHERE id = ?`).run(sessionId);\n\n    return {\n      deleted: session.changes > 0,\n      counts: {\n        prompts: prompts.changes,\n        spores: spores.changes,\n        attachments: attachments.changes,\n        graphEdges: edges.changes,\n        resolutionEvents: resEvents.changes,\n      },\n    };\n  })();\n\n  return {\n    ...result,\n    deletedSporeIds: sporeIds,\n    deletedAttachmentPaths: attachmentPaths,\n  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+{"version":3,"sources":["../src/db/queries/sessions.ts"],"sourcesContent":["/**\n * Session CRUD query helpers.\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 { getTeamMachineId } from '@myco/daemon/team-context.js';\nimport { syncRow } from '@myco/db/queries/team-outbox.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of sessions returned by listSessions when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n/** Session status value when a session is closed normally. */\nconst STATUS_COMPLETED = 'completed';\n\n/** Default session status for new sessions. */\nconst DEFAULT_STATUS = 'active';\n\n/** Default prompt count for new sessions. */\nconst DEFAULT_PROMPT_COUNT = 0;\n\n/** Default tool count for new sessions. */\nconst DEFAULT_TOOL_COUNT = 0;\n\n/** Default processed flag for new sessions. */\nconst DEFAULT_PROCESSED = 0;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting/upserting a session. */\nexport interface SessionInsert {\n  id: string;\n  agent: string;\n  started_at: number;\n  created_at: number;\n  user?: string | null;\n  project_root?: string | null;\n  branch?: string | null;\n  ended_at?: number | null;\n  status?: string;\n  prompt_count?: number;\n  tool_count?: number;\n  title?: string | null;\n  summary?: string | null;\n  transcript_path?: string | null;\n  parent_session_id?: string | null;\n  parent_session_reason?: string | null;\n  processed?: number;\n  content_hash?: string | null;\n  machine_id?: string;\n}\n\n/** Row shape returned from session queries (all columns). */\nexport interface SessionRow {\n  id: string;\n  agent: string;\n  user: string | null;\n  project_root: string | null;\n  branch: string | null;\n  started_at: number;\n  ended_at: number | null;\n  status: string;\n  prompt_count: number;\n  tool_count: number;\n  title: string | null;\n  summary: string | null;\n  transcript_path: string | null;\n  parent_session_id: string | null;\n  parent_session_reason: string | null;\n  processed: number;\n  content_hash: string | null;\n  embedded: number;\n  created_at: number;\n  machine_id: string;\n  synced_at: number | null;\n}\n\n/** Updatable fields for `updateSession`. */\nexport interface SessionUpdate {\n  agent?: string;\n  user?: string | null;\n  project_root?: string | null;\n  branch?: string | null;\n  ended_at?: number | null;\n  status?: string;\n  prompt_count?: number;\n  tool_count?: number;\n  title?: string | null;\n  summary?: string | null;\n  transcript_path?: string | null;\n  parent_session_id?: string | null;\n  parent_session_reason?: string | null;\n  processed?: number;\n  content_hash?: string | null;\n}\n\n/** Filter options for `listSessions`. */\nexport interface ListSessionsOptions {\n  limit?: number;\n  offset?: number;\n  status?: string;\n  agent?: string;\n  search?: string;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst SESSION_COLUMNS = [\n  'id',\n  'agent',\n  '\"user\"',\n  'project_root',\n  'branch',\n  'started_at',\n  'ended_at',\n  'status',\n  'prompt_count',\n  'tool_count',\n  'title',\n  'summary',\n  'transcript_path',\n  'parent_session_id',\n  'parent_session_reason',\n  'processed',\n  'content_hash',\n  'embedded',\n  'created_at',\n  'machine_id',\n  'synced_at',\n] as const;\n\nconst SELECT_COLUMNS = SESSION_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/**\n * Normalize a SQLite result row into a typed SessionRow.\n *\n * The quoted \"user\" column comes back as `user` in the result object.\n */\nfunction toSessionRow(row: Record<string, unknown>): SessionRow {\n  return {\n    id: row.id as string,\n    agent: row.agent as string,\n    user: (row.user as string) ?? null,\n    project_root: (row.project_root as string) ?? null,\n    branch: (row.branch as string) ?? null,\n    started_at: row.started_at as number,\n    ended_at: (row.ended_at as number) ?? null,\n    status: row.status as string,\n    prompt_count: row.prompt_count as number,\n    tool_count: row.tool_count as number,\n    title: (row.title as string) ?? null,\n    summary: (row.summary as string) ?? null,\n    transcript_path: (row.transcript_path as string) ?? null,\n    parent_session_id: (row.parent_session_id as string) ?? null,\n    parent_session_reason: (row.parent_session_reason as string) ?? null,\n    processed: row.processed as number,\n    content_hash: (row.content_hash as string) ?? null,\n    embedded: (row.embedded as number) ?? 0,\n    created_at: row.created_at as number,\n    machine_id: (row.machine_id as string) ?? 'local',\n    synced_at: (row.synced_at as number) ?? null,\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a session or update it if the id already exists.\n *\n * On conflict the row is updated with the values from `data`, preserving\n * any columns not supplied via COALESCE with EXCLUDED values.\n */\nexport function upsertSession(data: SessionInsert): SessionRow {\n  const db = getDatabase();\n\n  db.prepare(\n    `INSERT INTO sessions (\n       id, agent, \"user\", project_root, branch,\n       started_at, ended_at, status, prompt_count, tool_count,\n       title, summary, transcript_path,\n       parent_session_id, parent_session_reason,\n       processed, content_hash, created_at, machine_id\n     ) VALUES (\n       ?, ?, ?, ?, ?,\n       ?, ?, ?, ?, ?,\n       ?, ?, ?,\n       ?, ?,\n       ?, ?, ?, ?\n     )\n     ON CONFLICT (id) DO UPDATE SET\n       agent                 = EXCLUDED.agent,\n       \"user\"                = EXCLUDED.\"user\",\n       project_root          = EXCLUDED.project_root,\n       branch                = EXCLUDED.branch,\n       started_at            = EXCLUDED.started_at,\n       ended_at              = COALESCE(EXCLUDED.ended_at, sessions.ended_at),\n       status                = COALESCE(EXCLUDED.status, sessions.status),\n       prompt_count          = CASE WHEN ? THEN EXCLUDED.prompt_count ELSE sessions.prompt_count END,\n       tool_count            = CASE WHEN ? THEN EXCLUDED.tool_count ELSE sessions.tool_count END,\n       title                 = COALESCE(EXCLUDED.title, sessions.title),\n       summary               = COALESCE(EXCLUDED.summary, sessions.summary),\n       transcript_path       = COALESCE(EXCLUDED.transcript_path, sessions.transcript_path),\n       parent_session_id     = EXCLUDED.parent_session_id,\n       parent_session_reason = EXCLUDED.parent_session_reason,\n       processed             = COALESCE(EXCLUDED.processed, sessions.processed),\n       content_hash          = EXCLUDED.content_hash`,\n  ).run(\n    data.id,\n    data.agent,\n    data.user ?? null,\n    data.project_root ?? null,\n    data.branch ?? null,\n    data.started_at,\n    data.ended_at ?? null,\n    data.status ?? DEFAULT_STATUS,\n    data.prompt_count ?? DEFAULT_PROMPT_COUNT,\n    data.tool_count ?? DEFAULT_TOOL_COUNT,\n    data.title ?? null,\n    data.summary ?? null,\n    data.transcript_path ?? null,\n    data.parent_session_id ?? null,\n    data.parent_session_reason ?? null,\n    data.processed ?? DEFAULT_PROCESSED,\n    data.content_hash ?? null,\n    data.created_at,\n    data.machine_id ?? getTeamMachineId(),\n    data.prompt_count !== undefined ? 1 : 0,\n    data.tool_count !== undefined ? 1 : 0,\n  );\n\n  const row = toSessionRow(\n    db.prepare(`SELECT ${SELECT_COLUMNS} FROM sessions WHERE id = ?`).get(data.id) as Record<string, unknown>,\n  );\n\n  syncRow('sessions', row);\n\n  return row;\n}\n\n/**\n * Retrieve a single session by id.\n *\n * @returns the session row, or null if not found.\n */\nexport function getSession(id: string): SessionRow | null {\n  const db = getDatabase();\n\n  const row = db.prepare(\n    `SELECT ${SELECT_COLUMNS} FROM sessions WHERE id = ?`,\n  ).get(id) as Record<string, unknown> | undefined;\n\n  if (!row) return null;\n  return toSessionRow(row);\n}\n\n/** Build WHERE clause and bound params from session filter options. */\nfunction buildSessionsWhere(\n  options: Omit<ListSessionsOptions, 'limit' | 'offset'>,\n): { where: string; params: unknown[] } {\n  const conditions: string[] = [];\n  const params: unknown[] = [];\n\n  if (options.status !== undefined) {\n    conditions.push(`status = ?`);\n    params.push(options.status);\n  }\n\n  if (options.agent !== undefined) {\n    conditions.push(`agent = ?`);\n    params.push(options.agent);\n  }\n\n  if (options.search !== undefined && options.search.length > 0) {\n    conditions.push(`(title LIKE ? OR id LIKE ?)`);\n    const pattern = `%${options.search}%`;\n    params.push(pattern, pattern);\n  }\n\n  return {\n    where: conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '',\n    params,\n  };\n}\n\n/**\n * List sessions with optional filters, ordered by created_at DESC.\n */\nexport function listSessions(\n  options: ListSessionsOptions = {},\n): SessionRow[] {\n  const db = getDatabase();\n  const { where, params } = buildSessionsWhere(options);\n  const limit = options.limit ?? 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AS promptCount,\n       (SELECT COUNT(*) FROM spores WHERE session_id = ?) AS sporeCount,\n       (SELECT COUNT(*) FROM attachments WHERE session_id = ?) AS attachmentCount,\n       (SELECT COUNT(*) FROM graph_edges WHERE session_id = ?) AS graphEdgeCount`,\n  ).get(sessionId, sessionId, sessionId, sessionId) as SessionImpact;\n\n  return row;\n}\n\n/**\n * Delete a session and ALL related data in a single transaction.\n *\n * Returns counts of deleted rows and IDs needed for post-transaction\n * cleanup (vault files, embedding vectors).\n */\nexport function deleteSessionCascade(sessionId: string): DeleteCascadeResult {\n  const db = getDatabase();\n\n  const zeroCounts: DeleteCascadeResult = {\n    deleted: false,\n    counts: { prompts: 0, spores: 0, attachments: 0, graphEdges: 0, resolutionEvents: 0 },\n    deletedSporeIds: [],\n    deletedAttachmentPaths: [],\n  };\n\n  // Check session exists first\n  const exists = db.prepare(`SELECT id FROM sessions WHERE id = ?`).get(sessionId);\n  if (!exists) return zeroCounts;\n\n  // Collect IDs/paths needed for post-transaction cleanup before deleting\n  const sporeIds = (db.prepare(\n    `SELECT id FROM spores WHERE session_id = ?`,\n  ).all(sessionId) as { id: string }[]).map((r) => r.id);\n\n  const attachmentPaths = (db.prepare(\n    `SELECT file_path FROM attachments WHERE session_id = ?`,\n  ).all(sessionId) as { file_path: string }[]).map((r) => r.file_path);\n\n  // Run all deletes in a single transaction.\n  //\n  // Order matters — foreign_keys = ON is set in client.ts, so every DELETE\n  // is checked immediately. Child rows must be removed before their parents:\n  //   - spores.prompt_batch_id     → prompt_batches(id)   [spores BEFORE prompt_batches]\n  //   - plans.prompt_batch_id      → prompt_batches(id)   [plans BEFORE prompt_batches]\n  //   - resolution_events.spore_id → spores(id)           [resolution_events BEFORE spores]\n  //   - skill_usage.session_id     → sessions(id) NOT NULL\n  //   - plans.session_id           → sessions(id)\n  // resolution_events can reference spores across sessions (e.g. a later\n  // session supersedes an earlier session's spore), so we match by either\n  // session_id OR spore_id-in-this-session to catch cross-session references.\n  const result = db.transaction(() => {\n    db.prepare(`DELETE FROM activities WHERE session_id = ?`).run(sessionId);\n    const attachments = db.prepare(`DELETE FROM attachments WHERE session_id = ?`).run(sessionId);\n    db.prepare(`DELETE FROM plans WHERE session_id = ?`).run(sessionId);\n    db.prepare(`DELETE FROM skill_usage WHERE session_id = ?`).run(sessionId);\n    const resEvents = db.prepare(\n      `DELETE FROM resolution_events\n       WHERE session_id = ?\n          OR spore_id IN (SELECT id FROM spores WHERE session_id = ?)`,\n    ).run(sessionId, sessionId);\n    const edges = db.prepare(`DELETE FROM graph_edges WHERE session_id = ?`).run(sessionId);\n    const spores = db.prepare(`DELETE FROM spores WHERE session_id = ?`).run(sessionId);\n    const prompts = db.prepare(`DELETE FROM prompt_batches WHERE session_id = ?`).run(sessionId);\n    const session = db.prepare(`DELETE FROM sessions WHERE id = ?`).run(sessionId);\n\n    return {\n      deleted: session.changes > 0,\n      counts: {\n        prompts: prompts.changes,\n        spores: spores.changes,\n        attachments: attachments.changes,\n        graphEdges: edges.changes,\n        resolutionEvents: resEvents.changes,\n      },\n    };\n  })();\n\n  return {\n    ...result,\n    deletedSporeIds: sporeIds,\n    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package/dist/{chunk-X5IXK5KO.js → chunk-TIAYBVSI.js}

@@ -6,36 +6,106 @@ import path3 from "path";
 
 // src/symbionts/toml-helpers.ts
 var TOML_SECTION_RE = /^\[([^\]]+)\]/;
-function findTomlSectionEnd(raw, searchStart, serverName) {
-  const subsectionPrefix = `mcp_servers.${serverName}.`;
+function findTomlSectionEnd(raw, searchStart, sectionName) {
+  const subsectionPrefix = `${sectionName}.`;
   const rawLines = raw.slice(searchStart).split("\n");
   let offset = searchStart;
   for (const line of rawLines) {
     offset += line.length + 1;
     const m = line.match(TOML_SECTION_RE);
-    if (m && !m[1].startsWith(subsectionPrefix) && m[1] !== `mcp_servers.${serverName}`) {
+    if (m && !m[1].startsWith(subsectionPrefix) && m[1] !== sectionName) {
       return offset - line.length - 1;
     }
   }
   return raw.length;
 }
+function formatTomlScalarLine(key, val) {
+  if (typeof val === "string") return `${key} = "${val}"`;
+  if (typeof val === "boolean") return `${key} = ${val}`;
+  if (typeof val === "number" && Number.isFinite(val)) return `${key} = ${val}`;
+  if (Array.isArray(val)) {
+    return `${key} = [${val.map((v) => `"${v}"`).join(", ")}]`;
+  }
+  return null;
+}
+function upsertTomlSection(raw, sectionName, values) {
+  const sectionHeader = `[${sectionName}]`;
+  const lines = [sectionHeader];
+  for (const [key, val] of Object.entries(values)) {
+    const line = formatTomlScalarLine(key, val);
+    if (line !== null) lines.push(line);
+  }
+  const block = lines.join("\n");
+  if (raw.includes(sectionHeader)) {
+    const startIdx = raw.indexOf(sectionHeader);
+    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, sectionName);
+    const before = raw.slice(0, startIdx).trimEnd();
+    const after = raw.slice(endIdx);
+    const separator2 = before ? "\n\n" : "";
+    return (before + separator2 + block + after).trimEnd() + "\n";
+  }
+  const separator = raw.trim() ? "\n\n" : "";
+  return (raw.trimEnd() + separator + block).trimEnd() + "\n";
+}
+function removeTomlSectionKeys(raw, sectionName, keys) {
+  const sectionHeader = `[${sectionName}]`;
+  if (!raw.includes(sectionHeader)) return raw;
+  const startIdx = raw.indexOf(sectionHeader);
+  const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, sectionName);
+  const sectionBody = raw.slice(startIdx + sectionHeader.length, endIdx);
+  const keyRes = keys.map((k) => new RegExp(`^\\s*${escapeRegExp(k)}\\s*=`));
+  const bodyLines = sectionBody.split("\n");
+  const kept = [];
+  let removedAny = false;
+  let subtableSeen = false;
+  for (const line of bodyLines) {
+    if (subtableSeen || TOML_SECTION_RE.test(line.trim())) {
+      subtableSeen = true;
+      kept.push(line);
+      continue;
+    }
+    if (keyRes.some((re) => re.test(line))) {
+      removedAny = true;
+      continue;
+    }
+    kept.push(line);
+  }
+  if (!removedAny) return raw;
+  const hasRemainingKeys = kept.some((line) => {
+    const trimmed = line.trim();
+    if (!trimmed || trimmed.startsWith("#")) return false;
+    if (TOML_SECTION_RE.test(trimmed)) return false;
+    return /=/.test(trimmed);
+  });
+  const before = raw.slice(0, startIdx).trimEnd();
+  let rebuilt;
+  if (hasRemainingKeys) {
+    const newBody = kept.join("\n");
+    const separator = before ? "\n\n" : "";
+    rebuilt = before + separator + sectionHeader + newBody;
+  } else {
+    const trailing = kept.join("\n").trimStart();
+    const separator = before && trailing ? "\n\n" : "";
+    rebuilt = before + separator + trailing;
+  }
+  return rebuilt.trimEnd() + (rebuilt.trim() ? "\n" : "");
+}
+function escapeRegExp(s) {
+  return s.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+}
 function buildTomlMcpSection(raw, serverName, server) {
-  const sectionHeader = `[mcp_servers.${serverName}]`;
+  const sectionName = `mcp_servers.${serverName}`;
+  const sectionHeader = `[${sectionName}]`;
   const lines = [sectionHeader];
   for (const [key, val] of Object.entries(server)) {
     if (key === "env" && typeof val === "object" && val !== null) continue;
-    if (typeof val === "string") {
-      lines.push(`${key} = "${val}"`);
-    } else if (Array.isArray(val)) {
-      lines.push(`${key} = [${val.map((v) => `"${v}"`).join(", ")}]`);
-    } else if (typeof val === "boolean") {
-      lines.push(`${key} = ${val}`);
-    }
+    const line = formatTomlScalarLine(key, val);
+    if (line !== null) lines.push(line);
   }
   const env = server.env;
   if (env && Object.keys(env).length > 0) {
     lines.push("");
-    lines.push(`[mcp_servers.${serverName}.env]`);
+    lines.push(`[${sectionName}.env]`);
     for (const [key, val] of Object.entries(env)) {
       lines.push(`${key} = "${val}"`);
     }
@@ -44,7 +114,7 @@ function buildTomlMcpSection(raw, serverName, server) {
   let updated;
   if (raw.includes(sectionHeader)) {
     const startIdx = raw.indexOf(sectionHeader);
-    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, serverName);
+    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, sectionName);
     const before = raw.slice(0, startIdx).trimEnd();
     const after = raw.slice(endIdx);
     const separator = before ? "\n\n" : "";
@@ -628,7 +698,8 @@ ${desired.join("\n")}
   }
   /**
    * Merge settings template into the target settings file.
-   * Deep merges objects and deduplicates arrays.
+   * JSON targets: deep-merges objects and deduplicates arrays.
+   * TOML targets: emits each top-level template key as a [section] with scalar children.
    */
   installSettings() {
     const reg = this.manifest.registration;
@@ -636,16 +707,41 @@ ${desired.join("\n")}
     const template = this.loadTemplate("settings");
     if (!template) return false;
     const targetPath = path3.join(this.projectRoot, reg.settingsTarget);
+    const settingsFormat = reg.settingsFormat ?? "json";
+    if (settingsFormat === "toml") {
+      return this.installSettingsToml(targetPath, template);
+    }
     const existing = readJsonFile(targetPath);
     const merged = deepMergeSettings(existing, template);
     writeJsonFile(targetPath, merged);
     return true;
   }
+  /**
+   * Merge a settings template into a TOML config file.
+   * Each top-level key in the template becomes a [section] header, with its
+   * children written as scalar key = value lines. Existing sections and keys
+   * outside the template (including unrelated sections like [mcp_servers.*])
+   * are preserved.
+   */
+  installSettingsToml(targetPath, template) {
+    let raw = "";
+    try {
+      raw = fs3.readFileSync(targetPath, "utf-8");
+    } catch {
+    }
+    for (const [sectionName, values] of Object.entries(template)) {
+      if (!values || typeof values !== "object" || Array.isArray(values)) continue;
+      raw = upsertTomlSection(raw, sectionName, values);
+    }
+    fs3.mkdirSync(path3.dirname(targetPath), { recursive: true });
+    fs3.writeFileSync(targetPath, raw, "utf-8");
+    return true;
+  }
   /**
    * Remove Myco entries from the target settings file.
    * Template-driven: loads the settings template and removes matching values.
-   * Arrays: filter out values present in the template.
-   * Objects: delete keys present in the template.
+   * JSON: arrays filtered by template values, object keys deleted by name.
+   * TOML: removes each template key from its section; empty sections are dropped.
    */
   uninstallSettings() {
     const reg = this.manifest.registration;
@@ -653,6 +749,10 @@ ${desired.join("\n")}
     const template = this.loadTemplate("settings");
     if (!template) return false;
     const targetPath = path3.join(this.projectRoot, reg.settingsTarget);
+    const settingsFormat = reg.settingsFormat ?? "json";
+    if (settingsFormat === "toml") {
+      return this.uninstallSettingsToml(targetPath, template);
+    }
     const settings = readJsonFile(targetPath);
     if (Object.keys(settings).length === 0) return false;
     const changed = deepRemoveSettings(settings, template);
@@ -660,6 +760,41 @@ ${desired.join("\n")}
     writeOrDeleteJsonFile(targetPath, settings);
     return true;
   }
+  /**
+   * Remove template-defined keys from TOML settings file.
+   * For each section in the template, deletes only the keys the template owns;
+   * other keys and unrelated sections stay intact. Empty sections are stripped.
+   * Deletes the file entirely if no TOML content remains.
+   */
+  uninstallSettingsToml(targetPath, template) {
+    let raw = "";
+    try {
+      raw = fs3.readFileSync(targetPath, "utf-8");
+    } catch {
+      return false;
+    }
+    if (!raw.trim()) return false;
+    let changed = false;
+    for (const [sectionName, values] of Object.entries(template)) {
+      if (!values || typeof values !== "object" || Array.isArray(values)) continue;
+      const keys = Object.keys(values);
+      const next = removeTomlSectionKeys(raw, sectionName, keys);
+      if (next !== raw) {
+        raw = next;
+        changed = true;
+      }
+    }
+    if (!changed) return false;
+    if (!raw.trim()) {
+      try {
+        fs3.unlinkSync(targetPath);
+      } catch {
+      }
+    } else {
+      fs3.writeFileSync(targetPath, raw, "utf-8");
+    }
+    return true;
+  }
   /** Remove Myco hook groups from the target settings file. */
   uninstallHooks() {
     const reg = this.manifest.registration;
@@ -719,7 +854,7 @@ ${desired.join("\n")}
     const sectionHeader = `[mcp_servers.${MYCO_MCP_SERVER_NAME}]`;
     if (!raw.includes(sectionHeader)) return false;
     const startIdx = raw.indexOf(sectionHeader);
-    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, MYCO_MCP_SERVER_NAME);
+    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, `mcp_servers.${MYCO_MCP_SERVER_NAME}`);
     const before = raw.slice(0, startIdx).trimEnd();
     const after = raw.slice(endIdx).trimStart();
     const updated = (before + (before && after ? "\n\n" : "") + after).trimEnd();
@@ -854,4 +989,4 @@ export {
   SymbiontInstaller,
   syncSkillSymlinks
 };
-//# sourceMappingURL=chunk-X5IXK5KO.js.map
+//# sourceMappingURL=chunk-TIAYBVSI.js.map

package/dist/chunk-TIAYBVSI.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/symbionts/installer.ts","../src/symbionts/toml-helpers.ts","../src/symbionts/settings-merge.ts","../src/symbionts/json-helpers.ts","../src/symbionts/install-helpers.ts"],"sourcesContent":["import type { SymbiontManifest } from './manifest-schema.js';\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport { findTomlSectionEnd, buildTomlMcpSection, upsertTomlSection, removeTomlSectionKeys } from './toml-helpers.js';\nimport { deepMergeSettings, deepRemoveSettings } from './settings-merge.js';\nimport { readJsonFile, writeJsonFile, writeOrDeleteJsonFile } from './json-helpers.js';\nimport { ensureAgentsMd, ensureSymlink, isMycoHookGroup } from './install-helpers.js';\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: canonical per-skill entries + infrastructure artifacts.\n    // Agent-specific targets (e.g. .claude/skills/) use local .gitignore files\n    // instead of polluting the project-level .gitignore.\n    const desired = [\n      ...skillNames.map((name) => `${CANONICAL_SKILLS_DIR}/${name}`),\n      WRANGLER_CACHE_DIR,\n    ];\n\n    const gitignorePath = path.join(this.projectRoot, '.gitignore');\n    let content = '';\n    try { content = fs.readFileSync(gitignorePath, 'utf-8'); } catch { /* doesn't exist yet */ }\n\n    // Strip existing Myco block and any legacy entries\n    const stripped = this.stripMycoGitignoreBlock(content, skillNames);\n\n    // Build the new block\n    const desiredBlock = desired.length > 0\n      ? `${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      ensureLocalSkillsGitignore(agentSkillsDir);\n    }\n\n    return true;\n  }\n\n  /**\n   * Merge settings template into the target settings file.\n   * JSON targets: deep-merges objects and deduplicates arrays.\n   * TOML targets: emits each top-level template key as a [section] with scalar children.\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 settingsFormat = reg.settingsFormat ?? 'json';\n\n    if (settingsFormat === 'toml') {\n      return this.installSettingsToml(targetPath, template);\n    }\n\n    const existing = readJsonFile(targetPath);\n    const merged = deepMergeSettings(existing, template);\n    writeJsonFile(targetPath, merged);\n    return true;\n  }\n\n  /**\n   * Merge a settings template into a TOML config file.\n   * Each top-level key in the template becomes a [section] header, with its\n   * children written as scalar key = value lines. Existing sections and keys\n   * outside the template (including unrelated sections like [mcp_servers.*])\n   * are preserved.\n   */\n  private installSettingsToml(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 [sectionName, values] of Object.entries(template)) {\n      if (!values || typeof values !== 'object' || Array.isArray(values)) continue;\n      raw = upsertTomlSection(raw, sectionName, values 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   * Remove Myco entries from the target settings file.\n   * Template-driven: loads the settings template and removes matching values.\n   * JSON: arrays filtered by template values, object keys deleted by name.\n   * TOML: removes each template key from its section; empty sections are dropped.\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 settingsFormat = reg.settingsFormat ?? 'json';\n\n    if (settingsFormat === 'toml') {\n      return this.uninstallSettingsToml(targetPath, template);\n    }\n\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  /**\n   * Remove template-defined keys from TOML settings file.\n   * For each section in the template, deletes only the keys the template owns;\n   * other keys and unrelated sections stay intact. Empty sections are stripped.\n   * Deletes the file entirely if no TOML content remains.\n   */\n  private uninstallSettingsToml(targetPath: string, template: Record<string, unknown>): boolean {\n    let raw = '';\n    try { raw = fs.readFileSync(targetPath, 'utf-8'); } catch { return false; }\n    if (!raw.trim()) return false;\n\n    let changed = false;\n    for (const [sectionName, values] of Object.entries(template)) {\n      if (!values || typeof values !== 'object' || Array.isArray(values)) continue;\n      const keys = Object.keys(values as Record<string, unknown>);\n      const next = removeTomlSectionKeys(raw, sectionName, keys);\n      if (next !== raw) {\n        raw = next;\n        changed = true;\n      }\n    }\n\n    if (!changed) return false;\n\n    if (!raw.trim()) {\n      try { fs.unlinkSync(targetPath); } catch { /* ignore */ }\n    } else {\n      fs.writeFileSync(targetPath, raw, 'utf-8');\n    }\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.${MYCO_MCP_SERVER_NAME}]`;\n    if (!raw.includes(sectionHeader)) return false;\n\n    const startIdx = raw.indexOf(sectionHeader);\n    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, `mcp_servers.${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 ? '\\n\\n' : '') + after).trimEnd();\n\n    if (!updated.trim()) {\n      try { fs.unlinkSync(targetPath); } catch { /* ignore */ }\n    } else {\n      fs.writeFileSync(targetPath, updated + '\\n', 'utf-8');\n    }\n    return true;\n  }\n\n  /** Remove skill symlinks (canonical + agent-specific). */\n  uninstallSkills(): 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    let removed = false;\n\n    // Remove agent-specific symlinks\n    if (reg.skillsTarget !== CANONICAL_SKILLS_DIR) {\n      for (const name of skillNames) {\n        const link = path.join(this.projectRoot, reg.skillsTarget, name);\n        try { fs.unlinkSync(link); removed = true; } catch { /* doesn't exist */ }\n      }\n      // Remove agent skills dir if now empty (rmdirSync fails atomically if non-empty)\n      try { fs.rmdirSync(path.join(this.projectRoot, reg.skillsTarget)); } catch { /* not empty or missing */ }\n    }\n\n    // Remove canonical symlinks\n    const canonicalDir = path.join(this.projectRoot, CANONICAL_SKILLS_DIR);\n    for (const name of skillNames) {\n      const link = path.join(canonicalDir, name);\n      try { fs.unlinkSync(link); removed = true; } catch { /* doesn't exist */ }\n    }\n    // Remove empty dirs (rmdirSync fails atomically if non-empty)\n    try { fs.rmdirSync(canonicalDir); } catch { /* not empty or missing */ }\n    try { fs.rmdirSync(path.join(this.projectRoot, '.agents')); } catch { /* not empty or missing */ }\n\n    return removed;\n  }\n\n  /** Remove Myco entries from project .gitignore. */\n  private cleanGitignore(): void {\n    const gitignorePath = path.join(this.projectRoot, '.gitignore');\n    let content = '';\n    try { content = fs.readFileSync(gitignorePath, 'utf-8'); } catch { return; }\n\n    const cleaned = this.stripMycoGitignoreBlock(content, this.listSkillDirs()).trim();\n    if (cleaned) {\n      fs.writeFileSync(gitignorePath, cleaned + '\\n', 'utf-8');\n    } else {\n      try { fs.unlinkSync(gitignorePath); } catch { /* ignore */ }\n    }\n  }\n}\n\n/**\n * Create agent-specific symlinks for a skill in `.agents/skills/<name>`.\n *\n * Reads all symbiont manifests to find skillsTarget paths that differ\n * from the canonical `.agents/skills/` directory, then creates relative\n * symlinks from each target to the canonical location.\n *\n * Called by vault_write_skill after writing a generated skill to disk.\n * Also handles removal: when `remove` is true, deletes the symlinks.\n */\nexport function syncSkillSymlinks(\n  projectRoot: string,\n  skillName: string,\n  opts?: { remove?: boolean },\n): void {\n  // Resolve manifests dir — try sibling (source layout) then dist layout\n  // (tsup bundles into dist/chunk-*.js, but manifests are at dist/src/symbionts/manifests/)\n  const selfDir = path.dirname(new URL(import.meta.url).pathname);\n  const candidates = [\n    path.join(selfDir, 'manifests'),\n    path.join(selfDir, 'src', 'symbionts', 'manifests'),\n  ];\n  const manifestDir = candidates.find((d) => fs.existsSync(d));\n  if (!manifestDir) return;\n\n  const targets = new Set<string>();\n  for (const file of fs.readdirSync(manifestDir).filter((f) => f.endsWith('.yaml'))) {\n    try {\n      const content = fs.readFileSync(path.join(manifestDir, file), 'utf-8');\n      const match = content.match(/skillsTarget:\\s*(.+)/);\n      if (match) targets.add(match[1].trim());\n    } catch { /* skip unreadable manifests */ }\n  }\n\n  for (const target of targets) {\n    if (target === CANONICAL_SKILLS_DIR) continue; // canonical is the source, not a link target\n\n    const agentSkillsDir = path.join(projectRoot, target);\n    const linkPath = path.join(agentSkillsDir, skillName);\n\n    if (opts?.remove) {\n      try { fs.unlinkSync(linkPath); } catch { /* doesn't exist */ }\n      try { fs.rmdirSync(agentSkillsDir); } catch { /* not empty or missing */ }\n    } else {\n      fs.mkdirSync(agentSkillsDir, { recursive: true });\n      const canonicalDir = path.join(projectRoot, CANONICAL_SKILLS_DIR);\n      const relTarget = path.join(path.relative(agentSkillsDir, canonicalDir), skillName);\n      ensureSymlink(linkPath, relTarget);\n      // Ensure a local .gitignore ignores all symlinks in this directory.\n      // Localized to the agent's skills dir — doesn't pollute the project .gitignore.\n      ensureLocalSkillsGitignore(agentSkillsDir);\n    }\n  }\n}\n\n/** Content for the local .gitignore that ignores Myco-created symlinks. */\nconst LOCAL_SKILLS_GITIGNORE = `# Myco-managed symlinks — generated skills are symlinked here automatically.\n# The canonical location for all skills is .agents/skills/.\n#\n# To add your own skill to this directory, un-ignore it:\n#   !my-skill\n*\n!.gitignore\n`;\n\n/**\n * Write a .gitignore inside an agent's skills directory that ignores all\n * symlinks Myco creates there. Idempotent — skips if already present.\n */\nfunction ensureLocalSkillsGitignore(agentSkillsDir: string): void {\n  const gitignorePath = path.join(agentSkillsDir, '.gitignore');\n  try {\n    if (fs.readFileSync(gitignorePath, 'utf-8') === LOCAL_SKILLS_GITIGNORE) return;\n  } catch { /* doesn't exist — proceed */ }\n  fs.writeFileSync(gitignorePath, LOCAL_SKILLS_GITIGNORE, 'utf-8');\n}\n","/** TOML section header pattern. */\nconst TOML_SECTION_RE = /^\\[([^\\]]+)\\]/;\n\n/**\n * Find where a named TOML section ends.\n *\n * Walks forward from `searchStart` until it hits a section header that is\n * NEITHER the named section itself NOR any of its subtables (headers that\n * start with `${sectionName}.`). Returns `raw.length` if the section extends\n * to the end of the file.\n */\nexport function findTomlSectionEnd(\n  raw: string,\n  searchStart: number,\n  sectionName: string,\n): number {\n  const subsectionPrefix = `${sectionName}.`;\n  const rawLines = raw.slice(searchStart).split('\\n');\n  let offset = searchStart;\n  for (const line of rawLines) {\n    offset += line.length + 1;\n    const m = line.match(TOML_SECTION_RE);\n    if (m && !m[1].startsWith(subsectionPrefix) && m[1] !== sectionName) {\n      return offset - line.length - 1;\n    }\n  }\n  return raw.length;\n}\n\n/** Format a single TOML key = value line from a JS value. Skips unsupported types. */\nfunction formatTomlScalarLine(key: string, val: unknown): string | null {\n  if (typeof val === 'string') return `${key} = \"${val}\"`;\n  if (typeof val === 'boolean') return `${key} = ${val}`;\n  if (typeof val === 'number' && Number.isFinite(val)) return `${key} = ${val}`;\n  if (Array.isArray(val)) {\n    return `${key} = [${val.map((v: unknown) => `\"${v}\"`).join(', ')}]`;\n  }\n  return null;\n}\n\n/**\n * Insert or replace a top-level TOML section with the given scalar key/value pairs.\n *\n * - Scalar values (string, boolean, number, string[]) are written as `key = value`.\n * - Nested objects are ignored — use {@link buildTomlMcpSection} or call\n *   `upsertTomlSection` once per subtable if you need nested tables.\n * - Idempotent: running twice with the same inputs produces identical output.\n * - Preserves content before and after the section.\n */\nexport function upsertTomlSection(\n  raw: string,\n  sectionName: string,\n  values: Record<string, unknown>,\n): string {\n  const sectionHeader = `[${sectionName}]`;\n\n  const lines: string[] = [sectionHeader];\n  for (const [key, val] of Object.entries(values)) {\n    const line = formatTomlScalarLine(key, val);\n    if (line !== null) lines.push(line);\n  }\n  const block = lines.join('\\n');\n\n  if (raw.includes(sectionHeader)) {\n    const startIdx = raw.indexOf(sectionHeader);\n    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, sectionName);\n    const before = raw.slice(0, startIdx).trimEnd();\n    const after = raw.slice(endIdx);\n    const separator = before ? '\\n\\n' : '';\n    return (before + separator + block + after).trimEnd() + '\\n';\n  }\n\n  const separator = raw.trim() ? '\\n\\n' : '';\n  return (raw.trimEnd() + separator + block).trimEnd() + '\\n';\n}\n\n/**\n * Remove specific keys from a top-level TOML section.\n *\n * - Only the listed keys are removed. Other keys in the section are preserved.\n * - If the section ends up with no content after removal, the whole section\n *   (header and body) is stripped.\n * - Returns the updated string; equal to the input if no changes were made.\n */\nexport function removeTomlSectionKeys(\n  raw: string,\n  sectionName: string,\n  keys: string[],\n): string {\n  const sectionHeader = `[${sectionName}]`;\n  if (!raw.includes(sectionHeader)) return raw;\n\n  const startIdx = raw.indexOf(sectionHeader);\n  const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, sectionName);\n  const sectionBody = raw.slice(startIdx + sectionHeader.length, endIdx);\n\n  const keyRes = keys.map((k) => new RegExp(`^\\\\s*${escapeRegExp(k)}\\\\s*=`));\n  const bodyLines = sectionBody.split('\\n');\n  const kept: string[] = [];\n  let removedAny = false;\n  let subtableSeen = false;\n  for (const line of bodyLines) {\n    // Once we hit a subtable header, everything after stays (keys belong to the parent)\n    if (subtableSeen || TOML_SECTION_RE.test(line.trim())) {\n      subtableSeen = true;\n      kept.push(line);\n      continue;\n    }\n    if (keyRes.some((re) => re.test(line))) {\n      removedAny = true;\n      continue;\n    }\n    kept.push(line);\n  }\n  if (!removedAny) return raw;\n\n  // Determine whether the parent section still has any key = value lines.\n  const hasRemainingKeys = kept.some((line) => {\n    const trimmed = line.trim();\n    if (!trimmed || trimmed.startsWith('#')) return false;\n    if (TOML_SECTION_RE.test(trimmed)) return false;\n    return /=/.test(trimmed);\n  });\n\n  const before = raw.slice(0, startIdx).trimEnd();\n  let rebuilt: string;\n  if (hasRemainingKeys) {\n    const newBody = kept.join('\\n');\n    const separator = before ? '\\n\\n' : '';\n    rebuilt = before + separator + sectionHeader + newBody;\n  } else {\n    // Drop the header entirely; keep any trailing subtables we preserved above.\n    const trailing = kept.join('\\n').trimStart();\n    const separator = before && trailing ? '\\n\\n' : '';\n    rebuilt = before + separator + trailing;\n  }\n  return rebuilt.trimEnd() + (rebuilt.trim() ? '\\n' : '');\n}\n\nfunction escapeRegExp(s: string): string {\n  return s.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n}\n\n/**\n * Build/update a specific mcp_servers entry in a TOML string.\n * Pure transformation — returns updated content without writing to disk.\n *\n * Handles the MCP-specific `env` subtable pattern; for plain sections use\n * {@link upsertTomlSection}.\n */\nexport function buildTomlMcpSection(\n  raw: string,\n  serverName: string,\n  server: Record<string, unknown>,\n): string {\n  const sectionName = `mcp_servers.${serverName}`;\n  const sectionHeader = `[${sectionName}]`;\n\n  // Build the TOML block for this server\n  const lines: string[] = [sectionHeader];\n  for (const [key, val] of Object.entries(server)) {\n    if (key === 'env' && typeof val === 'object' && val !== null) continue; // Handle env as subtable\n    const line = formatTomlScalarLine(key, val);\n    if (line !== null) lines.push(line);\n  }\n\n  // Add env subtable if present\n  const env = server.env as Record<string, string> | undefined;\n  if (env && Object.keys(env).length > 0) {\n    lines.push('');\n    lines.push(`[${sectionName}.env]`);\n    for (const [key, val] of Object.entries(env)) {\n      lines.push(`${key} = \"${val}\"`);\n    }\n  }\n\n  const block = lines.join('\\n');\n\n  let updated: string;\n  if (raw.includes(sectionHeader)) {\n    const startIdx = raw.indexOf(sectionHeader);\n    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, sectionName);\n    const before = raw.slice(0, startIdx).trimEnd();\n    const after = raw.slice(endIdx);\n    const separator = before ? '\\n\\n' : '';\n    updated = (before + separator + block + after).trimEnd() + '\\n';\n  } else {\n    // Append new section\n    const separator = raw.trim() ? '\\n\\n' : '';\n    updated = (raw.trimEnd() + separator + block).trimEnd() + '\\n';\n  }\n\n  return updated;\n}\n","/** Deep merge two settings objects. Arrays are appended + deduplicated; objects recurse. */\nexport function deepMergeSettings(\n  target: Record<string, unknown>,\n  source: Record<string, unknown>,\n): Record<string, unknown> {\n  const result = { ...target };\n  for (const [key, sourceVal] of Object.entries(source)) {\n    const targetVal = result[key];\n    if (Array.isArray(sourceVal) && Array.isArray(targetVal)) {\n      result[key] = [...new Set([...targetVal, ...sourceVal])];\n    } else if (isPlainObject(sourceVal) && isPlainObject(targetVal)) {\n      result[key] = deepMergeSettings(\n        targetVal as Record<string, unknown>,\n        sourceVal as Record<string, unknown>,\n      );\n    } else {\n      result[key] = sourceVal;\n    }\n  }\n  return result;\n}\n\nexport function isPlainObject(val: unknown): val is Record<string, unknown> {\n  return typeof val === 'object' && val !== null && !Array.isArray(val);\n}\n\n/**\n * Remove values from target that match the template structure.\n * Arrays: filter out values present in the template array.\n * Objects: delete keys present in the template object, recurse into nested objects.\n * Returns true if anything was removed.\n */\nexport function deepRemoveSettings(\n  target: Record<string, unknown>,\n  template: Record<string, unknown>,\n): boolean {\n  let changed = false;\n  for (const [key, templateVal] of Object.entries(template)) {\n    const targetVal = target[key];\n    if (targetVal === undefined) continue;\n\n    if (Array.isArray(templateVal) && Array.isArray(targetVal)) {\n      // Filter out values that appear in the template array\n      const templateSet = new Set(templateVal.map(String));\n      const filtered = targetVal.filter((v) => !templateSet.has(String(v)));\n      if (filtered.length !== targetVal.length) {\n        if (filtered.length > 0) {\n          target[key] = filtered;\n        } else {\n          delete target[key];\n        }\n        changed = true;\n      }\n    } else if (isPlainObject(templateVal) && 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package/dist/{chunk-TQO4PF5K.js → chunk-TPTF3R77.js}

@@ -1,16 +1,16 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   isProcessAlive
-} from "./chunk-6GG2IVNV.js";
+} from "./chunk-35FAQCKJ.js";
 import {
   loadConfig
-} from "./chunk-4BQ5QE76.js";
+} from "./chunk-XAXQ72L3.js";
 import {
   getDatabase
 } from "./chunk-MYX5NCRH.js";
 import {
   DIGEST_TIERS
-} from "./chunk-TRA3R4EC.js";
+} from "./chunk-34NHDRWI.js";
 
 // src/db/queries/embeddings.ts
 var EMBEDDABLE_TABLES = ["sessions", "spores", "plans", "artifacts"];
@@ -184,4 +184,4 @@ export {
   getEmbeddingQueueDepth,
   gatherStats
 };
-//# sourceMappingURL=chunk-TQO4PF5K.js.map
+//# sourceMappingURL=chunk-TPTF3R77.js.map

package/dist/chunk-U5EW2VIQ.js

@@ -0,0 +1,86 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+
+// src/agent/tools/skill-staging.ts
+import {
+  existsSync,
+  mkdirSync,
+  readFileSync,
+  readdirSync,
+  rmSync,
+  statSync,
+  writeFileSync
+} from "fs";
+import { join, resolve } from "path";
+function stagingRoot(vaultDir) {
+  return resolve(vaultDir, "staging", "skills");
+}
+function stagingPath(vaultDir, candidateId) {
+  return join(stagingRoot(vaultDir), candidateId, "SKILL.md");
+}
+function stagingManifestPath(vaultDir, candidateId) {
+  return join(stagingRoot(vaultDir), candidateId, "manifest.json");
+}
+function writeStagedSkill(vaultDir, candidateId, content) {
+  const path = stagingPath(vaultDir, candidateId);
+  mkdirSync(resolve(path, ".."), { recursive: true });
+  writeFileSync(path, content, "utf-8");
+  return path;
+}
+function readStagedSkill(vaultDir, candidateId) {
+  const path = stagingPath(vaultDir, candidateId);
+  if (!existsSync(path)) return null;
+  return readFileSync(path, "utf-8");
+}
+function writeStagedManifest(vaultDir, candidateId, manifest) {
+  const path = stagingManifestPath(vaultDir, candidateId);
+  mkdirSync(resolve(path, ".."), { recursive: true });
+  writeFileSync(path, JSON.stringify(manifest, null, 2), "utf-8");
+  return path;
+}
+function readStagedManifest(vaultDir, candidateId) {
+  const path = stagingManifestPath(vaultDir, candidateId);
+  if (!existsSync(path)) return null;
+  try {
+    return JSON.parse(readFileSync(path, "utf-8"));
+  } catch {
+    return null;
+  }
+}
+function cleanupStagedSkill(vaultDir, candidateId) {
+  const dir = resolve(stagingRoot(vaultDir), candidateId);
+  try {
+    rmSync(dir, { recursive: true, force: true });
+  } catch {
+  }
+}
+function listStaleStagingDirs(vaultDir, maxAgeMs) {
+  const root = stagingRoot(vaultDir);
+  if (!existsSync(root)) return [];
+  const cutoff = Date.now() - maxAgeMs;
+  const stale = [];
+  for (const entry of readdirSync(root, { withFileTypes: true })) {
+    if (!entry.isDirectory()) continue;
+    const dirPath = join(root, entry.name);
+    try {
+      const st = statSync(dirPath);
+      if (st.mtimeMs < cutoff) {
+        stale.push(entry.name);
+      }
+    } catch {
+    }
+  }
+  return stale;
+}
+
+export {
+  stagingRoot,
+  stagingPath,
+  stagingManifestPath,
+  writeStagedSkill,
+  readStagedSkill,
+  writeStagedManifest,
+  readStagedManifest,
+  cleanupStagedSkill,
+  listStaleStagingDirs
+};
+//# sourceMappingURL=chunk-U5EW2VIQ.js.map