@goondocks/myco 0.20.1 → 0.21.0

package/dist/chunk-MYOZLMB2.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/db/schema-ddl.ts","../src/constants/skill-candidate-status.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    supersedes      TEXT,\n    created_at      INTEGER NOT NULL,\n    updated_at      INTEGER NOT NULL,\n    approved_at     INTEGER,\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    embedded        INTEGER DEFAULT 0,\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  'CREATE INDEX IF NOT EXISTS idx_sessions_created_at ON sessions (created_at)',\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 * Canonical string values for skill_candidates.status.\n *\n * The skill lifecycle uses four states:\n *   - identified: discovered by skill-survey, awaiting human review\n *   - approved:   human approved; queued for skill-generate\n *   - generated:  vault_finalize_skill promoted the staged skill to live\n *   - dismissed:  retired (human or agent)\n *\n * See docs/superpowers/plans/2026-04-08-skill-lifecycle-audit-and-staging.md\n * for the lifecycle transitions and who is allowed to make each one.\n */\nexport const CANDIDATE_STATUS = {\n  IDENTIFIED: 'identified',\n  APPROVED: 'approved',\n  GENERATED: 'generated',\n  DISMISSED: 'dismissed',\n} as const;\n\nexport type SkillCandidateStatus = (typeof CANDIDATE_STATUS)[keyof typeof CANDIDATE_STATUS];\n\n/**\n * Statuses the agent-facing vault_skill_candidates tool is allowed to set\n * on an update. Human-only transitions (approved) and internal-only\n * transitions (generated, via vault_finalize_skill) are excluded.\n */\nexport const AGENT_SETTABLE_STATUSES: readonly SkillCandidateStatus[] = [\n  CANDIDATE_STATUS.IDENTIFIED,\n  CANDIDATE_STATUS.DISMISSED,\n];\n\n/**\n * Statuses REST callers (UI + MCP myco_skill_candidates) are allowed to\n * set. 'generated' is internal — only vault_finalize_skill sets it, and\n * that path calls updateCandidate directly rather than going through REST.\n */\nexport const REST_SETTABLE_STATUSES: readonly SkillCandidateStatus[] = [\n  CANDIDATE_STATUS.IDENTIFIED,\n  CANDIDATE_STATUS.APPROVED,\n  CANDIDATE_STATUS.DISMISSED,\n];\n\n/**\n * Composite UI filter value that the REST handler translates into a\n * multi-status query (`status IN ('approved', 'generated')`). Kept here\n * so the UI and backend share a single source of truth for the wire\n * encoding.\n */\nexport const PIPELINE_FILTER_VALUE = `${CANDIDATE_STATUS.APPROVED},${CANDIDATE_STATUS.GENERATED}`;\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 { CANDIDATE_STATUS } from '@myco/constants/skill-candidate-status.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  { version: 10, migrate: (db) => migrateV9ToV10(db) },\n  { version: 11, migrate: (db) => migrateV10ToV11(db) },\n  { version: 12, migrate: (db) => migrateV11ToV12(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/**\n * Version 10 adds an audit trail for skill candidate approvals.\n *\n *   - skill_candidates.approved_at INTEGER (nullable) — timestamp of the\n *     first transition into status='approved'. Auto-managed by\n *     updateCandidate going forward.\n *\n * Backfill: rows currently in status 'approved' or 'generated' get\n * approved_at set to the migration timestamp. This is a one-time,\n * deliberately-imprecise assumption — the true approval time is lost\n * for existing rows, so we record \"as of the migration, these were\n * considered approved\" rather than inventing timestamps.\n *\n * Rows in 'identified' or 'dismissed' state keep approved_at = NULL.\n *\n * Idempotent: the ALTER is wrapped in try/catch so re-runs tolerate the\n * existing column; the backfill uses `WHERE approved_at IS NULL` so it\n * never overwrites a previously-recorded timestamp.\n */\nfunction migrateV9ToV10(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    try {\n      db.exec('ALTER TABLE skill_candidates ADD COLUMN approved_at INTEGER');\n    } catch {\n      // Column already exists -- safe to ignore on re-run\n    }\n\n    const now = epochSeconds();\n    db.prepare(\n      `UPDATE skill_candidates\n         SET approved_at = ?\n       WHERE approved_at IS NULL\n         AND status IN (?, ?)`,\n    ).run(now, CANDIDATE_STATUS.APPROVED, CANDIDATE_STATUS.GENERATED);\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`,\n    ).run(10, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Version 11 adds supersedes tracking to skill candidates.\n *\n *   - skill_candidates.supersedes TEXT (nullable) — JSON array of skill\n *     record names that this candidate would replace. Used by the skill\n *     survey task to create domain-level candidates that explicitly\n *     subsume existing narrow skills.\n *\n * Idempotent: the ALTER is wrapped in try/catch so re-runs tolerate the\n * existing column.\n */\nfunction migrateV10ToV11(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    try {\n      db.exec('ALTER TABLE skill_candidates ADD COLUMN supersedes TEXT');\n    } catch {\n      // Column already exists -- safe to ignore on re-run\n    }\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`,\n    ).run(11, epochSeconds());\n\n    db.exec('COMMIT');\n  } catch (err) {\n    db.exec('ROLLBACK');\n    throw err;\n  }\n}\n\n/**\n * Version 12 adds embedding support for skill records.\n *\n *   - skill_records.embedded INTEGER DEFAULT 0 — flag for the embedding\n *     pipeline to know which rows still need vectors.\n *\n * Idempotent: the ALTER is wrapped in try/catch so re-runs tolerate the\n * existing column.\n */\nfunction migrateV11ToV12(db: Database): void {\n  db.exec('BEGIN');\n  try {\n    try {\n      db.exec('ALTER TABLE skill_records ADD COLUMN embedded INTEGER DEFAULT 0');\n    } catch {\n      // Column already exists\n    }\n\n    db.prepare(\n      `INSERT INTO schema_version (version, applied_at)\n       VALUES (?, ?)\n       ON CONFLICT (version) DO NOTHING`,\n    ).run(12, 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. 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package/dist/chunk-SRXTSI25.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/config/loader.ts","../src/config/appearance-values.ts","../src/config/schema.ts","../src/config/migrations.ts","../src/utils/deep-merge.ts"],"sourcesContent":["import fs from 'node:fs';\nimport path from 'node:path';\nimport YAML from 'yaml';\nimport { MycoConfigSchema, type MycoConfig, type BackupConfig, type TeamConfig } from './schema.js';\nimport { runMigrations, CURRENT_MIGRATION_VERSION } from './migrations.js';\nimport { deepMerge } from '../utils/deep-merge.js';\n\nexport const CONFIG_FILENAME = 'myco.yaml';\nexport const LOCAL_CONFIG_FILENAME = 'local.yaml';\n\nfunction localConfigPath(vaultDir: string): string {\n  // vaultDir already points at `.myco/` (see resolveVaultDir), so local.yaml\n  // sits alongside myco.yaml in the vault — no extra `.myco/` prefix.\n  return path.join(vaultDir, LOCAL_CONFIG_FILENAME);\n}\n\n/** Config overlay uses replace semantics: arrays in source overwrite arrays in target. */\nexport function deepMergeConfig<T extends Record<string, unknown>>(target: T, source: Partial<T>): T {\n  return deepMerge(target, source, { arrayStrategy: 'replace' });\n}\n\nexport function loadConfig(vaultDir: string): MycoConfig {\n  const configPath = path.join(vaultDir, CONFIG_FILENAME);\n\n  if (!fs.existsSync(configPath)) {\n    throw new Error(`myco.yaml not found in ${vaultDir}`);\n  }\n\n  const raw = fs.readFileSync(configPath, 'utf-8');\n  const parsed = YAML.parse(raw) as Record<string, unknown>;\n\n  // Detect v1 config and guide migration\n  if (parsed.version === 1 || (parsed.intelligence as Record<string, unknown>)?.backend) {\n    throw new Error(\n      'Myco config uses v1 format. Run /myco:setup-llm to reconfigure for v2.',\n    );\n  }\n\n  // --- v2 → v3 migration ---\n  let v2Migrated = false;\n  if (parsed.version === 2) {\n    // Extract intelligence.embedding to top-level embedding\n    const intel = parsed.intelligence as Record<string, unknown> | undefined;\n    const embeddingConfig = intel?.embedding as Record<string, unknown> | undefined;\n    if (embeddingConfig && !parsed.embedding) {\n      // Map v2 'lm-studio' to v3 'openai-compatible' for embedding provider\n      if (embeddingConfig.provider === 'lm-studio') {\n        embeddingConfig.provider = 'openai-compatible';\n      }\n      parsed.embedding = embeddingConfig;\n    }\n\n    // Keep daemon.port and daemon.log_level, drop grace_period and max_log_size\n    const daemon = parsed.daemon as Record<string, unknown> | undefined;\n    if (daemon) {\n      const { port, log_level } = daemon;\n      parsed.daemon = { port: port ?? null, log_level: log_level ?? 'info' };\n    }\n\n    // Keep capture basics, drop token-related fields; migrate artifact_watch → plan_dirs\n    const capture = parsed.capture as Record<string, unknown> | undefined;\n    if (capture) {\n      const { transcript_paths, artifact_watch, plan_dirs, artifact_extensions, buffer_max_events } = capture;\n      parsed.capture = {\n        transcript_paths,\n        plan_dirs: plan_dirs ?? artifact_watch,\n        artifact_extensions,\n        buffer_max_events,\n      };\n    }\n\n    // Drop removed top-level sections\n    delete parsed.intelligence;\n    delete parsed.context;\n    delete parsed.team;\n    delete parsed.digest;\n    delete parsed.pipeline;\n\n    // Set version to 3\n    parsed.version = 3;\n    v2Migrated = true;\n\n    process.stderr.write('[myco migration] Migrated config from v2 to v3\\n');\n  }\n\n  // Run numbered migrations (for v3+ forward migrations)\n  const migrationsRan = runMigrations(parsed, vaultDir, (msg) => {\n    process.stderr.write(`[myco migration] ${msg}\\n`);\n  });\n\n  // Parse with Zod to fill in defaults for new config sections\n  const config = MycoConfigSchema.parse(parsed);\n\n  // Write back if v2→v3 migration ran, numbered migrations ran, or new defaults were added\n  const needsWrite = v2Migrated\n    || migrationsRan\n    || (parsed.config_version as number ?? 0) < CURRENT_MIGRATION_VERSION\n    || parsed.version !== config.version;\n\n  if (needsWrite) {\n    const fullConfig = JSON.parse(JSON.stringify(config)) as Record<string, unknown>;\n    fs.writeFileSync(configPath, YAML.stringify(fullConfig), 'utf-8');\n  }\n\n  return config;\n}\n\nexport function saveConfig(vaultDir: string, config: MycoConfig): void {\n  // Validate before writing — OAK lesson: validate on write, not just read.\n  // This is the single parse point for all write paths.\n  const validated = MycoConfigSchema.parse(config);\n\n  const configPath = path.join(vaultDir, CONFIG_FILENAME);\n  fs.mkdirSync(vaultDir, { recursive: true });\n  fs.writeFileSync(configPath, YAML.stringify(validated), 'utf-8');\n}\n\nexport function updateConfig(\n  vaultDir: string,\n  fn: (config: MycoConfig) => MycoConfig,\n): MycoConfig {\n  const current = loadConfig(vaultDir);\n  const updated = fn(current);\n  saveConfig(vaultDir, updated);\n  return updated;\n}\n\nexport function updateBackupConfig(\n  vaultDir: string,\n  backup: Partial<BackupConfig>,\n): MycoConfig {\n  return updateConfig(vaultDir, (config) => ({\n    ...config,\n    backup: { ...config.backup, ...backup },\n  }));\n}\n\n/**\n * Extract the set of enabled symbiont names from config.\n * Returns null when the `symbionts` section is absent (pre-existing installs),\n * signalling callers to fall back to their own heuristic.\n */\nexport function getEnabledSymbiontNames(config: MycoConfig): Set<string> | null {\n  if (!config.symbionts) return null;\n  return new Set(\n    Object.entries(config.symbionts)\n      .filter(([, entry]) => entry.enabled)\n      .map(([name]) => name),\n  );\n}\n\nexport function updateTeamConfig(\n  vaultDir: string,\n  team: Partial<TeamConfig>,\n): MycoConfig {\n  return updateConfig(vaultDir, (config) => ({\n    ...config,\n    team: { ...config.team, ...team },\n  }));\n}\n\n/** Return raw local overrides, or `{}` if the file is missing, empty, malformed, or not a mapping. */\nexport function loadLocalConfig(vaultDir: string): Partial<MycoConfig> {\n  const filePath = localConfigPath(vaultDir);\n  if (!fs.existsSync(filePath)) return {};\n  const raw = fs.readFileSync(filePath, 'utf-8').trim();\n  if (!raw) return {};\n\n  let parsed: unknown;\n  try {\n    parsed = YAML.parse(raw);\n  } catch (err) {\n    process.stderr.write(`[myco config] Failed to parse ${filePath}; ignoring local overrides. ${(err as Error).message}\\n`);\n    return {};\n  }\n\n  if (!parsed || typeof parsed !== 'object' || Array.isArray(parsed)) {\n    process.stderr.write(`[myco config] ${filePath} must contain a YAML mapping; ignoring local overrides.\\n`);\n    return {};\n  }\n\n  return parsed as Partial<MycoConfig>;\n}\n\n/** Load project config and overlay local overrides on top (leaf-level deep merge). */\nexport function loadMergedConfig(vaultDir: string): MycoConfig {\n  const project = loadConfig(vaultDir);\n  const local = loadLocalConfig(vaultDir);\n  const merged = deepMergeConfig(project as Record<string, unknown>, local as Record<string, unknown>);\n  return MycoConfigSchema.parse(merged);\n}\n\n/**\n * Write local.yaml only when the serialized contents differ from `current`.\n * Skips the write (and mkdirSync) on a no-op to avoid noisy file mtimes.\n */\nfunction writeLocalYamlIfChanged<T>(vaultDir: string, current: T, next: T): T {\n  const existingYaml = YAML.stringify(current);\n  const nextYaml = YAML.stringify(next);\n  if (existingYaml === nextYaml) return next;\n\n  fs.mkdirSync(vaultDir, { recursive: true });\n  fs.writeFileSync(localConfigPath(vaultDir), nextYaml, 'utf-8');\n  return next;\n}\n\n/** Write a partial to <vaultDir>/local.yaml, deep-merging with existing local content. */\nexport function saveLocalConfig(vaultDir: string, patch: Partial<MycoConfig>): Partial<MycoConfig> {\n  const existing = loadLocalConfig(vaultDir);\n  const next = deepMergeConfig(existing as Record<string, unknown>, patch as Record<string, unknown>) as Partial<MycoConfig>;\n  return writeLocalYamlIfChanged(vaultDir, existing, next);\n}\n\n/**\n * Callback-style update for local config. Replace-semantics: the value\n * returned by `fn` is written verbatim (so callers can remove keys by\n * omitting them). Callers that want merge-semantics should spread\n * `...local` inside their callback, or use `saveLocalConfig` directly.\n */\nexport function updateLocalConfig(\n  vaultDir: string,\n  fn: (local: Partial<MycoConfig>) => Partial<MycoConfig>,\n): Partial<MycoConfig> {\n  const current = loadLocalConfig(vaultDir);\n  return writeLocalYamlIfChanged(vaultDir, current, fn(current));\n}\n","/**\n * Appearance enum values shared between the Zod schema (server) and the UI.\n *\n * This file MUST stay free of Node built-ins and other server-only imports\n * so it can be consumed by browser code without pulling in the full schema\n * dependency graph.\n */\n\nexport const APPEARANCE_THEMES = ['sage', 'moss', 'terracotta', 'dusk', 'plum', 'slate'] as const;\nexport const APPEARANCE_MODES = ['light', 'dark', 'system'] as const;\nexport const APPEARANCE_FONTS = ['default', 'geist-mono', 'system', 'sf-mono', 'fira-code', 'jetbrains-mono'] as const;\nexport const APPEARANCE_DENSITIES = ['compact', 'normal', 'comfy'] as const;\n\nexport type AppearanceTheme = typeof APPEARANCE_THEMES[number];\nexport type AppearanceMode = typeof APPEARANCE_MODES[number];\nexport type AppearanceFont = typeof APPEARANCE_FONTS[number];\nexport type AppearanceDensity = typeof APPEARANCE_DENSITIES[number];\n\nexport interface AppearanceValues {\n  theme: AppearanceTheme;\n  mode: AppearanceMode;\n  font: AppearanceFont;\n  density: AppearanceDensity;\n}\n","import { z } from 'zod';\nimport { SCHEDULABLE_POWER_STATES } from '@myco/constants.js';\n\nconst EmbeddingProviderSchema = z.object({\n  provider: z.enum(['ollama', 'openai-compatible', 'openrouter', 'openai']).default('ollama'),\n  model: z.string().default('bge-m3'),\n  base_url: z.string().url().optional(),\n});\n\nconst DaemonSchema = z.object({\n  port: z.number().int().min(1024).max(65535).nullable().default(null),\n  log_level: z.enum(['debug', 'info', 'warn', 'error']).default('info'),\n  log_retention_days: z.number().int().min(1).max(365).default(30),\n  /**\n   * Time without new prompts before an active session is auto-completed (ms).\n   * Intelligence tasks (full-intelligence, skill-survey, etc.) only process\n   * settled sessions, so this threshold directly controls how fresh their\n   * inputs are. Defaults to 1 hour.\n   */\n  stale_session_threshold_ms: z.number().int().min(60_000).default(60 * 60 * 1000),\n});\n\nconst CaptureSchema = z.object({\n  transcript_paths: z.array(z.string()).default([]),\n  plan_dirs: z.array(z.string()).default([]),\n  ignore_plan_dirs_in_git: z.boolean().default(false),\n  artifact_extensions: z.array(z.string()).default(['.md']),\n  buffer_max_events: z.number().int().positive().default(500),\n});\n\n/** Provider config shape used in both task-level and phase-level overrides. */\nconst ProviderOverrideSchema = z.object({\n  type: z.enum(['anthropic', 'ollama', 'lmstudio']),\n  base_url: z.string().optional(),\n  model: z.string().optional(),\n  /** Context window size for local models (Ollama num_ctx, LM Studio context_length). */\n  context_length: z.number().int().positive().optional(),\n});\n\n/** Per-phase overrides within a task — keyed by phase name. */\nconst PhaseOverrideSchema = z.object({\n  provider: ProviderOverrideSchema.optional(),\n  model: z.string().optional(),\n  maxTurns: z.number().int().positive().optional(),\n});\n\n/** Per-task schedule override — partial, merges with YAML defaults. */\nconst ScheduleOverrideSchema = z.object({\n  enabled: z.boolean().optional(),\n  intervalSeconds: z.number().int().positive().optional(),\n  runIn: z.array(z.enum([...SCHEDULABLE_POWER_STATES])).optional(),\n  preCondition: z.enum(['has-unprocessed-batches', 'has-active-skills', 'has-approved-candidates']).optional(),\n}).optional();\n\n/** Per-task config override — stored in myco.yaml under agent.tasks. */\nconst TaskProviderOverrideSchema = z.object({\n  provider: ProviderOverrideSchema.optional(),\n  model: z.string().optional(),\n  maxTurns: z.number().int().positive().optional(),\n  timeoutSeconds: z.number().int().positive().optional(),\n  phases: z.record(z.string(), PhaseOverrideSchema).optional(),\n  schedule: ScheduleOverrideSchema,\n  /** Task-specific params — keys and types vary per task. */\n  params: z.record(z.string(), z.union([z.string(), z.number(), z.boolean()])).optional(),\n});\n\nconst ContextSchema = z.object({\n  /** Which digest tier to inject at session start. */\n  digest_tier: z.number().int().default(5000),\n  /** Enable semantic spore search on each user prompt. */\n  prompt_search: z.boolean().default(true),\n  /** Max spores to inject per prompt (0-10). */\n  prompt_max_spores: z.number().int().min(0).max(10).default(3),\n});\n\nconst AgentSchema = z.object({\n  /** Number of batches between event-driven summary triggers (0 to disable). */\n  summary_batch_interval: z.number().int().min(0).default(5),\n  /** Global toggle for PowerManager-scheduled agent tasks. */\n  scheduled_tasks_enabled: z.boolean().default(true),\n  /** Global toggle for event-driven agent tasks (title-summary). */\n  event_tasks_enabled: z.boolean().default(true),\n  /** Global default provider — applies to all tasks unless overridden per-task. */\n  provider: ProviderOverrideSchema.optional(),\n  /** Global default model — applies to all tasks unless overridden per-task. */\n  model: z.string().optional(),\n  /** Per-task overrides keyed by task name. */\n  tasks: z.record(z.string(), TaskProviderOverrideSchema).optional(),\n});\n\nconst BackupSchema = z.object({\n  /** Override directory for backup files. Supports ~ for home directory. When unset, defaults to .myco/backups. */\n  dir: z.string().optional(),\n});\n\nconst MaintenanceSchema = z.object({\n  /** Automatically run PRAGMA optimize on a schedule. */\n  auto_optimize: z.boolean().default(true),\n  /** How often to run auto-optimize, in hours (1–720). */\n  auto_optimize_interval_hours: z.number().int().min(1).max(720).default(24),\n});\n\nconst TeamSchema = z.object({\n  /** Whether team sync is enabled. */\n  enabled: z.boolean().default(false),\n  /** Cloudflare Worker URL for team sync. */\n  worker_url: z.string().url().optional(),\n  /** Team identifier for sync grouping. */\n  team_id: z.string().optional(),\n  /** Sync interval in minutes. */\n  interval_minutes: z.number().int().min(1).max(1440).default(15),\n});\n\nconst SkillsSchema = z.object({\n  /** Auto-generate candidates above this confidence score. */\n  confidence_threshold: z.number().min(0).max(1).default(0.7),\n  /** Flag unused skills after this many days. */\n  usage_stale_days: z.number().int().positive().default(30),\n});\n\nconst NotificationsSchema = z.object({\n  /** Master switch — disables all notifications when false. */\n  enabled: z.boolean().default(true),\n  /** Allow browser system notifications (Notification API). */\n  system_notifications: z.boolean().default(false),\n  /** Default display mode for new notification types. */\n  default_mode: z.enum(['banner', 'summary']).default('summary'),\n  /** Per-domain settings. Keys are domain names from the registry. */\n  domains: z.record(z.string(), z.object({\n    enabled: z.boolean().default(true),\n    /** Override display mode for this domain. Omit to use global default_mode. */\n    mode: z.enum(['banner', 'summary']).optional(),\n  })).default({}),\n});\n\nconst SymbiontEntrySchema = z.object({\n  enabled: z.boolean().default(true),\n});\n\nexport {\n  APPEARANCE_THEMES,\n  APPEARANCE_MODES,\n  APPEARANCE_FONTS,\n  APPEARANCE_DENSITIES,\n  type AppearanceValues,\n} from './appearance-values.js';\n\nimport {\n  APPEARANCE_THEMES,\n  APPEARANCE_MODES,\n  APPEARANCE_FONTS,\n  APPEARANCE_DENSITIES,\n} from './appearance-values.js';\n\nexport const AppearanceConfigSchema = z.object({\n  theme: z.enum(APPEARANCE_THEMES).default('sage'),\n  mode: z.enum(APPEARANCE_MODES).default('dark'),\n  font: z.enum(APPEARANCE_FONTS).default('default'),\n  density: z.enum(APPEARANCE_DENSITIES).default('normal'),\n}).default({ theme: 'sage', mode: 'dark', font: 'default', density: 'normal' });\n\nexport type AppearanceConfig = z.infer<typeof AppearanceConfigSchema>;\n\nexport const MycoConfigSchema = z.preprocess(\n  (raw: unknown) => {\n    if (raw && typeof raw === 'object' && 'curation' in raw && !('agent' in raw)) {\n      const { curation, ...rest } = raw as Record<string, unknown>;\n      return { ...rest, agent: curation };\n    }\n    return raw;\n  },\n  z.object({\n    version: z.literal(3),\n    config_version: z.number().int().nonnegative().default(0),\n    embedding: EmbeddingProviderSchema.default(() => EmbeddingProviderSchema.parse({})),\n    daemon: DaemonSchema.default(() => DaemonSchema.parse({})),\n    capture: CaptureSchema.default(() => CaptureSchema.parse({})),\n    agent: AgentSchema.default(() => AgentSchema.parse({})),\n    context: ContextSchema.default(() => ContextSchema.parse({})),\n    backup: BackupSchema.default(() => BackupSchema.parse({})),\n    maintenance: MaintenanceSchema.default(() => MaintenanceSchema.parse({})),\n    team: TeamSchema.default(() => TeamSchema.parse({})),\n    skills: SkillsSchema.default(() => SkillsSchema.parse({})),\n    notifications: NotificationsSchema.default(() => NotificationsSchema.parse({})),\n    appearance: AppearanceConfigSchema,\n    symbionts: z.record(z.string(), SymbiontEntrySchema).optional(),\n  }),\n);\n\nexport type MycoConfig = z.output<typeof MycoConfigSchema>;\nexport type EmbeddingProviderConfig = z.infer<typeof EmbeddingProviderSchema>;\nexport type TaskProviderOverride = z.infer<typeof TaskProviderOverrideSchema>;\nexport type PhaseOverride = z.infer<typeof PhaseOverrideSchema>;\nexport type ScheduleOverride = z.infer<typeof ScheduleOverrideSchema>;\nexport type ContextConfig = z.infer<typeof ContextSchema>;\nexport type BackupConfig = z.infer<typeof BackupSchema>;\nexport type TeamConfig = z.infer<typeof TeamSchema>;\nexport type SkillsConfig = z.infer<typeof SkillsSchema>;\nexport type NotificationsConfig = z.infer<typeof NotificationsSchema>;\nexport type SymbiontEntry = z.infer<typeof SymbiontEntrySchema>;\n","/**\n * Config and vault migrations — run once per version, tracked by config_version.\n *\n * Each migration has a version number, a name, and a function that receives\n * the raw parsed YAML doc and the vault directory. Migrations run in order\n * and are skipped if config_version is already past them.\n *\n * To add a new migration:\n * 1. Add an entry to MIGRATIONS with the next version number\n * 2. Write the migrate function — it receives the mutable doc and vaultDir\n * 3. The framework handles version tracking and writing the config back\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\n\nexport interface Migration {\n  version: number;\n  name: string;\n  migrate: (doc: Record<string, unknown>, vaultDir: string) => void;\n}\n\n/** Regex matching both quoted and unquoted YAML: type: memory, type: \"memory\", type: 'memory' */\nconst MEMORY_TYPE_PATTERN = /type:\\s*[\"']?memory[\"']?/g;\n\nexport const MIGRATIONS: Migration[] = [\n  {\n    version: 1,\n    name: 'rename-memories-to-spores',\n    migrate: (doc, vaultDir) => {\n      // Config: rename context.layers.memories → context.layers.spores\n      const context = doc.context as Record<string, unknown> | undefined;\n      const layers = context?.layers as Record<string, unknown> | undefined;\n      if (layers && 'memories' in layers && !('spores' in layers)) {\n        layers.spores = layers.memories;\n        delete layers.memories;\n      }\n\n      // Vault: rename memories/ directory → spores/\n      const memoriesDir = path.join(vaultDir, 'memories');\n      const sporesDir = path.join(vaultDir, 'spores');\n\n      if (!fs.existsSync(memoriesDir)) return;\n\n      if (fs.existsSync(sporesDir)) {\n        // Both exist (interrupted migration) — merge remaining files\n        const moveRemaining = (srcDir: string, destDir: string): void => {\n          for (const entry of fs.readdirSync(srcDir, { withFileTypes: true })) {\n            const srcPath = path.join(srcDir, entry.name);\n            const destPath = path.join(destDir, entry.name);\n            if (entry.isDirectory()) {\n              if (!fs.existsSync(destPath)) fs.mkdirSync(destPath, { recursive: true });\n              moveRemaining(srcPath, destPath);\n            } else if (!fs.existsSync(destPath)) {\n              fs.renameSync(srcPath, destPath);\n            }\n          }\n        };\n        moveRemaining(memoriesDir, sporesDir);\n        fs.rmSync(memoriesDir, { recursive: true, force: true });\n      } else {\n        fs.renameSync(memoriesDir, sporesDir);\n      }\n\n      // Update frontmatter type: memory → type: spore (handles quoted and unquoted)\n      const walkUpdate = (dir: string): void => {\n        for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {\n          const fullPath = path.join(dir, entry.name);\n          if (entry.isDirectory()) { walkUpdate(fullPath); continue; }\n          if (!entry.name.endsWith('.md')) continue;\n          const content = fs.readFileSync(fullPath, 'utf-8');\n          MEMORY_TYPE_PATTERN.lastIndex = 0;\n          if (MEMORY_TYPE_PATTERN.test(content)) {\n            MEMORY_TYPE_PATTERN.lastIndex = 0;\n            fs.writeFileSync(fullPath, content.replace(MEMORY_TYPE_PATTERN, 'type: spore'));\n          }\n        }\n      };\n      walkUpdate(sporesDir);\n\n      // Legacy: update wikilink references in Markdown files (pre-SQLite migration): [[memories/...]] → [[spores/...]]\n      const walkLinks = (dir: string): void => {\n        for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {\n          const fullPath = path.join(dir, entry.name);\n          if (entry.isDirectory()) { walkLinks(fullPath); continue; }\n          if (!entry.name.endsWith('.md')) continue;\n          const content = fs.readFileSync(fullPath, 'utf-8');\n          if (content.includes('memories/')) {\n            fs.writeFileSync(fullPath, content.replace(/memories\\//g, 'spores/'));\n          }\n        }\n      };\n      walkLinks(vaultDir);\n    },\n  },\n  {\n    version: 2,\n    name: 'consolidation-boolean-to-object',\n    migrate: (doc) => {\n      const digest = doc.digest as Record<string, unknown> | undefined;\n      if (!digest) return;\n\n      const consolidation = digest.consolidation;\n      if (typeof consolidation === 'boolean') {\n        digest.consolidation = { enabled: consolidation, max_tokens: 2048 };\n      }\n    },\n  },\n  {\n    version: 3,\n    name: 'schedule-to-task-level',\n    migrate(doc: Record<string, unknown>, _vaultDir: string): void {\n      const agent = (doc.agent ?? {}) as Record<string, unknown>;\n      const skills = (doc.skills ?? {}) as Record<string, unknown>;\n      const tasks = ((agent.tasks ?? {}) as Record<string, Record<string, unknown>>);\n\n      /** Default interval for full-intelligence task (5 minutes). */\n      const DEFAULT_INTELLIGENCE_INTERVAL_SECONDS = 300;\n\n      const VALID_SCHEDULE_STATES = ['active', 'idle', 'sleep'] as const;\n\n      // Migrate agent.auto_run + interval_seconds → full-intelligence schedule\n      if ('auto_run' in agent || 'interval_seconds' in agent) {\n        const fiTask = tasks['full-intelligence'] ?? {};\n        fiTask.schedule = {\n          enabled: agent.auto_run ?? true,\n          intervalSeconds: agent.interval_seconds ?? DEFAULT_INTELLIGENCE_INTERVAL_SECONDS,\n        };\n        tasks['full-intelligence'] = fiTask;\n        delete agent.auto_run;\n        delete agent.interval_seconds;\n      }\n\n      // Migrate skills.auto_survey → skill-survey schedule\n      if ('auto_survey' in skills) {\n        const ssTask = tasks['skill-survey'] ?? {};\n        ssTask.schedule = {\n          enabled: skills.auto_survey ?? false,\n        };\n        tasks['skill-survey'] = ssTask;\n        delete skills.auto_survey;\n      }\n\n      // Migrate skills.auto_evolve + evolve_cadence → skill-evolve schedule\n      if ('auto_evolve' in skills || 'evolve_cadence' in skills) {\n        const seTask = tasks['skill-evolve'] ?? {};\n        const schedule: Record<string, unknown> = {\n          enabled: skills.auto_evolve ?? false,\n        };\n        if ('evolve_cadence' in skills) {\n          const cadence = String(skills.evolve_cadence);\n          schedule.runIn = VALID_SCHEDULE_STATES.includes(cadence as typeof VALID_SCHEDULE_STATES[number])\n            ? [cadence]\n            : ['idle']; // fallback to safe default\n        }\n        seTask.schedule = schedule;\n        tasks['skill-evolve'] = seTask;\n        delete skills.auto_evolve;\n        delete skills.evolve_cadence;\n      }\n\n      // Write back tasks if any were created\n      if (Object.keys(tasks).length > 0) {\n        agent.tasks = tasks;\n      }\n      doc.agent = agent;\n      doc.skills = skills;\n    },\n  },\n  {\n    version: 4,\n    name: 'rename-cloud-provider-to-anthropic',\n    migrate(doc: Record<string, unknown>, _vaultDir: string): void {\n      // Rename `provider.type: cloud` -> `provider.type: anthropic` everywhere\n      // it appears in the agent config: global default, per-task, per-phase.\n      const renameProvider = (provider: unknown): void => {\n        if (\n          provider &&\n          typeof provider === 'object' &&\n          (provider as Record<string, unknown>).type === 'cloud'\n        ) {\n          (provider as Record<string, unknown>).type = 'anthropic';\n        }\n      };\n\n      const agent = doc.agent as Record<string, unknown> | undefined;\n      if (!agent) return;\n\n      // Global default provider\n      renameProvider(agent.provider);\n\n      // Per-task overrides\n      const tasks = agent.tasks as Record<string, Record<string, unknown>> | undefined;\n      if (tasks) {\n        for (const taskConfig of Object.values(tasks)) {\n          renameProvider(taskConfig.provider);\n\n          // Per-phase overrides within a task\n          const phases = taskConfig.phases as Record<string, Record<string, unknown>> | undefined;\n          if (phases) {\n            for (const phaseConfig of Object.values(phases)) {\n              renameProvider(phaseConfig.provider);\n            }\n          }\n        }\n      }\n    },\n  },\n  {\n    version: 5,\n    name: 'seed-settings-notification-domain-default',\n    migrate(doc: Record<string, unknown>, _vaultDir: string): void {\n      const notifications = (doc.notifications ??= {}) as Record<string, unknown>;\n      const domains = (notifications.domains ??= {}) as Record<string, unknown>;\n      const settings = (domains.settings ??= {}) as Record<string, unknown>;\n\n      if (!('enabled' in settings)) settings.enabled = true;\n      if (!('mode' in settings)) settings.mode = 'banner';\n    },\n  },\n];\n\n/** Current migration version — the highest version in MIGRATIONS. */\nexport const CURRENT_MIGRATION_VERSION = MIGRATIONS[MIGRATIONS.length - 1]?.version ?? 0;\n\n/**\n * Run all pending migrations on the raw config doc.\n * Returns true if any migrations ran (caller should reindex).\n */\nexport function runMigrations(\n  doc: Record<string, unknown>,\n  vaultDir: string,\n  log?: (message: string) => void,\n): boolean {\n  const currentVersion = (doc.config_version as number) ?? 0;\n  let ran = false;\n\n  for (const migration of MIGRATIONS) {\n    if (migration.version <= currentVersion) continue;\n\n    migration.migrate(doc, vaultDir);\n    doc.config_version = migration.version;\n    ran = true;\n  }\n\n  if (ran) {\n    const from = currentVersion;\n    const to = (doc.config_version as number) ?? 0;\n    log?.(`Migrated config from v${from} to v${to}`);\n  }\n\n  return ran;\n}\n","export interface DeepMergeOptions {\n  /** How to reconcile arrays found at the same key in both target and source. */\n  arrayStrategy: 'replace' | 'union';\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 * Deep-merge source into target at the leaf.\n *\n * - `arrayStrategy: 'replace'` — arrays in source overwrite arrays in target (config overlay semantics).\n * - `arrayStrategy: 'union'` — arrays are concatenated and deduplicated (symbiont settings merge semantics).\n *\n * Non-object, non-array leaves: source overwrites target.\n * `undefined` values in source are skipped (target value preserved).\n */\nexport function deepMerge<T extends Record<string, unknown>>(\n  target: T,\n  source: Partial<T>,\n  options: DeepMergeOptions,\n): T {\n  const result: Record<string, unknown> = { ...target };\n  for (const [key, value] of Object.entries(source)) {\n    if (value === undefined) continue;\n    const existing = result[key];\n    if (Array.isArray(value) && Array.isArray(existing)) {\n      result[key] = options.arrayStrategy === 'union'\n        ? 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package/dist/chunk-US4LNCAT.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/config/updates.ts"],"sourcesContent":["import type { MycoConfig, EmbeddingProviderConfig, ContextConfig, TaskProviderOverride, PhaseOverride } from './schema.js';\nimport { setAtPath } from '../utils/dot-path.js';\n\n/**\n * Set a value at a dot-separated path, returning a new config object.\n * Creates intermediate objects along the path as needed.\n */\nexport function withValue(config: MycoConfig, dotPath: string, value: unknown): MycoConfig {\n  const clone = structuredClone(config) as MycoConfig & Record<string, unknown>;\n  setAtPath(clone, dotPath, value);\n  return clone as MycoConfig;\n}\n\n/** Provider override shape used in task config updates. Null means delete. */\ninterface ProviderInput {\n  type: 'anthropic' | 'ollama' | 'lmstudio';\n  model?: string;\n  base_url?: string;\n  context_length?: number;\n}\n\n/** Phase override input. Null fields mean delete. */\ninterface PhaseInput {\n  provider?: ProviderInput | null;\n  model?: string | null;\n  maxTurns?: number | null;\n}\n\n/** Input shape for task config updates. Null values mean \"delete this field\". */\nexport interface TaskConfigUpdate {\n  provider?: ProviderInput | null;\n  model?: string | null;\n  maxTurns?: number | null;\n  timeoutSeconds?: number | null;\n  phases?: Record<string, PhaseInput | null> | null;\n  schedule?: { enabled?: boolean; intervalSeconds?: number; runIn?: ('active' | 'idle' | 'sleep')[] } | null;\n}\n\n/**\n * Apply partial task config updates, returning a new config object.\n * Null values delete fields. 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package/dist/cli-UWBAOHLL.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/cli.ts"],"sourcesContent":["#!/usr/bin/env node\nimport { loadEnv } from './cli/shared.js';\nimport { resolveVaultDir } from './vault/resolve.js';\nimport fs from 'node:fs';\nimport path from 'node:path';\n\nloadEnv();\n\nconst USAGE = `Usage: myco <command> [args]\n\nCommands:\n  init [options]           Initialize a new vault\n  update                   Update vault files and agent registration\n  remove [--remove-vault]    Remove Myco from this project (vault preserved by default)\n  remove --symbiont <name>   Unregister a single agent and remove from config\n  config <get|set> [args]  Get or set vault config values\n  detect-providers         Detect available LLM/embedding providers (JSON)\n  verify                   Test LLM and embedding connectivity\n  stats                    Vault health, index counts, vector count\n  search <query>           Combined FTS + vector search with scores\n  vectors <query>          Raw vector search with similarity scores\n  session [id|latest]      Show a session\n  logs [options]           View daemon logs\n  setup-llm [options]      Configure LLM and embedding providers\n  setup-digest [options]   Configure digest and capture settings\n  agent [options]          Run the intelligence agent\n  task <subcommand>        Manage agent task definitions\n  team <init|upgrade>      Provision or upgrade team sync infrastructure\n  doctor [--fix]          Check vault health and repair issues\n  open                     Open the dashboard in your browser\n  restart                  Restart the daemon\n  version                  Show plugin version\n  mcp                     Start the MCP stdio server\n  hook <name>             Run a hook (session-start, session-end, stop, user-prompt-submit, post-tool-use, post-tool-use-failure, subagent-start, subagent-stop, stop-failure, task-completed, pre-compact, post-compact)\n  daemon --vault <dir>    Start the daemon process\n`;\n\nasync function main(): Promise<void> {\n  const [cmd, ...args] = process.argv.slice(2);\n  if (!cmd || cmd === '--help' || cmd === '-h') {\n    process.stdout.write(USAGE);\n    return;\n  }\n\n  if (cmd === 'init') return (await import('./cli/init.js')).run(args);\n  if (cmd === 'detect-providers') return (await import('./cli/detect-providers.js')).run(args);\n  if (cmd === 'version' || cmd === '--version' || cmd === '-v') {\n    const { getPluginVersion } = await import('./version.js');\n    console.log(getPluginVersion());\n    return;\n  }\n  if (cmd === 'mcp') return (await import('./mcp/server.js')).main();\n  if (cmd === 'hook') {\n    const hookName = args[0];\n    const HOOK_DISPATCH: Record<string, () => Promise<{ main: () => Promise<void> }>> = {\n      'session-start': () => import('./hooks/session-start.js'),\n      'session-end': () => import('./hooks/session-end.js'),\n      'stop': () => import('./hooks/stop.js'),\n      'user-prompt-submit': () => import('./hooks/user-prompt-submit.js'),\n      'post-tool-use': () => import('./hooks/post-tool-use.js'),\n      'post-tool-use-failure': () => import('./hooks/post-tool-use-failure.js'),\n      'subagent-start': () => import('./hooks/subagent-start.js'),\n      'subagent-stop': () => import('./hooks/subagent-stop.js'),\n      'stop-failure': () => import('./hooks/stop-failure.js'),\n      'task-completed': () => import('./hooks/task-completed.js'),\n      'pre-compact': () => import('./hooks/pre-compact.js'),\n      'post-compact': () => import('./hooks/post-compact.js'),\n    };\n    const loader = HOOK_DISPATCH[hookName];\n    if (!loader) {\n      console.error(`Unknown hook: ${hookName}. 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package/dist/doctor-UUUOVDZS.js.map

@@ -1 +0,0 @@
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With --fix, attempts to repair issues it can handle automatically.\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport { isProcessAlive } from './shared.js';\nimport { MYCO_MCP_SERVER_NAME } from '../symbionts/installer.js';\n\n// --- Named constants (no magic literals) ---\n\n\n/** Filename of the vault config file. */\nconst CONFIG_FILENAME = 'myco.yaml';\n\n/** Filename of the daemon state file. */\nconst DAEMON_STATE_FILENAME = 'daemon.json';\n\n/** Filename of the SQLite database. */\nconst DB_FILENAME = 'myco.db';\n\n/** Column width for the check name in output. */\nconst NAME_COL_WIDTH = 17;\n\n/** Prefix for indented continuation lines (e.g. multi-line agent output). */\nconst CONTINUATION_INDENT = ' '.repeat(NAME_COL_WIDTH);\n\n// --- Types ---\n\nexport interface DoctorCheck {\n  name: string;\n  status: 'ok' | 'fail' | 'warn';\n  detail: string;\n  fixable: boolean;\n}\n\n// --- Checks ---\n\n/** Check that myco.yaml exists and parses. Returns the parsed config on success. */\nasync function checkVault(vaultDir: string): Promise<{ check: DoctorCheck; config: import('../config/schema.js').MycoConfig | null }> {\n  const configPath = path.join(vaultDir, CONFIG_FILENAME);\n  if (!fs.existsSync(configPath)) {\n    return { check: { name: 'Vault', status: 'fail', detail: `${CONFIG_FILENAME} not found in ${vaultDir}`, fixable: false }, config: null };\n  }\n  try {\n    const { loadMergedConfig } = await import('../config/loader.js');\n    const config = loadMergedConfig(vaultDir);\n    return { check: { name: 'Vault', status: 'ok', detail: `.myco/ (v${config.version})`, fixable: false }, config };\n  } catch (err) {\n    return { check: { name: 'Vault', status: 'fail', detail: `${CONFIG_FILENAME} parse error: ${(err as Error).message}`, fixable: false }, config: null };\n  }\n}\n\n/** Check that the SQLite database exists and can be queried. */\nasync function checkDatabase(vaultDir: string): Promise<DoctorCheck> {\n  const dbPath = path.join(vaultDir, DB_FILENAME);\n  if (!fs.existsSync(dbPath)) {\n    return { name: 'Database', status: 'fail', detail: `${DB_FILENAME} not found — run \\`myco init\\``, fixable: false };\n  }\n  try {\n    const { initDatabase, closeDatabase, vaultDbPath } = await import('../db/client.js');\n    const db = initDatabase(vaultDbPath(vaultDir));\n    const row = db.prepare('SELECT count(*) AS cnt FROM sessions').get() as { cnt: number } | undefined;\n    const count = row?.cnt ?? 0;\n    closeDatabase();\n    return { name: 'Database', status: 'ok', detail: `${DB_FILENAME} (${count.toLocaleString()} sessions)`, fixable: false };\n  } catch (err) {\n    // Ensure DB is closed even on error\n    try { const { closeDatabase } = await import('../db/client.js'); closeDatabase(); } catch { /* ignore */ }\n    return { name: 'Database', status: 'fail', detail: `Database error: ${(err as Error).message}`, fixable: false };\n  }\n}\n\n/** Check that the intelligence (agent) provider is configured. */\nasync function checkIntelligence(config: import('../config/schema.js').MycoConfig): Promise<DoctorCheck> {\n  try {\n    const provider = config.agent.provider;\n\n    if (!provider) {\n      return { name: 'Intelligence', status: 'warn', detail: 'No agent provider configured — run `myco init` to set up', fixable: false };\n    }\n\n    const label = `${provider.type}${provider.model ? ` / ${provider.model}` : ''}`;\n\n    if (provider.type === 'anthropic') {\n      return { name: 'Intelligence', status: 'ok', detail: `${label} (SDK handles auth)`, fixable: false };\n    }\n\n    // Local provider — check reachability\n    if (provider.type === 'ollama' || provider.type === 'lmstudio') {\n      const { checkLocalProvider } = await import('../intelligence/provider-check.js');\n      const status = await checkLocalProvider(provider.type, provider.base_url);\n      if (!status.available) {\n        return { name: 'Intelligence', status: 'warn', detail: `${label} (not reachable)`, fixable: false };\n      }\n      return { name: 'Intelligence', status: 'ok', detail: label, fixable: false };\n    }\n\n    return { name: 'Intelligence', status: 'ok', detail: label, fixable: false };\n  } catch (err) {\n    return { name: 'Intelligence', status: 'fail', detail: `Intelligence check failed: ${(err as Error).message}`, fixable: false };\n  }\n}\n\n/** Check that the embedding provider is configured and reachable. */\nasync function checkEmbeddings(config: import('../config/schema.js').MycoConfig): Promise<DoctorCheck> {\n  try {\n    const { createEmbeddingProvider } = await import('../intelligence/llm.js');\n    const provider = createEmbeddingProvider(config.embedding);\n    const available = await provider.isAvailable();\n    const label = `${config.embedding.provider} / ${config.embedding.model}`;\n    if (available) {\n      return { name: 'Embeddings', status: 'ok', detail: label, fixable: false };\n    }\n    return { name: 'Embeddings', status: 'warn', detail: `${label} (not reachable)`, fixable: false };\n  } catch (err) {\n    return { name: 'Embeddings', status: 'fail', detail: `Embedding check failed: ${(err as Error).message}`, fixable: false };\n  }\n}\n\n/** Check symbiont detection and registration status. */\nasync function checkAgents(vaultDir: string, config: import('../config/schema.js').MycoConfig | null): Promise<DoctorCheck[]> {\n  try {\n    const { detectSymbionts } = await import('../symbionts/detect.js');\n    const { getEnabledSymbiontNames } = await import('../config/loader.js');\n    const projectRoot = path.dirname(vaultDir);\n    const detected = detectSymbionts(projectRoot);\n\n    const enabledNames = config ? getEnabledSymbiontNames(config) : null;\n\n    if (detected.length === 0 && !enabledNames) {\n      return [{ name: 'Agents', status: 'warn', detail: 'No symbionts detected', fixable: false }];\n    }\n\n    const checks: DoctorCheck[] = [];\n    for (const d of detected) {\n      const registered = isSymbiontRegistered(d, projectRoot);\n      const enabled = enabledNames ? enabledNames.has(d.manifest.name) : registered;\n\n      if (enabled && registered) {\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'ok',\n          detail: `${d.manifest.displayName} (enabled, registered)`,\n          fixable: false,\n        });\n      } else if (enabled && !registered) {\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'warn',\n          detail: `${d.manifest.displayName} (enabled but not registered — run \\`myco update\\`)`,\n          fixable: false,\n        });\n      } else if (!enabled && registered) {\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'warn',\n          detail: `${d.manifest.displayName} (registered but not enabled — run \\`myco remove --symbiont ${d.manifest.name}\\`)`,\n          fixable: false,\n        });\n      } else {\n        // Detected but neither enabled nor registered\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'ok',\n          detail: `${d.manifest.displayName} (detected, not enabled)`,\n          fixable: false,\n        });\n      }\n    }\n\n    if (checks.length === 0) {\n      return [{ name: 'Agents', status: 'warn', detail: 'No symbionts detected or enabled', fixable: false }];\n    }\n\n    return checks;\n  } catch (err) {\n    return [{ name: 'Agents', status: 'fail', detail: `Agent check failed: ${(err as Error).message}`, fixable: false }];\n  }\n}\n\n/** Check if a symbiont has the Myco MCP server registered. */\nfunction isSymbiontRegistered(\n  d: import('../symbionts/detect.js').DetectedSymbiont,\n  projectRoot: string,\n): boolean {\n  try {\n    const mcpTarget = d.manifest.registration?.mcpTarget;\n    if (!mcpTarget) return false;\n\n    const mcpFile = path.join(projectRoot, mcpTarget);\n    const raw = fs.readFileSync(mcpFile, 'utf-8');\n\n    // TOML: check for section header\n    if (mcpTarget.endsWith('.toml')) {\n      return raw.includes(`[mcp_servers.${MYCO_MCP_SERVER_NAME}]`);\n    }\n\n    // JSON: check for server entry under the configured key (defaults to 'mcpServers').\n    // opencode uses 'mcp' — without the manifest lookup, doctor reports opencode as\n    // unregistered even after a successful install.\n    const config = JSON.parse(raw) as Record<string, unknown>;\n    const serversKey = d.manifest.registration?.mcpServersKey ?? 'mcpServers';\n    const servers = config[serversKey] as Record<string, unknown> | undefined;\n    return !!servers?.[MYCO_MCP_SERVER_NAME];\n  } catch { /* config missing or malformed */ }\n  return false;\n}\n\n/** Check the daemon state file and process liveness. */\nasync function checkDaemon(vaultDir: string): Promise<DoctorCheck> {\n  const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);\n  if (!fs.existsSync(daemonFile)) {\n    return { name: 'Daemon', status: 'warn', detail: 'Not running (no daemon.json)', fixable: false };\n  }\n  try {\n    const state = JSON.parse(fs.readFileSync(daemonFile, 'utf-8')) as { pid?: number; port?: number };\n    if (!state.pid) {\n      return { name: 'Daemon', status: 'warn', detail: 'daemon.json exists but no PID', fixable: true };\n    }\n    if (isProcessAlive(state.pid)) {\n      return { name: 'Daemon', status: 'ok', detail: `PID ${state.pid}, port ${state.port ?? 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Returns descriptions of actions taken. */\nexport async function fix(vaultDir: string, checks: DoctorCheck[]): Promise<string[]> {\n  const actions: string[] = [];\n\n  for (const check of checks) {\n    if (!check.fixable || check.status === 'ok') continue;\n\n    // Fix stale daemon.json\n    if (check.name === 'Daemon' && check.detail.includes('Stale')) {\n      const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);\n      fs.unlinkSync(daemonFile);\n      actions.push('Removed stale daemon.json');\n    }\n\n    // Fix malformed daemon.json\n    if (check.name === 'Daemon' && check.detail.includes('parse error')) {\n      const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);\n      fs.unlinkSync(daemonFile);\n      actions.push('Removed malformed daemon.json');\n    }\n\n    // Advise on database issues\n    if (check.name === 'Database' && check.status === 'fail') {\n      actions.push('Run `myco init` to initialize the database');\n    }\n  }\n\n  return actions;\n}\n\n// --- Output formatting ---\n\n/** Status label width (visible characters). */\nconst STATUS_COL_WIDTH = 6;\n\nconst STATUS_LABELS: Record<DoctorCheck['status'], { text: string; color: string }> = {\n  ok: { text: 'ok', color: '\\x1b[32m' },\n  fail: { text: 'FAIL', color: '\\x1b[31m' },\n  warn: { text: '!!', color: '\\x1b[33m' },\n};\n\nfunction formatCheck(check: DoctorCheck): string {\n  const name = check.name ? check.name.padEnd(NAME_COL_WIDTH) : CONTINUATION_INDENT;\n  const { text, color } = STATUS_LABELS[check.status];\n  const paddedText = text.padEnd(STATUS_COL_WIDTH);\n  return `  ${name}${color}${paddedText}\\x1b[0m${check.detail}`;\n}\n\n// --- CLI entry point ---\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const shouldFix = args.includes('--fix');\n\n  console.log('\\nmyco doctor\\n');\n\n  const checks = await runChecks(vaultDir);\n\n  for (const check of checks) {\n    console.log(formatCheck(check));\n  }\n\n  const issues = checks.filter(c => c.status !== 'ok');\n  const fixable = issues.filter(c => c.fixable);\n\n  console.log('');\n\n  if (issues.length === 0) {\n    console.log('  All checks passed.\\n');\n    return;\n  }\n\n  console.log(`  ${issues.length} issue(s) found.`);\n\n  if (shouldFix) {\n    const actions = await fix(vaultDir, checks);\n    if (actions.length > 0) {\n      console.log('');\n      for (const action of actions) {\n        console.log(`  Fixed: ${action}`);\n      }\n      console.log('');\n    } else {\n      console.log('  No auto-fixable issues.\\n');\n    }\n  } else if (fixable.length > 0) {\n    console.log(`  Run \\`myco doctor --fix\\` to repair ${fixable.length} fixable issue(s).\\n`);\n  } else {\n    console.log('');\n  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