@goondocks/myco 0.15.1 → 0.16.0

package/dist/chunk-DJQOYEK3.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/db/schema-ddl.ts","../src/db/migrations.ts","../src/db/schema.ts"],"sourcesContent":["/**\n * DDL constants for all Myco vault tables, FTS5 virtual tables,\n * sync triggers, and secondary indexes.\n *\n * Extracted from schema.ts for readability -- these are pure string\n * constants with no runtime behaviour.\n */\n\n// ---------------------------------------------------------------------------\n// Table DDL statements\n// ---------------------------------------------------------------------------\n\nconst SCHEMA_VERSION_TABLE = `\n  CREATE TABLE IF NOT EXISTS schema_version (\n    version    INTEGER PRIMARY KEY,\n    applied_at INTEGER NOT NULL\n  )`;\n\n// -- Capture Layer ----------------------------------------------------------\n\nconst SESSIONS_TABLE = `\n  CREATE TABLE IF NOT EXISTS sessions (\n    id                     TEXT PRIMARY KEY,\n    agent                  TEXT NOT NULL,\n    \"user\"                 TEXT,\n    project_root           TEXT,\n    branch                 TEXT,\n    started_at             INTEGER NOT NULL,\n    ended_at               INTEGER,\n    status                 TEXT DEFAULT 'active',\n    prompt_count           INTEGER DEFAULT 0,\n    tool_count             INTEGER DEFAULT 0,\n    title                  TEXT,\n    summary                TEXT,\n    transcript_path        TEXT,\n    parent_session_id      TEXT,\n    parent_session_reason  TEXT,\n    processed              INTEGER DEFAULT 0,\n    content_hash           TEXT UNIQUE,\n    created_at             INTEGER NOT NULL,\n    embedded               INTEGER DEFAULT 0,\n    machine_id             TEXT NOT NULL DEFAULT 'local',\n    synced_at              INTEGER\n  )`;\n\nconst PROMPT_BATCHES_TABLE = `\n  CREATE TABLE IF NOT EXISTS prompt_batches (\n    id                INTEGER PRIMARY KEY AUTOINCREMENT,\n    session_id        TEXT NOT NULL REFERENCES sessions(id),\n    prompt_number     INTEGER,\n    user_prompt       TEXT,\n    response_summary  TEXT,\n    classification    TEXT,\n    started_at        INTEGER,\n    ended_at          INTEGER,\n    status            TEXT DEFAULT 'active',\n    activity_count    INTEGER DEFAULT 0,\n    processed         INTEGER DEFAULT 0,\n    content_hash      TEXT UNIQUE,\n    created_at        INTEGER NOT NULL,\n    machine_id        TEXT NOT NULL DEFAULT 'local',\n    synced_at         INTEGER\n  )`;\n\nconst ACTIVITIES_TABLE = `\n  CREATE TABLE IF NOT EXISTS activities (\n    id                   INTEGER PRIMARY KEY AUTOINCREMENT,\n    session_id           TEXT NOT NULL REFERENCES sessions(id),\n    prompt_batch_id      INTEGER REFERENCES prompt_batches(id),\n    tool_name            TEXT NOT NULL,\n    tool_input           TEXT,\n    tool_output_summary  TEXT,\n    file_path            TEXT,\n    files_affected       TEXT,\n    duration_ms          INTEGER,\n    success              INTEGER DEFAULT 1,\n    error_message        TEXT,\n    timestamp            INTEGER NOT NULL,\n    processed            INTEGER DEFAULT 0,\n    content_hash         TEXT UNIQUE,\n    created_at           INTEGER NOT NULL\n  )`;\n\nconst PLANS_TABLE = `\n  CREATE TABLE IF NOT EXISTS plans (\n    id               TEXT PRIMARY KEY,\n    status           TEXT DEFAULT 'active',\n    author           TEXT,\n    title            TEXT,\n    content          TEXT,\n    source_path      TEXT,\n    tags             TEXT,\n    session_id       TEXT REFERENCES sessions(id),\n    prompt_batch_id  INTEGER REFERENCES prompt_batches(id),\n    content_hash     TEXT,\n    processed        INTEGER DEFAULT 0,\n    created_at       INTEGER NOT NULL,\n    updated_at       INTEGER,\n    embedded         INTEGER DEFAULT 0,\n    machine_id       TEXT NOT NULL DEFAULT 'local',\n    synced_at        INTEGER\n  )`;\n\nconst ARTIFACTS_TABLE = `\n  CREATE TABLE IF NOT EXISTS artifacts (\n    id               TEXT PRIMARY KEY,\n    artifact_type    TEXT,\n    source_path      TEXT NOT NULL,\n    title            TEXT NOT NULL,\n    content          TEXT,\n    last_captured_by TEXT,\n    tags             TEXT,\n    created_at       INTEGER NOT NULL,\n    updated_at       INTEGER,\n    embedded         INTEGER DEFAULT 0,\n    machine_id       TEXT NOT NULL DEFAULT 'local',\n    synced_at        INTEGER\n  )`;\n\nconst TEAM_MEMBERS_TABLE = `\n  CREATE TABLE IF NOT EXISTS team_members (\n    id          TEXT PRIMARY KEY,\n    \"user\"      TEXT NOT NULL,\n    role        TEXT,\n    joined      TEXT,\n    tags        TEXT,\n    machine_id  TEXT NOT NULL DEFAULT 'local',\n    synced_at   INTEGER\n  )`;\n\nconst ATTACHMENTS_TABLE = `\n  CREATE TABLE IF NOT EXISTS attachments (\n    id              TEXT PRIMARY KEY,\n    session_id      TEXT REFERENCES sessions(id),\n    prompt_batch_id INTEGER REFERENCES prompt_batches(id),\n    file_path       TEXT NOT NULL,\n    media_type      TEXT,\n    description     TEXT,\n    data            BLOB,\n    content_hash    TEXT,\n    created_at      INTEGER NOT NULL\n  )`;\n\n// -- Intelligence Layer -----------------------------------------------------\n\nconst AGENTS_TABLE = `\n  CREATE TABLE IF NOT EXISTS agents (\n    id                  TEXT PRIMARY KEY,\n    name                TEXT NOT NULL,\n    provider            TEXT,\n    model               TEXT,\n    system_prompt_hash  TEXT,\n    config              TEXT,\n    source              TEXT NOT NULL DEFAULT 'built-in',\n    system_prompt       TEXT,\n    max_turns           INTEGER,\n    timeout_seconds     INTEGER,\n    tool_access         TEXT,\n    enabled             INTEGER NOT NULL DEFAULT 1,\n    created_at          INTEGER NOT NULL,\n    updated_at          INTEGER\n  )`;\n\nconst SPORES_TABLE = `\n  CREATE TABLE IF NOT EXISTS spores (\n    id                TEXT PRIMARY KEY,\n    agent_id          TEXT NOT NULL REFERENCES agents(id),\n    session_id        TEXT REFERENCES sessions(id),\n    prompt_batch_id   INTEGER REFERENCES prompt_batches(id),\n    observation_type  TEXT NOT NULL,\n    status            TEXT DEFAULT 'active',\n    content           TEXT NOT NULL,\n    context           TEXT,\n    importance        INTEGER DEFAULT 5,\n    file_path         TEXT,\n    tags              TEXT,\n    content_hash      TEXT UNIQUE,\n    properties        TEXT,\n    created_at        INTEGER NOT NULL,\n    updated_at        INTEGER,\n    embedded          INTEGER DEFAULT 0,\n    machine_id        TEXT NOT NULL DEFAULT 'local',\n    synced_at         INTEGER\n  )`;\n\nconst ENTITIES_TABLE = `\n  CREATE TABLE IF NOT EXISTS entities (\n    id          TEXT PRIMARY KEY,\n    agent_id    TEXT NOT NULL REFERENCES agents(id),\n    type        TEXT NOT NULL,\n    name        TEXT NOT NULL,\n    properties  TEXT,\n    first_seen  INTEGER NOT NULL,\n    last_seen   INTEGER NOT NULL,\n    status      TEXT DEFAULT 'active',\n    machine_id  TEXT NOT NULL DEFAULT 'local',\n    synced_at   INTEGER,\n    UNIQUE (agent_id, type, name)\n  )`;\n\nconst GRAPH_EDGES_TABLE = `\n  CREATE TABLE IF NOT EXISTS graph_edges (\n    id              TEXT PRIMARY KEY,\n    agent_id        TEXT NOT NULL REFERENCES agents(id),\n    source_id       TEXT NOT NULL,\n    source_type     TEXT NOT NULL,\n    target_id       TEXT NOT NULL,\n    target_type     TEXT NOT NULL,\n    type            TEXT NOT NULL,\n    session_id      TEXT,\n    confidence      REAL DEFAULT 1.0,\n    properties      TEXT,\n    created_at      INTEGER NOT NULL,\n    machine_id      TEXT NOT NULL DEFAULT 'local',\n    synced_at       INTEGER\n  )`;\n\nconst ENTITY_MENTIONS_TABLE = `\n  CREATE TABLE IF NOT EXISTS entity_mentions (\n    entity_id   TEXT NOT NULL REFERENCES entities(id),\n    note_id     TEXT NOT NULL,\n    note_type   TEXT NOT NULL,\n    agent_id    TEXT NOT NULL REFERENCES agents(id),\n    machine_id  TEXT NOT NULL DEFAULT 'local',\n    synced_at   INTEGER,\n    UNIQUE (entity_id, note_id, note_type, agent_id)\n  )`;\n\nconst RESOLUTION_EVENTS_TABLE = `\n  CREATE TABLE IF NOT EXISTS resolution_events (\n    id            TEXT PRIMARY KEY,\n    agent_id      TEXT NOT NULL REFERENCES agents(id),\n    spore_id      TEXT NOT NULL REFERENCES spores(id),\n    action        TEXT NOT NULL,\n    new_spore_id  TEXT,\n    reason        TEXT,\n    session_id    TEXT,\n    created_at    INTEGER NOT NULL,\n    machine_id    TEXT NOT NULL DEFAULT 'local',\n    synced_at     INTEGER\n  )`;\n\nconst DIGEST_EXTRACTS_TABLE = `\n  CREATE TABLE IF NOT EXISTS digest_extracts (\n    id              INTEGER PRIMARY KEY AUTOINCREMENT,\n    agent_id        TEXT NOT NULL REFERENCES agents(id),\n    tier            INTEGER NOT NULL,\n    content         TEXT NOT NULL,\n    substrate_hash  TEXT,\n    generated_at    INTEGER NOT NULL,\n    machine_id      TEXT NOT NULL DEFAULT 'local',\n    synced_at       INTEGER,\n    UNIQUE (agent_id, tier)\n  )`;\n\n// -- Agent State Layer ------------------------------------------------------\n\nconst AGENT_RUNS_TABLE = `\n  CREATE TABLE IF NOT EXISTS agent_runs (\n    id            TEXT PRIMARY KEY,\n    agent_id      TEXT NOT NULL REFERENCES agents(id),\n    task          TEXT,\n    instruction   TEXT,\n    status        TEXT DEFAULT 'pending',\n    started_at    INTEGER,\n    completed_at  INTEGER,\n    tokens_used   INTEGER,\n    cost_usd      REAL,\n    actions_taken TEXT,\n    error         TEXT\n  )`;\n\nconst AGENT_REPORTS_TABLE = `\n  CREATE TABLE IF NOT EXISTS agent_reports (\n    id          INTEGER PRIMARY KEY AUTOINCREMENT,\n    run_id      TEXT NOT NULL REFERENCES agent_runs(id),\n    agent_id    TEXT NOT NULL REFERENCES agents(id),\n    action      TEXT NOT NULL,\n    summary     TEXT NOT NULL,\n    details     TEXT,\n    created_at  INTEGER NOT NULL\n  )`;\n\nconst AGENT_TURNS_TABLE = `\n  CREATE TABLE IF NOT EXISTS agent_turns (\n    id                   INTEGER PRIMARY KEY AUTOINCREMENT,\n    run_id               TEXT NOT NULL REFERENCES agent_runs(id),\n    agent_id             TEXT NOT NULL REFERENCES agents(id),\n    turn_number          INTEGER NOT NULL,\n    tool_name            TEXT NOT NULL,\n    tool_input           TEXT,\n    tool_output_summary  TEXT,\n    started_at           INTEGER,\n    completed_at         INTEGER\n  )`;\n\nconst AGENT_TASKS_TABLE = `\n  CREATE TABLE IF NOT EXISTS agent_tasks (\n    id              TEXT PRIMARY KEY,\n    agent_id        TEXT NOT NULL REFERENCES agents(id),\n    source          TEXT NOT NULL DEFAULT 'built-in',\n    display_name    TEXT,\n    description     TEXT,\n    prompt          TEXT NOT NULL,\n    is_default      INTEGER DEFAULT 0,\n    tool_overrides  TEXT,\n    model           TEXT,\n    config          TEXT,\n    created_at      INTEGER NOT NULL,\n    updated_at      INTEGER\n  )`;\n\nconst AGENT_STATE_TABLE = `\n  CREATE TABLE IF NOT EXISTS agent_state (\n    agent_id    TEXT NOT NULL REFERENCES agents(id),\n    key         TEXT NOT NULL,\n    value       TEXT NOT NULL,\n    updated_at  INTEGER NOT NULL,\n    PRIMARY KEY (agent_id, key)\n  )`;\n\n// -- Sync Layer -------------------------------------------------------------\n\nexport const TEAM_OUTBOX_TABLE = `\n  CREATE TABLE IF NOT EXISTS team_outbox (\n    id          INTEGER PRIMARY KEY AUTOINCREMENT,\n    table_name  TEXT NOT NULL,\n    row_id      TEXT NOT NULL,\n    operation   TEXT NOT NULL DEFAULT 'upsert',\n    payload     TEXT NOT NULL,\n    machine_id  TEXT NOT NULL,\n    created_at  INTEGER NOT NULL,\n    sent_at     INTEGER,\n    retry_count    INTEGER NOT NULL DEFAULT 0,\n    last_attempt_at INTEGER\n  )`;\n\n// -- Logging Layer ----------------------------------------------------------\n\nexport const LOG_ENTRIES_TABLE = `\n  CREATE TABLE IF NOT EXISTS log_entries (\n    id          INTEGER PRIMARY KEY AUTOINCREMENT,\n    timestamp   TEXT    NOT NULL,\n    level       TEXT    NOT NULL,\n    component   TEXT    NOT NULL,\n    kind        TEXT    NOT NULL,\n    message     TEXT    NOT NULL,\n    data        TEXT,\n    session_id  TEXT\n  )`;\n\n// -- Skills Layer -----------------------------------------------------------\n\nexport const SKILL_CANDIDATES_TABLE = `\n  CREATE TABLE IF NOT EXISTS skill_candidates (\n    id              TEXT PRIMARY KEY,\n    agent_id        TEXT NOT NULL REFERENCES agents(id),\n    machine_id      TEXT NOT NULL DEFAULT 'local',\n    topic           TEXT NOT NULL,\n    rationale       TEXT NOT NULL,\n    confidence      REAL NOT NULL DEFAULT 0.0,\n    status          TEXT NOT NULL DEFAULT 'identified',\n    source_ids      TEXT NOT NULL DEFAULT '[]',\n    skill_id        TEXT,\n    created_at      INTEGER NOT NULL,\n    updated_at      INTEGER NOT NULL,\n    synced_at       INTEGER\n  )`;\n\nexport const SKILL_RECORDS_TABLE = `\n  CREATE TABLE IF NOT EXISTS skill_records (\n    id              TEXT PRIMARY KEY,\n    agent_id        TEXT NOT NULL REFERENCES agents(id),\n    machine_id      TEXT NOT NULL DEFAULT 'local',\n    name            TEXT NOT NULL UNIQUE,\n    display_name    TEXT NOT NULL,\n    description     TEXT NOT NULL,\n    status          TEXT NOT NULL DEFAULT 'active',\n    generation      INTEGER NOT NULL DEFAULT 1,\n    candidate_id    TEXT REFERENCES skill_candidates(id),\n    source_ids      TEXT NOT NULL DEFAULT '[]',\n    path            TEXT NOT NULL,\n    usage_count     INTEGER NOT NULL DEFAULT 0,\n    last_used_at    INTEGER,\n    created_at      INTEGER NOT NULL,\n    updated_at      INTEGER NOT NULL,\n    properties      TEXT NOT NULL DEFAULT '{}',\n    synced_at       INTEGER\n  )`;\n\nexport const SKILL_LINEAGE_TABLE = `\n  CREATE TABLE IF NOT EXISTS skill_lineage (\n    id               TEXT PRIMARY KEY,\n    skill_id         TEXT NOT NULL REFERENCES skill_records(id),\n    generation       INTEGER NOT NULL,\n    action           TEXT NOT NULL,\n    rationale        TEXT NOT NULL,\n    source_ids_added TEXT NOT NULL DEFAULT '[]',\n    content_snapshot TEXT NOT NULL,\n    created_at       INTEGER NOT NULL\n  )`;\n\nexport const SKILL_USAGE_TABLE = `\n  CREATE TABLE IF NOT EXISTS skill_usage (\n    id          TEXT PRIMARY KEY,\n    skill_id    TEXT NOT NULL REFERENCES skill_records(id),\n    session_id  TEXT NOT NULL REFERENCES sessions(id),\n    machine_id  TEXT NOT NULL DEFAULT 'local',\n    detected_at INTEGER NOT NULL\n  )`;\n\n// -- Notifications Layer ----------------------------------------------------\n\nexport const NOTIFICATIONS_TABLE = `\n  CREATE TABLE IF NOT EXISTS notifications (\n    id          TEXT PRIMARY KEY,\n    domain      TEXT NOT NULL,\n    type        TEXT NOT NULL,\n    level       TEXT NOT NULL DEFAULT 'info',\n    title       TEXT NOT NULL,\n    message     TEXT,\n    mode        TEXT NOT NULL DEFAULT 'banner',\n    status      TEXT NOT NULL DEFAULT 'unread',\n    link        TEXT,\n    metadata    TEXT,\n    created_at  INTEGER NOT NULL\n  )`;\n\n// -- FTS5 Virtual Tables ----------------------------------------------------\n\nexport const FTS_TABLES = [\n  `CREATE VIRTUAL TABLE IF NOT EXISTS prompt_batches_fts\n     USING fts5(user_prompt, response_summary, content='prompt_batches', content_rowid='id')`,\n\n  `CREATE VIRTUAL TABLE IF NOT EXISTS activities_fts\n     USING fts5(tool_name, tool_input, file_path, content='activities', content_rowid='id')`,\n\n  `CREATE VIRTUAL TABLE IF NOT EXISTS log_entries_fts\n     USING fts5(message, content='log_entries', content_rowid='id')`,\n\n  `CREATE VIRTUAL TABLE IF NOT EXISTS spores_fts\n     USING fts5(content, content='spores', content_rowid='rowid')`,\n\n  `CREATE VIRTUAL TABLE IF NOT EXISTS sessions_fts\n     USING fts5(title, summary, content='sessions', content_rowid='rowid')`,\n\n  // FTS5 sync triggers for log_entries (external-content table)\n  `CREATE TRIGGER IF NOT EXISTS log_entries_ai AFTER INSERT ON log_entries BEGIN\n     INSERT INTO log_entries_fts(rowid, message) VALUES (new.id, new.message);\n   END`,\n\n  `CREATE TRIGGER IF NOT EXISTS log_entries_ad AFTER DELETE ON log_entries BEGIN\n     INSERT INTO log_entries_fts(log_entries_fts, rowid, message) VALUES('delete', old.id, old.message);\n   END`,\n\n  // FTS5 sync triggers for prompt_batches\n  `CREATE TRIGGER IF NOT EXISTS prompt_batches_fts_ai AFTER INSERT ON prompt_batches BEGIN\n     INSERT INTO prompt_batches_fts(rowid, user_prompt, response_summary) VALUES (new.id, new.user_prompt, new.response_summary);\n   END`,\n\n  `CREATE TRIGGER IF NOT EXISTS prompt_batches_fts_au AFTER UPDATE OF user_prompt, response_summary ON prompt_batches BEGIN\n     INSERT INTO prompt_batches_fts(prompt_batches_fts, rowid, user_prompt, response_summary) VALUES('delete', old.id, old.user_prompt, old.response_summary);\n     INSERT INTO prompt_batches_fts(rowid, user_prompt, response_summary) VALUES (new.id, new.user_prompt, new.response_summary);\n   END`,\n\n  `CREATE TRIGGER IF NOT EXISTS prompt_batches_fts_ad AFTER DELETE ON prompt_batches BEGIN\n     INSERT INTO prompt_batches_fts(prompt_batches_fts, rowid, user_prompt, response_summary) VALUES('delete', old.id, old.user_prompt, old.response_summary);\n   END`,\n\n  // FTS5 sync triggers for spores\n  `CREATE TRIGGER IF NOT EXISTS spores_fts_ai AFTER INSERT ON spores BEGIN\n     INSERT INTO spores_fts(rowid, content) VALUES (new.rowid, new.content);\n   END`,\n\n  `CREATE TRIGGER IF NOT EXISTS spores_fts_au AFTER UPDATE OF content ON spores BEGIN\n     INSERT INTO spores_fts(spores_fts, rowid, content) VALUES('delete', old.rowid, old.content);\n     INSERT INTO spores_fts(rowid, content) VALUES (new.rowid, new.content);\n   END`,\n\n  `CREATE TRIGGER IF NOT EXISTS spores_fts_ad AFTER DELETE ON spores BEGIN\n     INSERT INTO spores_fts(spores_fts, rowid, content) VALUES('delete', old.rowid, old.content);\n   END`,\n\n  // FTS5 sync triggers for sessions\n  `CREATE TRIGGER IF NOT EXISTS sessions_fts_ai AFTER INSERT ON sessions BEGIN\n     INSERT INTO sessions_fts(rowid, title, summary) VALUES (new.rowid, new.title, new.summary);\n   END`,\n\n  `CREATE TRIGGER IF NOT EXISTS sessions_fts_au AFTER UPDATE OF title, summary ON sessions BEGIN\n     INSERT INTO sessions_fts(sessions_fts, rowid, title, summary) VALUES('delete', old.rowid, old.title, old.summary);\n     INSERT INTO sessions_fts(rowid, title, summary) VALUES (new.rowid, new.title, new.summary);\n   END`,\n\n  `CREATE TRIGGER IF NOT EXISTS sessions_fts_ad AFTER DELETE ON sessions BEGIN\n     INSERT INTO sessions_fts(sessions_fts, rowid, title, summary) VALUES('delete', old.rowid, old.title, old.summary);\n   END`,\n];\n\n// -- Indexes ----------------------------------------------------------------\n\nexport const SECONDARY_INDEXES = [\n  // Sessions\n  'CREATE INDEX IF NOT EXISTS idx_sessions_status ON sessions (status)',\n  'CREATE INDEX IF NOT EXISTS idx_sessions_processed ON sessions (processed)',\n  'CREATE INDEX IF NOT EXISTS idx_sessions_started_at ON sessions (started_at)',\n  'CREATE INDEX IF NOT EXISTS idx_sessions_agent ON sessions (agent)',\n\n  // Prompt batches\n  'CREATE INDEX IF NOT EXISTS idx_prompt_batches_session_id ON prompt_batches (session_id)',\n  'CREATE INDEX IF NOT EXISTS idx_prompt_batches_processed ON prompt_batches (processed)',\n  'CREATE INDEX IF NOT EXISTS idx_prompt_batches_status ON prompt_batches (status)',\n\n  // Activities\n  'CREATE INDEX IF NOT EXISTS idx_activities_session_id ON activities (session_id)',\n  'CREATE INDEX IF NOT EXISTS idx_activities_prompt_batch_id ON activities (prompt_batch_id)',\n  'CREATE INDEX IF NOT EXISTS idx_activities_tool_name ON activities (tool_name)',\n  'CREATE INDEX IF NOT EXISTS idx_activities_timestamp ON activities (timestamp)',\n  'CREATE INDEX IF NOT EXISTS idx_activities_processed ON activities (processed)',\n\n  // Spores\n  'CREATE INDEX IF NOT EXISTS idx_spores_agent_id ON spores (agent_id)',\n  'CREATE INDEX IF NOT EXISTS idx_spores_session_id ON spores (session_id)',\n  'CREATE INDEX IF NOT EXISTS idx_spores_status ON spores (status)',\n  'CREATE INDEX IF NOT EXISTS idx_spores_observation_type ON spores (observation_type)',\n  'CREATE INDEX IF NOT EXISTS idx_spores_created_at ON spores (created_at)',\n\n  // Entities\n  'CREATE INDEX IF NOT EXISTS idx_entities_agent_id ON entities (agent_id)',\n  'CREATE INDEX IF NOT EXISTS idx_entities_type ON entities (type)',\n\n  // Graph edges\n  'CREATE INDEX IF NOT EXISTS idx_graph_edges_source ON graph_edges (source_id, source_type)',\n  'CREATE INDEX IF NOT EXISTS idx_graph_edges_target ON graph_edges (target_id, target_type)',\n  'CREATE INDEX IF NOT EXISTS idx_graph_edges_type ON graph_edges (type)',\n  'CREATE INDEX IF NOT EXISTS idx_graph_edges_agent ON graph_edges (agent_id)',\n  'CREATE INDEX IF NOT EXISTS idx_graph_edges_source_type ON graph_edges (source_id, type)',\n\n  // Entity mentions\n  'CREATE INDEX IF NOT EXISTS idx_entity_mentions_entity_id ON entity_mentions (entity_id)',\n  'CREATE INDEX IF NOT EXISTS idx_entity_mentions_agent_id ON entity_mentions (agent_id)',\n\n  // Resolution events\n  'CREATE INDEX IF NOT EXISTS idx_resolution_events_spore_id ON resolution_events (spore_id)',\n  'CREATE INDEX IF NOT EXISTS idx_resolution_events_agent_id ON resolution_events (agent_id)',\n\n  // Digest extracts\n  'CREATE INDEX IF NOT EXISTS idx_digest_extracts_agent_id ON digest_extracts (agent_id)',\n\n  // Agent runs\n  'CREATE INDEX IF NOT EXISTS idx_agent_runs_agent_id ON agent_runs (agent_id)',\n  'CREATE INDEX IF NOT EXISTS idx_agent_runs_status ON agent_runs (status)',\n  'CREATE INDEX IF NOT EXISTS idx_agent_runs_agent_status ON agent_runs (agent_id, status)',\n  'CREATE INDEX IF NOT EXISTS idx_agent_runs_task_completed ON agent_runs (task, status, completed_at)',\n\n  // Agent reports\n  'CREATE INDEX IF NOT EXISTS idx_agent_reports_run_id ON agent_reports (run_id)',\n\n  // Agent turns\n  'CREATE INDEX IF NOT EXISTS idx_agent_turns_run_id ON agent_turns (run_id)',\n\n  // Agent tasks\n  'CREATE INDEX IF NOT EXISTS idx_agent_tasks_agent_id ON agent_tasks (agent_id)',\n\n  // Plans\n  'CREATE INDEX IF NOT EXISTS idx_plans_session_id ON plans (session_id)',\n  'CREATE INDEX IF NOT EXISTS idx_plans_source_path ON plans (source_path)',\n  'CREATE INDEX IF NOT EXISTS idx_plans_content_hash ON plans (content_hash)',\n  // Attachments\n  'CREATE INDEX IF NOT EXISTS idx_attachments_file_path ON attachments (file_path)',\n\n  // Team outbox\n  'CREATE INDEX IF NOT EXISTS idx_team_outbox_pending ON team_outbox (sent_at, created_at)',\n  'CREATE INDEX IF NOT EXISTS idx_team_outbox_table_name ON team_outbox (table_name)',\n  'CREATE INDEX IF NOT EXISTS idx_team_outbox_row_lookup ON team_outbox (table_name, row_id)',\n\n  // Machine ID (synced tables)\n  'CREATE INDEX IF NOT EXISTS idx_sessions_machine_id ON sessions (machine_id)',\n  'CREATE INDEX IF NOT EXISTS idx_spores_machine_id ON spores (machine_id)',\n  'CREATE INDEX IF NOT EXISTS idx_graph_edges_machine_id ON graph_edges (machine_id)',\n\n  // Skill candidates\n  'CREATE INDEX IF NOT EXISTS idx_skill_candidates_agent_id ON skill_candidates (agent_id)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_candidates_status ON skill_candidates (status)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_candidates_machine_id ON skill_candidates (machine_id)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_candidates_agent_status ON skill_candidates (agent_id, status)',\n\n  // Skill records\n  'CREATE INDEX IF NOT EXISTS idx_skill_records_agent_id ON skill_records (agent_id)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_records_status ON skill_records (status)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_records_name ON skill_records (name)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_records_machine_id ON skill_records (machine_id)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_records_agent_status ON skill_records (agent_id, status)',\n\n  // Skill lineage\n  'CREATE INDEX IF NOT EXISTS idx_skill_lineage_skill_id ON skill_lineage (skill_id)',\n\n  // Skill usage\n  'CREATE INDEX IF NOT EXISTS idx_skill_usage_skill_id ON skill_usage (skill_id)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_usage_session_id ON skill_usage (session_id)',\n  'CREATE INDEX IF NOT EXISTS idx_skill_usage_skill_session ON skill_usage (skill_id, session_id)',\n\n  // Log entries\n  'CREATE INDEX IF NOT EXISTS idx_log_entries_timestamp ON log_entries (timestamp)',\n  'CREATE INDEX IF NOT EXISTS idx_log_entries_level ON log_entries (level)',\n  'CREATE INDEX IF NOT EXISTS idx_log_entries_component ON log_entries (component)',\n  'CREATE INDEX IF NOT EXISTS idx_log_entries_kind ON log_entries (kind)',\n  'CREATE INDEX IF NOT EXISTS idx_log_entries_session_id ON log_entries (session_id)',\n\n  // Notifications\n  'CREATE INDEX IF NOT EXISTS idx_notifications_status ON notifications (status)',\n  'CREATE INDEX IF NOT EXISTS idx_notifications_domain ON notifications (domain)',\n  'CREATE INDEX IF NOT EXISTS idx_notifications_created_at ON notifications (created_at)',\n  'CREATE INDEX IF NOT EXISTS idx_notifications_status_created ON notifications (status, created_at)',\n];\n\n// -- Ordered table creation -------------------------------------------------\n\nexport const TABLE_DDLS = [\n  SCHEMA_VERSION_TABLE,\n  // Capture layer (order matters for FK references)\n  SESSIONS_TABLE,\n  PROMPT_BATCHES_TABLE,\n  ACTIVITIES_TABLE,\n  PLANS_TABLE,\n  ARTIFACTS_TABLE,\n  TEAM_MEMBERS_TABLE,\n  ATTACHMENTS_TABLE,\n  // Intelligence layer\n  AGENTS_TABLE,\n  SPORES_TABLE,\n  ENTITIES_TABLE,\n  GRAPH_EDGES_TABLE,\n  ENTITY_MENTIONS_TABLE,\n  RESOLUTION_EVENTS_TABLE,\n  DIGEST_EXTRACTS_TABLE,\n  // Agent state layer\n  AGENT_RUNS_TABLE,\n  AGENT_REPORTS_TABLE,\n  AGENT_TURNS_TABLE,\n  AGENT_TASKS_TABLE,\n  AGENT_STATE_TABLE,\n  // Skills layer\n  SKILL_CANDIDATES_TABLE,\n  SKILL_RECORDS_TABLE,\n  SKILL_LINEAGE_TABLE,\n  SKILL_USAGE_TABLE,\n  // Sync layer\n  TEAM_OUTBOX_TABLE,\n  // Logging layer\n  LOG_ENTRIES_TABLE,\n  // Notifications layer\n  NOTIFICATIONS_TABLE,\n];\n","/**\n * Schema migrations for the Myco vault database.\n *\n * Each migration is a function that upgrades the database from version N-1 to N.\n * The MIGRATIONS registry provides a declarative list that createSchema() can\n * iterate over instead of hand-coding version checks.\n */\n\nimport type { Database } from 'better-sqlite3';\nimport { epochSeconds, DEFAULT_MACHINE_ID } from '@myco/constants.js';\nimport {\n  LOG_ENTRIES_TABLE,\n  TEAM_OUTBOX_TABLE,\n  SKILL_CANDIDATES_TABLE,\n  SKILL_RECORDS_TABLE,\n  SKILL_LINEAGE_TABLE,\n  SKILL_USAGE_TABLE,\n  NOTIFICATIONS_TABLE,\n} from './schema-ddl.js';\n\n// ---------------------------------------------------------------------------\n// Migration interface + registry\n// ---------------------------------------------------------------------------\n\nexport interface Migration {\n  version: number;\n  migrate: (db: Database, machineId: string) => void;\n}\n\nexport const MIGRATIONS: Migration[] = [\n  { version: 2, migrate: (db) => migrateV1ToV2(db) },\n  { version: 3, migrate: (db) => migrateV2ToV3(db) },\n  { version: 4, migrate: migrateV3ToV4 },\n  { version: 5, migrate: (db) => migrateV4ToV5(db) },\n  { version: 6, migrate: (db) => migrateV5ToV6(db) },\n  { version: 7, migrate: migrateV6ToV7 },\n  { version: 8, migrate: (db) => migrateV7ToV8(db) },\n  { version: 9, migrate: (db) => migrateV8ToV9(db) },\n];\n\n// ---------------------------------------------------------------------------\n// Individual migration functions\n// ---------------------------------------------------------------------------\n\n/**\n * Migrate a version-1 database to version-2.\n *\n * Version 2 adds:\n *   - plans.session_id, plans.prompt_batch_id, plans.content_hash\n *   - attachments.data, attachments.content_hash\n *   - indexes: idx_plans_session_id, idx_plans_source_path, idx_plans_content_hash\n *\n * Each ALTER TABLE is wrapped in try/catch so re-running is safe -- SQLite\n * throws \"duplicate column name\" if the column already exists, which we ignore.\n */\nfunction migrateV1ToV2(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    const alterStatements = [\n      'ALTER TABLE plans ADD COLUMN session_id TEXT REFERENCES sessions(id)',\n      'ALTER TABLE plans ADD COLUMN prompt_batch_id INTEGER REFERENCES prompt_batches(id)',\n      'ALTER TABLE plans ADD COLUMN content_hash TEXT',\n      'ALTER TABLE attachments ADD COLUMN data BLOB',\n      'ALTER TABLE attachments ADD COLUMN content_hash TEXT',\n    ];\n\n    for (const stmt of alterStatements) {\n      try {\n        db.exec(stmt);\n      } catch {\n        // Column already exists -- safe to ignore on re-run\n      }\n    }\n\n    // Indexes use IF NOT EXISTS so they are idempotent\n    const newIndexes = [\n      'CREATE INDEX IF NOT EXISTS idx_plans_session_id ON plans (session_id)',\n      'CREATE INDEX IF NOT EXISTS idx_plans_source_path ON plans (source_path)',\n      'CREATE INDEX IF NOT EXISTS idx_plans_content_hash ON plans (content_hash)',\n      'CREATE INDEX IF NOT EXISTS idx_attachments_file_path ON attachments (file_path)',\n    ];\n\n    for (const idx of newIndexes) {\n      db.exec(idx);\n    }\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`\n    ).run(2, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Migrate a version-2 database to version-3.\n *\n * Version 3 adds:\n *   - log_entries table\n *   - log_entries_fts virtual table (FTS5)\n *   - indexes: idx_log_entries_timestamp, _level, _component, _kind, _session_id\n *\n * Uses `CREATE ... IF NOT EXISTS` throughout for idempotency.\n */\nfunction migrateV2ToV3(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    db.exec(LOG_ENTRIES_TABLE);\n\n    db.exec(\n      `CREATE VIRTUAL TABLE IF NOT EXISTS log_entries_fts\n         USING fts5(message, content='log_entries', content_rowid='id')`\n    );\n\n    // FTS5 sync triggers for log_entries\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS log_entries_ai AFTER INSERT ON log_entries BEGIN\n         INSERT INTO log_entries_fts(rowid, message) VALUES (new.id, new.message);\n       END`\n    );\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS log_entries_ad AFTER DELETE ON log_entries BEGIN\n         INSERT INTO log_entries_fts(log_entries_fts, rowid, message) VALUES('delete', old.id, old.message);\n       END`\n    );\n\n    const newIndexes = [\n      'CREATE INDEX IF NOT EXISTS idx_log_entries_timestamp ON log_entries (timestamp)',\n      'CREATE INDEX IF NOT EXISTS idx_log_entries_level ON log_entries (level)',\n      'CREATE INDEX IF NOT EXISTS idx_log_entries_component ON log_entries (component)',\n      'CREATE INDEX IF NOT EXISTS idx_log_entries_kind ON log_entries (kind)',\n      'CREATE INDEX IF NOT EXISTS idx_log_entries_session_id ON log_entries (session_id)',\n    ];\n\n    for (const idx of newIndexes) {\n      db.exec(idx);\n    }\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`\n    ).run(3, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Migrate a version-3 database to version-4.\n *\n * Version 4 adds multi-machine support:\n *   - machine_id TEXT NOT NULL DEFAULT 'local' on all synced tables\n *   - synced_at INTEGER on all synced tables\n *   - team_outbox table + indexes\n *   - machine_id indexes on high-traffic tables\n *\n * Backfills existing rows with the provided machineId.\n */\nfunction migrateV3ToV4(db: Database, machineId: string): void {\n  db.exec('BEGIN');\n  try {\n    // Tables that need machine_id + synced_at columns\n    const syncedTables = [\n      'sessions',\n      'prompt_batches',\n      'spores',\n      'entities',\n      'graph_edges',\n      'entity_mentions',\n      'resolution_events',\n      'plans',\n      'artifacts',\n      'digest_extracts',\n      'team_members',\n    ];\n\n    for (const table of syncedTables) {\n      try {\n        db.exec(`ALTER TABLE ${table} ADD COLUMN machine_id TEXT NOT NULL DEFAULT 'local'`);\n      } catch {\n        // Column already exists -- safe to ignore on re-run\n      }\n      try {\n        db.exec(`ALTER TABLE ${table} ADD COLUMN synced_at INTEGER`);\n      } catch {\n        // Column already exists -- safe to ignore on re-run\n      }\n    }\n\n    // Backfill machine_id on existing rows\n    for (const table of syncedTables) {\n      db.prepare(`UPDATE ${table} SET machine_id = ? WHERE machine_id = 'local'`).run(machineId);\n    }\n\n    // Create team_outbox table\n    db.exec(TEAM_OUTBOX_TABLE);\n\n    // Create new indexes (IF NOT EXISTS for idempotency)\n    const newIndexes = [\n      'CREATE INDEX IF NOT EXISTS idx_team_outbox_pending ON team_outbox (sent_at, created_at)',\n      'CREATE INDEX IF NOT EXISTS idx_team_outbox_table_name ON team_outbox (table_name)',\n      'CREATE INDEX IF NOT EXISTS idx_team_outbox_row_lookup ON team_outbox (table_name, row_id)',\n      'CREATE INDEX IF NOT EXISTS idx_sessions_machine_id ON sessions (machine_id)',\n      'CREATE INDEX IF NOT EXISTS idx_spores_machine_id ON spores (machine_id)',\n      'CREATE INDEX IF NOT EXISTS idx_graph_edges_machine_id ON graph_edges (machine_id)',\n    ];\n\n    for (const idx of newIndexes) {\n      db.exec(idx);\n    }\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`\n    ).run(4, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Migrate a version-4 database to version-5.\n *\n * Version 5 adds the Skills layer:\n *   - skill_candidates table\n *   - skill_records table\n *   - skill_lineage table\n *   - skill_usage table\n *   - indexes for all new tables\n *\n * Uses `CREATE TABLE IF NOT EXISTS` throughout for idempotency.\n */\nfunction migrateV4ToV5(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    db.exec(SKILL_CANDIDATES_TABLE);\n    db.exec(SKILL_RECORDS_TABLE);\n    db.exec(SKILL_LINEAGE_TABLE);\n    db.exec(SKILL_USAGE_TABLE);\n\n    const newIndexes = [\n      'CREATE INDEX IF NOT EXISTS idx_skill_candidates_agent_id ON skill_candidates (agent_id)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_candidates_status ON skill_candidates (status)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_candidates_machine_id ON skill_candidates (machine_id)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_candidates_agent_status ON skill_candidates (agent_id, status)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_records_agent_id ON skill_records (agent_id)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_records_status ON skill_records (status)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_records_name ON skill_records (name)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_records_machine_id ON skill_records (machine_id)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_records_agent_status ON skill_records (agent_id, status)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_lineage_skill_id ON skill_lineage (skill_id)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_usage_skill_id ON skill_usage (skill_id)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_usage_session_id ON skill_usage (session_id)',\n      'CREATE INDEX IF NOT EXISTS idx_skill_usage_skill_session ON skill_usage (skill_id, session_id)',\n      'CREATE INDEX IF NOT EXISTS idx_agent_runs_task_completed ON agent_runs (task, status, completed_at)',\n    ];\n\n    for (const idx of newIndexes) {\n      db.exec(idx);\n    }\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`\n    ).run(5, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Migrate a version-5 database to version-6.\n *\n * Version 6 expands FTS5 coverage:\n *   - prompt_batches_fts gains response_summary column (drop + recreate)\n *   - spores_fts new virtual table (content column, hidden rowid)\n *   - sessions_fts new virtual table (title + summary, hidden rowid)\n *   - sync triggers for all three tables (insert / update / delete)\n *   - backfills FTS from existing data\n *\n * Uses `IF NOT EXISTS` throughout for idempotency where possible.\n * The prompt_batches_fts table must be dropped first since its column\n * definition changed.\n */\nfunction migrateV5ToV6(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    // Drop old prompt_batches_fts (column definition changed)\n    db.exec('DROP TABLE IF EXISTS prompt_batches_fts');\n\n    // Recreate with response_summary added\n    db.exec(\n      `CREATE VIRTUAL TABLE IF NOT EXISTS prompt_batches_fts\n         USING fts5(user_prompt, response_summary, content='prompt_batches', content_rowid='id')`,\n    );\n\n    // New FTS tables\n    db.exec(\n      `CREATE VIRTUAL TABLE IF NOT EXISTS spores_fts\n         USING fts5(content, content='spores', content_rowid='rowid')`,\n    );\n    db.exec(\n      `CREATE VIRTUAL TABLE IF NOT EXISTS sessions_fts\n         USING fts5(title, summary, content='sessions', content_rowid='rowid')`,\n    );\n\n    // Triggers for prompt_batches\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS prompt_batches_fts_ai AFTER INSERT ON prompt_batches BEGIN\n         INSERT INTO prompt_batches_fts(rowid, user_prompt, response_summary) VALUES (new.id, new.user_prompt, new.response_summary);\n       END`,\n    );\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS prompt_batches_fts_au AFTER UPDATE OF user_prompt, response_summary ON prompt_batches BEGIN\n         INSERT INTO prompt_batches_fts(prompt_batches_fts, rowid, user_prompt, response_summary) VALUES('delete', old.id, old.user_prompt, old.response_summary);\n         INSERT INTO prompt_batches_fts(rowid, user_prompt, response_summary) VALUES (new.id, new.user_prompt, new.response_summary);\n       END`,\n    );\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS prompt_batches_fts_ad AFTER DELETE ON prompt_batches BEGIN\n         INSERT INTO prompt_batches_fts(prompt_batches_fts, rowid, user_prompt, response_summary) VALUES('delete', old.id, old.user_prompt, old.response_summary);\n       END`,\n    );\n\n    // Triggers for spores\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS spores_fts_ai AFTER INSERT ON spores BEGIN\n         INSERT INTO spores_fts(rowid, content) VALUES (new.rowid, new.content);\n       END`,\n    );\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS spores_fts_au AFTER UPDATE OF content ON spores BEGIN\n         INSERT INTO spores_fts(spores_fts, rowid, content) VALUES('delete', old.rowid, old.content);\n         INSERT INTO spores_fts(rowid, content) VALUES (new.rowid, new.content);\n       END`,\n    );\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS spores_fts_ad AFTER DELETE ON spores BEGIN\n         INSERT INTO spores_fts(spores_fts, rowid, content) VALUES('delete', old.rowid, old.content);\n       END`,\n    );\n\n    // Triggers for sessions\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS sessions_fts_ai AFTER INSERT ON sessions BEGIN\n         INSERT INTO sessions_fts(rowid, title, summary) VALUES (new.rowid, new.title, new.summary);\n       END`,\n    );\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS sessions_fts_au AFTER UPDATE OF title, summary ON sessions BEGIN\n         INSERT INTO sessions_fts(sessions_fts, rowid, title, summary) VALUES('delete', old.rowid, old.title, old.summary);\n         INSERT INTO sessions_fts(rowid, title, summary) VALUES (new.rowid, new.title, new.summary);\n       END`,\n    );\n    db.exec(\n      `CREATE TRIGGER IF NOT EXISTS sessions_fts_ad AFTER DELETE ON sessions BEGIN\n         INSERT INTO sessions_fts(sessions_fts, rowid, title, summary) VALUES('delete', old.rowid, old.title, old.summary);\n       END`,\n    );\n\n    // Backfill FTS from existing data\n    db.exec(\n      `INSERT INTO prompt_batches_fts(rowid, user_prompt, response_summary)\n         SELECT rowid, user_prompt, response_summary FROM prompt_batches`,\n    );\n    db.exec(\n      `INSERT INTO spores_fts(rowid, content)\n         SELECT rowid, content FROM spores`,\n    );\n    db.exec(\n      `INSERT INTO sessions_fts(rowid, title, summary)\n         SELECT rowid, title, summary FROM sessions`,\n    );\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`,\n    ).run(6, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Migrate v6 -> v7: fix stale 'local' machine_id on ALL synced tables.\n *\n * The agent vault tools historically used DEFAULT_MACHINE_ID ('local')\n * instead of the resolved machine identity. This one-time data migration\n * fixes all affected records and re-queues them for team sync.\n */\nfunction migrateV6ToV7(db: Database, machineId: string): void {\n  if (machineId === 'local' || machineId === DEFAULT_MACHINE_ID) return; // Nothing to fix\n\n  db.exec('BEGIN');\n  try {\n    // entity_mentions excluded -- no `id` column (composite key: entity_id, note_id, note_type)\n    const tables = [\n      'sessions', 'prompt_batches', 'spores', 'entities', 'graph_edges',\n      'resolution_events', 'plans', 'artifacts',\n      'digest_extracts', 'skill_candidates', 'skill_records',\n    ];\n\n    for (const table of tables) {\n      try {\n        // Find rows that need fixing BEFORE updating\n        const staleRows = db.prepare(\n          `SELECT id FROM ${table} WHERE machine_id = 'local'`,\n        ).all() as Array<{ id: string }>;\n\n        if (staleRows.length === 0) continue;\n\n        // Fix machine_id and clear synced_at\n        db.prepare(\n          `UPDATE ${table} SET machine_id = ?, synced_at = NULL WHERE machine_id = 'local'`,\n        ).run(machineId);\n\n        // Clear stale outbox entries for affected rows only\n        for (const row of staleRows) {\n          db.prepare(\n            `DELETE FROM team_outbox WHERE table_name = ? AND row_id = ?`,\n          ).run(table, String(row.id));\n        }\n\n        // Re-enqueue only the fixed rows with full payload\n        const enqueueStmt = db.prepare(\n          `INSERT INTO team_outbox (table_name, row_id, operation, payload, machine_id, created_at)\n           VALUES (?, ?, 'upsert', ?, ?, ?)`,\n        );\n        const now = epochSeconds();\n        for (const stale of staleRows) {\n          const fresh = db.prepare(`SELECT * FROM ${table} WHERE id = ?`).get(stale.id) as Record<string, unknown>;\n          if (fresh) {\n            enqueueStmt.run(table, String(stale.id), JSON.stringify(fresh), machineId, now);\n          }\n        }\n      } catch (tableErr) {\n        // Skip if table doesn't exist; re-throw for other errors (I/O, constraint)\n        const msg = tableErr instanceof Error ? tableErr.message : String(tableErr);\n        if (!msg.includes('no such table')) throw tableErr;\n      }\n    }\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`,\n    ).run(7, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Migrate v7 -> v8: add notifications table.\n *\n * Uses `CREATE TABLE IF NOT EXISTS` for idempotency.\n */\nfunction migrateV7ToV8(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    db.exec(NOTIFICATIONS_TABLE);\n\n    const newIndexes = [\n      'CREATE INDEX IF NOT EXISTS idx_notifications_status ON notifications (status)',\n      'CREATE INDEX IF NOT EXISTS idx_notifications_domain ON notifications (domain)',\n      'CREATE INDEX IF NOT EXISTS idx_notifications_created_at ON notifications (created_at)',\n      'CREATE INDEX IF NOT EXISTS idx_notifications_status_created ON notifications (status, created_at)',\n    ];\n\n    for (const idx of newIndexes) {\n      db.exec(idx);\n    }\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`,\n    ).run(8, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Version 9 adds retry tracking to the team outbox:\n *   - retry_count INTEGER NOT NULL DEFAULT 0\n *   - last_attempt_at INTEGER\n *\n * Records exceeding the max retry count are dead-lettered (excluded from\n * pending queries) so they don't block the sync flush or deep sleep.\n */\nfunction migrateV8ToV9(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    db.exec('ALTER TABLE team_outbox ADD COLUMN retry_count INTEGER NOT NULL DEFAULT 0');\n    db.exec('ALTER TABLE team_outbox ADD COLUMN last_attempt_at INTEGER');\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`,\n    ).run(9, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n","/**\n * SQLite database schema -- all capture, intelligence, and agent state tables.\n *\n * Uses `CREATE TABLE IF NOT EXISTS` and `CREATE INDEX IF NOT EXISTS` throughout\n * for idempotency. Running `createSchema()` multiple times is always safe.\n *\n * Timestamp convention: all timestamps are INTEGER (Unix epoch seconds).\n * Content hashing: all `content_hash` columns are TEXT with UNIQUE constraint.\n * Embedding dimensions: 1024 (bge-m3 default) -- used by external sqlite-vec store.\n *\n * Vector columns live in a separate sqlite-vec virtual table, not inline.\n * Tables that participate in vector search carry an `embedded INTEGER DEFAULT 0`\n * flag so the embedder knows which rows still need vectors.\n */\n\nimport type { Database } from 'better-sqlite3';\nimport { epochSeconds, DEFAULT_MACHINE_ID } from '@myco/constants.js';\nimport { TABLE_DDLS, FTS_TABLES, SECONDARY_INDEXES } from './schema-ddl.js';\nimport { MIGRATIONS } from './migrations.js';\n\n/** Current schema version -- fresh start for the SQLite era. */\nexport const SCHEMA_VERSION = 9;\n\n// Re-export for backwards compat (other modules import from schema.ts)\nexport { DEFAULT_MACHINE_ID };\n\n/** Embedding vector dimensions (bge-m3 default). */\nexport const EMBEDDING_DIMENSIONS = 1024;\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\nfunction getCurrentVersion(db: Database): number {\n  const row = db.prepare(\n    'SELECT version FROM schema_version ORDER BY version DESC LIMIT 1'\n  ).get() as { version: number } | undefined;\n  return row?.version ?? 0;\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Create all database tables, indexes, and record the schema version.\n *\n * Fully idempotent -- safe to call on every startup. Uses `IF NOT EXISTS`\n * for all DDL and `ON CONFLICT DO NOTHING` for the version row.\n *\n * @param db -- better-sqlite3 Database instance.\n * @param machineId -- machine identifier for backfilling existing rows during\n *   v3->v4 and v6->v7 migrations. Defaults to `'local'` (tests, init).\n */\nexport function createSchema(db: Database, machineId: string = DEFAULT_MACHINE_ID): void {\n  // Fast-path: skip if already at current version\n  try {\n    const currentVersion = getCurrentVersion(db);\n    if (currentVersion === SCHEMA_VERSION) return;\n\n    // Run pending migrations in order\n    for (const migration of MIGRATIONS) {\n      const version = getCurrentVersion(db);\n      if (version < migration.version) {\n        migration.migrate(db, machineId);\n      }\n    }\n    return;\n  } catch {\n    // Table doesn't exist yet -- first run\n  }\n\n  // Fresh install: create all tables, FTS, indexes\n  for (const ddl of TABLE_DDLS) { db.exec(ddl); }\n  for (const ddl of FTS_TABLES) { db.exec(ddl); }\n  for (const idx of SECONDARY_INDEXES) { db.exec(idx); }\n\n  db.prepare(\n    `INSERT INTO schema_version (version, applied_at)\n     VALUES (?, ?)\n     ON CONFLICT (version) DO NOTHING`\n  ).run(SCHEMA_VERSION, 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package/dist/chunk-GYIA6XLB.js.map

@@ -1 +0,0 @@
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package/dist/chunk-SV6UCB2Z.js.map

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package/dist/chunk-TRA3R4EC.js.map

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extracted from this prompt batch. */\nexport const EDGE_TYPE_EXTRACTED_FROM = 'EXTRACTED_FROM';\n/** Wisdom spore was derived from (consolidated) this source spore. */\nexport const EDGE_TYPE_DERIVED_FROM = 'DERIVED_FROM';\n/** Session contains this prompt batch. */\nexport const EDGE_TYPE_HAS_BATCH = 'HAS_BATCH';\n// --- Query defaults ---\n/** Default row limit for query module list operations. */\nexport const QUERY_DEFAULT_LIST_LIMIT = 100;\n/** Default LIMIT for paginated list queries. */\nexport const DEFAULT_LIST_LIMIT = 50;\n/** Default confidence score for graph edges. */\nexport const GRAPH_EDGE_DEFAULT_CONFIDENCE = 1.0;\n\n// --- Query limits ---\n/** Max recent sessions to check for lineage heuristics. */\nexport const LINEAGE_RECENT_SESSIONS_LIMIT = 5;\n/** Max related spores to query for session notes. */\nexport const RELATED_SPORES_LIMIT = 50;\n\n// --- Context injection ---\n/** Max spores to inject per prompt. */\nexport const PROMPT_CONTEXT_MAX_SPORES = 3;\n/** Minimum similarity score for prompt context injection (0-1). */\nexport const PROMPT_CONTEXT_MIN_SIMILARITY = 0.3;\n/** Max token budget for session-start context injection. */\nexport const SESSION_CONTEXT_MAX_TOKENS = 500;\n/** Max token budget for per-prompt context injection. */\nexport const PROMPT_CONTEXT_MAX_TOKENS = 300;\n/** Minimum prompt length to trigger context search. */\nexport const PROMPT_CONTEXT_MIN_LENGTH = 10;\n\n/** Over-fetch multiplier for vector search to compensate for post-filtering. */\nexport const PROMPT_VECTOR_OVER_FETCH = 2;\n\n// --- Spore status filtering ---\n/** Spore statuses excluded from search results and context injection. */\nexport const EXCLUDED_SPORE_STATUSES = new Set(['superseded', 'archived']);\n\n// --- Agent identity ---\n/** Default agent ID for the built-in intelligence agent. */\nexport const DEFAULT_AGENT_ID = 'myco-agent';\n/** Agent ID for user-initiated MCP operations. */\nexport const USER_AGENT_ID = 'user';\n/** Agent name for user-initiated MCP operations. */\nexport const USER_AGENT_NAME = 'User (MCP)';\n\n// --- MCP tool defaults ---\n/** Default result limit for myco_search. */\nexport const MCP_SEARCH_DEFAULT_LIMIT = 10;\n/** Default result limit for myco_sessions. */\nexport const MCP_SESSIONS_DEFAULT_LIMIT = 20;\n/** Default result limit for myco_logs. */\nexport const MCP_LOGS_DEFAULT_LIMIT = 50;\n/** Default result limit for myco_skills and myco_skill_candidates. */\nexport const MCP_SKILLS_DEFAULT_LIMIT = 50;\n\n// --- Feed ---\n/** Default number of entries returned by the activity feed. */\nexport const FEED_DEFAULT_LIMIT = 50;\n\n// --- Digest — Tiers ---\n/** Available token-budget tiers for digest synthesis. */\nexport const DIGEST_TIERS = [1500, 5000, 10000] as const;\nexport type DigestTier = (typeof DIGEST_TIERS)[number];\n\n// --- Digest — Context window minimums per tier ---\n/** Minimum context window (tokens) required to run a digest at a given tier. */\nexport const DIGEST_TIER_MIN_CONTEXT: Record<number, number> = {\n  1500: 6500,\n  5000: 18500,\n  10000: 30500,\n};\n\n// --- Digest — Substrate ---\n/** Default minimum substrate notes required before a digest cycle runs. */\nexport const DIGEST_MIN_NOTES_FOR_CYCLE = 10;\n\n/** Scoring weights by note type when selecting substrate for synthesis. */\nexport const DIGEST_SUBSTRATE_TYPE_WEIGHTS: Record<string, number> = {\n  session: 3,\n  spore: 3,\n  plan: 2,\n  artifact: 1,\n  team: 1,\n};\n\n// --- LLM reasoning control ---\n/** Reasoning mode for all Myco LLM calls. Suppresses chain-of-thought tokens from reasoning models. */\nexport const LLM_REASONING_MODE = 'off' as const;\n\n// --- Digest — System prompt overhead estimate ---\n\n// --- Vault intelligence ---\n/** Max candidate spores after post-filtering for supersession check. */\nexport const SUPERSESSION_CANDIDATE_LIMIT = 5;\n\n/** Over-fetch from vector index before post-filtering by status/type. */\nexport const SUPERSESSION_VECTOR_FETCH_LIMIT = 20;\n\n/** Max output tokens for supersession LLM evaluation. */\nexport const SUPERSESSION_MAX_TOKENS = 256;\n\n/** Similarity threshold for clustering related spores in batch agent processing. */\nexport const AGENT_CLUSTER_SIMILARITY = 0.75;\n\n// --- Search ---\n/** Default number of results returned by vector search and fullTextSearch. */\nexport const SEARCH_RESULTS_DEFAULT_LIMIT = 20;\n/** Minimum cosine similarity score for semantic search results (0-1). */\nexport const SEARCH_SIMILARITY_THRESHOLD = 0.3;\n\n// --- Pipeline processing ---\n/** Default page size for pipeline items API listing. */\nexport const PIPELINE_ITEMS_DEFAULT_LIMIT = 50;\n\n// --- Pipeline retry ---\n/** Max retries for parse (structural) pipeline failures — fail fast. */\nexport const PIPELINE_PARSE_MAX_RETRIES = 1;\n/** Exponential backoff multiplier for successive pipeline retries. */\nexport const PIPELINE_BACKOFF_MULTIPLIER = 4;\n\n// --- Pipeline stages (ordered) ---\nexport const PIPELINE_STAGES = ['capture', 'extraction', 'embedding', 'consolidation', 'digest'] as const;\nexport type PipelineStage = typeof PIPELINE_STAGES[number];\n\n// --- Pipeline statuses ---\nexport const PIPELINE_STATUSES = ['pending', 'processing', 'succeeded', 'failed', 'blocked', 'skipped', 'poisoned'] as const;\nexport type PipelineStatus = typeof PIPELINE_STATUSES[number];\n\n// --- Provider roles for circuit breakers ---\nexport const PIPELINE_PROVIDER_ROLES = ['llm', 'embedding', 'digest-llm'] as const;\nexport type PipelineProviderRole = typeof PIPELINE_PROVIDER_ROLES[number];\n\n// --- Stage to provider role mapping ---\nexport const STAGE_PROVIDER_MAP: Record<PipelineStage, PipelineProviderRole | null> = {\n  capture: null,\n  extraction: 'llm',\n  embedding: 'embedding',\n  consolidation: 'digest-llm',\n  digest: 'digest-llm',\n};\n\n/**\n * Stages processed by the pipeline tick timer.\n * Capture is handled at registration time, digest is gated by the metabolism timer.\n */\nexport const PIPELINE_TICK_STAGES: PipelineStage[] = ['extraction', 'embedding', 'consolidation'];\n\n// --- Item type to applicable stages ---\n// Sessions skip consolidation — consolidation applies to the spores\n// extracted FROM sessions, not the session work item itself.\n// Lineage detection stays outside the pipeline (fire-and-forget, non-critical).\nexport const ITEM_STAGE_MAP: Record<string, PipelineStage[]> = {\n  session: ['capture', 'extraction', 'embedding', 'digest'],\n  spore: ['capture', 'embedding', 'consolidation', 'digest'],\n  artifact: ['capture', 'embedding', 'digest'],\n};\n\n// --- User task registry ---\n/** Subdirectory within the vault for user-created task YAML files. */\nexport const USER_TASKS_DIR = 'tasks';\n\n/** Source label for user-created tasks. */\nexport const USER_TASK_SOURCE = 'user';\n\n/** Source label for built-in tasks shipped with the package. */\nexport const BUILT_IN_SOURCE = 'built-in';\n\n/** Task name validation pattern (lowercase, hyphens, digits). */\nexport const TASK_NAME_PATTERN = /^[a-z0-9][a-z0-9-]*[a-z0-9]$|^[a-z0-9]$/;\n\n/** Maximum length for task names. */\nexport const MAX_TASK_NAME_LENGTH = 50;\n\n// --- Automatic consolidation ---\n/** Minimum cluster size required before asking LLM to consolidate. */\nexport const CONSOLIDATION_MIN_CLUSTER_SIZE = 3;\n\n/** Over-fetch from vector index before post-filtering by status/type. */\nexport const CONSOLIDATION_VECTOR_FETCH_LIMIT = 20;\n\n/** Max output tokens for consolidation LLM synthesis.\n *  Must be large enough for the full JSON response including content field. */\nexport const CONSOLIDATION_MAX_TOKENS = 2048;\n\n// --- Power management ---\n/** PowerManager states valid for task scheduling (excludes deep_sleep which halts all ticks). */\nexport const SCHEDULABLE_POWER_STATES = ['active', 'idle', 'sleep'] as const;\nexport type SchedulablePowerState = typeof SCHEDULABLE_POWER_STATES[number];\n\n/** Time without activity before transitioning to idle (ms). */\nexport const POWER_IDLE_THRESHOLD_MS = 5 * 60 * MS_PER_SECOND;\n/** Time without activity before transitioning to sleep (ms). */\nexport const POWER_SLEEP_THRESHOLD_MS = 30 * 60 * MS_PER_SECOND;\n/** Time without activity before transitioning to deep sleep (ms). */\nexport const POWER_DEEP_SLEEP_THRESHOLD_MS = 90 * 60 * MS_PER_SECOND;\n/** Job cycle interval during active/idle states (ms). */\nexport const POWER_ACTIVE_INTERVAL_MS = 60 * MS_PER_SECOND;\n/** Job cycle interval during sleep state (ms). */\nexport const POWER_SLEEP_INTERVAL_MS 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package/dist/chunk-X5IXK5KO.js.map

@@ -1 +0,0 @@
-{"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 } 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   * 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 ? '\\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/** Find where a [mcp_servers.<name>] section ends in a TOML string. */\nexport function findTomlSectionEnd(raw: string, searchStart: number, serverName: string): number {\n  const subsectionPrefix = `mcp_servers.${serverName}.`;\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] !== `mcp_servers.${serverName}`) {\n      return offset - line.length - 1;\n    }\n  }\n  return raw.length;\n}\n\n/**\n * Build/update a specific mcp_servers entry in a TOML string.\n * Pure transformation — returns updated content without writing to disk.\n */\nexport function buildTomlMcpSection(\n  raw: string,\n  serverName: string,\n  server: Record<string, unknown>,\n): string {\n  const sectionHeader = `[mcp_servers.${serverName}]`;\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    if (typeof val === 'string') {\n      lines.push(`${key} = \"${val}\"`);\n    } else if (Array.isArray(val)) {\n      lines.push(`${key} = [${val.map((v: unknown) => `\"${v}\"`).join(', ')}]`);\n    } else if (typeof val === 'boolean') {\n      lines.push(`${key} = ${val}`);\n    }\n  }\n\n  // Add env subtable if present\n  const env = server.env as Record<string, string> | undefined;\n  if (env && Object.keys(env).length > 0) {\n    lines.push('');\n    lines.push(`[mcp_servers.${serverName}.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, serverName);\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) && isPlainObject(targetVal)) {\n      // Recurse into nested objects, then prune if empty\n      if (deepRemoveSettings(targetVal, templateVal)) {\n        if (Object.keys(targetVal).length === 0) {\n          delete target[key];\n        }\n        changed = true;\n      }\n    } else {\n      // Scalar: delete if value matches\n      if (String(targetVal) === String(templateVal)) {\n        delete target[key];\n        changed = true;\n      }\n    }\n  }\n  return changed;\n}\n","import fs from 'node:fs';\nimport path from 'node:path';\n\nexport function readJsonFile(filePath: string): Record<string, unknown> {\n  try {\n    return JSON.parse(fs.readFileSync(filePath, 'utf-8'));\n  } catch {\n    return {};\n  }\n}\n\nexport function writeJsonFile(filePath: string, data: Record<string, unknown>): void {\n  fs.mkdirSync(path.dirname(filePath), { recursive: true });\n  fs.writeFileSync(filePath, JSON.stringify(data, null, 2) + '\\n', 'utf-8');\n}\n\n/** Write a JSON file, or delete it if the object is empty. */\nexport function writeOrDeleteJsonFile(filePath: string, data: Record<string, unknown>): void {\n  if (Object.keys(data).length === 0) {\n    try { fs.unlinkSync(filePath); } catch { /* ignore */ }\n  } else {\n    writeJsonFile(filePath, data);\n  }\n}\n","import 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). */\nexport function 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 */\nexport function 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/**\n * Create a starter AGENTS.md if the project doesn't have one.\n * Idempotent — skips if AGENTS.md already exists.\n */\nexport function ensureAgentsMd(projectRoot: string, packageRoot: string): void {\n  const agentsMdPath = path.join(projectRoot, 'AGENTS.md');\n  if (fs.existsSync(agentsMdPath)) return;\n\n  const candidates = [\n    path.join(packageRoot, 'src/symbionts/templates/agents-starter.md'),\n    path.join(packageRoot, 'dist/src/symbionts/templates/agents-starter.md'),\n  ];\n  for (const p of candidates) {\n    try {\n      const content = fs.readFileSync(p, 'utf-8');\n      fs.writeFileSync(agentsMdPath, content, 'utf-8');\n      return;\n    } catch { /* try next */ }\n  }\n}\n\nexport function ensureSymlink(linkPath: string, target: string): void {\n  try {\n    if (fs.readlinkSync(linkPath) === target) return;\n  } catch { /* does not exist or is not a symlink — proceed */ }\n  try { fs.rmSync(linkPath, { recursive: true, force: true }); } catch { /* ignore */ }\n  fs.symlinkSync(target, 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