@goondocks/myco 0.17.2 → 0.18.1

package/dist/{chunk-CTF7TQMJ.js → chunk-TLK46KKD.js}

@@ -1,11 +1,11 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   SymbiontInstaller
-} from "./chunk-VVGZL2HX.js";
+} from "./chunk-WYOE4IAX.js";
 import {
   LmStudioBackend,
   OllamaBackend
-} from "./chunk-ML6GTPZU.js";
+} from "./chunk-CML4MCYF.js";
 import {
   closeDatabase,
   initDatabase,
@@ -13,7 +13,7 @@ import {
 } from "./chunk-MYX5NCRH.js";
 import {
   DaemonClient
-} from "./chunk-XZWFMMJR.js";
+} from "./chunk-XWOQL4XN.js";
 
 // src/cli/shared.ts
 import fs from "fs";
@@ -69,11 +69,21 @@ secrets.env
 # Machine ID
 machine_id
 
+# Update tracking \u2014 per-machine state
+last-update-version
+restart-reason.json
+
 # Binary attachments \u2014 screenshots captured from transcripts
 attachments/
 
 # Team worker deployment \u2014 patched wrangler.toml + source copy
 .team-worker/
+
+# Runtime command alias \u2014 per-contributor override for which myco binary
+# the hook guard invokes. Default (file absent) is \`myco\`; \`make dev-link\`
+# writes \`myco-dev\`; users can hand-edit for PATH conflicts or pinning.
+# Never committed \u2014 different contributors use different aliases.
+runtime.command
 `;
 function registerSymbionts(manifests, projectRoot, packageRoot, verb) {
   let count = 0;
@@ -110,4 +120,4 @@ export {
   VAULT_GITIGNORE,
   registerSymbionts
 };
-//# sourceMappingURL=chunk-CTF7TQMJ.js.map
+//# sourceMappingURL=chunk-TLK46KKD.js.map

package/dist/chunk-TLK46KKD.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/shared.ts"],"sourcesContent":["import fs from 'node:fs';\nimport path from 'node:path';\nimport os from 'node:os';\nimport { OllamaBackend } from '../intelligence/ollama.js';\nimport { LmStudioBackend } from '../intelligence/lm-studio.js';\n\nimport { DaemonClient } from '../hooks/client.js';\nimport { initDatabase, closeDatabase, vaultDbPath } from '../db/client.js';\nimport { SymbiontInstaller } from '../symbionts/installer.js';\nimport type { SymbiontManifest } from '../symbionts/manifest-schema.js';\n\nexport { parseStringFlag, parseIntFlag } from '../logs/format.js';\n\n/**\n * Initialize the singleton database for direct CLI reads.\n * Used by CLI commands that only need reads (stats, search, session).\n * Does NOT require the daemon to be running — WAL mode allows concurrent reads.\n *\n * @returns a cleanup function that closes the database.\n */\nexport function initVaultDb(vaultDir: string): () => void {\n  initDatabase(vaultDbPath(vaultDir));\n  return closeDatabase;\n}\n\n/** Connect to the daemon, ensuring it's running. Exits on failure. */\nexport async function connectToDaemon(vaultDir: string): Promise<DaemonClient> {\n  const client = new DaemonClient(vaultDir);\n  const healthy = await client.ensureRunning();\n  if (!healthy) {\n    console.error('Failed to connect to daemon');\n    process.exit(1);\n  }\n  return client;\n}\n\n/** Load .env from cwd (not script location — that's the plugin install dir). */\nexport function loadEnv(): void {\n  const envPath = path.resolve(process.cwd(), '.env');\n  if (!fs.existsSync(envPath)) return;\n  for (const line of fs.readFileSync(envPath, 'utf-8').split('\\n')) {\n    const match = line.match(/^\\s*([^#=]+?)\\s*=\\s*(.*?)\\s*$/);\n    if (match && !process.env[match[1]]) {\n      process.env[match[1]] = match[2];\n    }\n  }\n}\n\nexport function isProcessAlive(pid: number): boolean {\n  try { process.kill(pid, 0); return true; } catch { return false; }\n}\n\n// --- Provider defaults (sourced from backend classes) ---\nexport const PROVIDER_DEFAULTS: Record<string, { base_url: string }> = {\n  ollama: { base_url: OllamaBackend.DEFAULT_BASE_URL },\n  'lm-studio': { base_url: LmStudioBackend.DEFAULT_BASE_URL },\n};\n\n\nexport const VAULT_GITIGNORE = `# SQLite database\nmyco.db*\nvectors.db*\n\n# Daemon state — per-machine, ephemeral\ndaemon.json\nbuffer/\nlogs/\n\n# Secrets — API keys for cloud providers\nsecrets.env\n\n# Machine ID\nmachine_id\n\n# Update tracking — per-machine state\nlast-update-version\nrestart-reason.json\n\n# Binary attachments — screenshots captured from transcripts\nattachments/\n\n# Team worker deployment — patched wrangler.toml + source copy\n.team-worker/\n\n# Runtime command alias — per-contributor override for which myco binary\n# the hook guard invokes. Default (file absent) is \\`myco\\`; \\`make dev-link\\`\n# writes \\`myco-dev\\`; users can hand-edit for PATH conflicts or pinning.\n# Never committed — different contributors use different aliases.\nruntime.command\n`;\n\n/** Collapse an absolute home-dir path to its `~/` form for portable config storage. */\nexport function collapseHomePath(absPath: string): string {\n  const home = os.homedir();\n  if (absPath.startsWith(home + path.sep) || absPath === home) {\n    return '~' + absPath.slice(home.length);\n  }\n  return absPath;\n}\n\n/**\n * Run the SymbiontInstaller for each symbiont manifest and log results.\n * Shared between myco init and myco update.\n */\nexport function registerSymbionts(\n  manifests: SymbiontManifest[],\n  projectRoot: string,\n  packageRoot: string,\n  verb: 'Registered' | 'Updated',\n): number {\n  let count = 0;\n  for (const manifest of manifests) {\n    try {\n      const installer = new SymbiontInstaller(manifest, projectRoot, packageRoot);\n      const result = installer.install();\n\n      const installed = [\n        result.hooks && 'hooks',\n        result.mcp && 'MCP server',\n        result.skills && 'skills',\n        result.settings && 'settings',\n        result.instructions && 'instructions',\n        result.pluginPackage && 'plugin deps',\n      ].filter(Boolean);\n\n      if (installed.length > 0) {\n        console.log(`  \\u2713 ${verb} ${manifest.displayName}: ${installed.join(', ')}`);\n        count++;\n      } else {\n        console.log(`  \\u2013 ${manifest.displayName}: no registration targets configured`);\n      }\n    } catch (err) {\n      console.error(`  \\u2717 Failed to register ${manifest.displayName}: ${(err as Error).message}`);\n    }\n  }\n  return count;\n}\n\n"],"mappings":";;;;;;;;;;;;;;;;;;AAAA,OAAO,QAAQ;AACf,OAAO,UAAU;AACjB,OAAO,QAAQ;AAkBR,SAAS,YAAY,UAA8B;AACxD,eAAa,YAAY,QAAQ,CAAC;AAClC,SAAO;AACT;AAGA,eAAsB,gBAAgB,UAAyC;AAC7E,QAAM,SAAS,IAAI,aAAa,QAAQ;AACxC,QAAM,UAAU,MAAM,OAAO,cAAc;AAC3C,MAAI,CAAC,SAAS;AACZ,YAAQ,MAAM,6BAA6B;AAC3C,YAAQ,KAAK,CAAC;AAAA,EAChB;AACA,SAAO;AACT;AAGO,SAAS,UAAgB;AAC9B,QAAM,UAAU,KAAK,QAAQ,QAAQ,IAAI,GAAG,MAAM;AAClD,MAAI,CAAC,GAAG,WAAW,OAAO,EAAG;AAC7B,aAAW,QAAQ,GAAG,aAAa,SAAS,OAAO,EAAE,MAAM,IAAI,GAAG;AAChE,UAAM,QAAQ,KAAK,MAAM,+BAA+B;AACxD,QAAI,SAAS,CAAC,QAAQ,IAAI,MAAM,CAAC,CAAC,GAAG;AACnC,cAAQ,IAAI,MAAM,CAAC,CAAC,IAAI,MAAM,CAAC;AAAA,IACjC;AAAA,EACF;AACF;AAEO,SAAS,eAAe,KAAsB;AACnD,MAAI;AAAE,YAAQ,KAAK,KAAK,CAAC;AAAG,WAAO;AAAA,EAAM,QAAQ;AAAE,WAAO;AAAA,EAAO;AACnE;AAGO,IAAM,oBAA0D;AAAA,EACrE,QAAQ,EAAE,UAAU,cAAc,iBAAiB;AAAA,EACnD,aAAa,EAAE,UAAU,gBAAgB,iBAAiB;AAC5D;AAGO,IAAM,kBAAkB;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AA6CxB,SAAS,kBACd,WACA,aACA,aACA,MACQ;AACR,MAAI,QAAQ;AACZ,aAAW,YAAY,WAAW;AAChC,QAAI;AACF,YAAM,YAAY,IAAI,kBAAkB,UAAU,aAAa,WAAW;AAC1E,YAAM,SAAS,UAAU,QAAQ;AAEjC,YAAM,YAAY;AAAA,QAChB,OAAO,SAAS;AAAA,QAChB,OAAO,OAAO;AAAA,QACd,OAAO,UAAU;AAAA,QACjB,OAAO,YAAY;AAAA,QACnB,OAAO,gBAAgB;AAAA,QACvB,OAAO,iBAAiB;AAAA,MAC1B,EAAE,OAAO,OAAO;AAEhB,UAAI,UAAU,SAAS,GAAG;AACxB,gBAAQ,IAAI,YAAY,IAAI,IAAI,SAAS,WAAW,KAAK,UAAU,KAAK,IAAI,CAAC,EAAE;AAC/E;AAAA,MACF,OAAO;AACL,gBAAQ,IAAI,YAAY,SAAS,WAAW,sCAAsC;AAAA,MACpF;AAAA,IACF,SAAS,KAAK;AACZ,cAAQ,MAAM,+BAA+B,SAAS,WAAW,KAAM,IAAc,OAAO,EAAE;AAAA,IAChG;AAAA,EACF;AACA,SAAO;AACT;","names":[]}

package/dist/{chunk-IGBHLFV5.js → chunk-TOER6RNC.js}

@@ -5,7 +5,7 @@ import {
 import {
   SEARCH_PREVIEW_CHARS,
   SEARCH_RESULTS_DEFAULT_LIMIT
-} from "./chunk-7DAH5GLC.js";
+} from "./chunk-CKJAWZQE.js";
 
 // src/db/queries/search.ts
 function fullTextSearch(query, options = {}) {
@@ -125,6 +125,9 @@ function hydrateSearchResults(vectorResults) {
   const artifactStmt = db.prepare(
     `SELECT id, title, content FROM artifacts WHERE id IN (SELECT value FROM json_each(?))`
   );
+  const skillStmt = db.prepare(
+    `SELECT id, name, display_name, description FROM skill_records WHERE id IN (SELECT value FROM json_each(?))`
+  );
   const sessionResults = byNamespace.get("sessions");
   if (sessionResults && sessionResults.length > 0) {
     const ids = sessionResults.map((r) => r.id);
@@ -195,6 +198,23 @@ function hydrateSearchResults(vectorResults) {
       });
     }
   }
+  const skillResults = byNamespace.get("skill_records");
+  if (skillResults && skillResults.length > 0) {
+    const ids = skillResults.map((r) => r.id);
+    const rows = skillStmt.all(JSON.stringify(ids));
+    const rowMap = new Map(rows.map((r) => [r.id, r]));
+    for (const vr of skillResults) {
+      const row = rowMap.get(vr.id);
+      if (!row) continue;
+      results.push({
+        id: row.id,
+        type: "skill",
+        title: row.display_name || row.name,
+        preview: row.description.slice(0, SEARCH_PREVIEW_CHARS),
+        score: vr.similarity
+      });
+    }
+  }
   results.sort((a, b) => b.score - a.score);
   return results;
 }
@@ -203,4 +223,4 @@ export {
   fullTextSearch,
   hydrateSearchResults
 };
-//# sourceMappingURL=chunk-IGBHLFV5.js.map
+//# sourceMappingURL=chunk-TOER6RNC.js.map

package/dist/chunk-TOER6RNC.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/db/queries/search.ts"],"sourcesContent":["/**\n * Full-text search using SQLite FTS5.\n *\n * Searches prompt_batches and activities via their FTS5 virtual tables.\n * Semantic search (vector similarity) is handled by the external VectorStore —\n * this module covers text-based retrieval only.\n *\n * All queries use parameterized placeholders throughout.\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport {\n  SEARCH_RESULTS_DEFAULT_LIMIT,\n  SEARCH_PREVIEW_CHARS,\n} from '@myco/constants.js';\nimport type { VectorSearchResult } from '@myco/daemon/embedding/types.js';\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** All result types that can appear in search results. */\nexport type SearchResultType =\n  | 'session'\n  | 'spore'\n  | 'plan'\n  | 'artifact'\n  | 'prompt_batch'\n  | 'activity'\n  | 'skill';\n\n/** A single result returned from full-text or semantic search. */\nexport interface SearchResult {\n  id: string;\n  type: SearchResultType;\n  title: string;\n  preview: string;\n  score: number;\n  session_id?: string;\n}\n\n/** Options for fullTextSearch. */\nexport interface SearchOptions {\n  /** Restrict results to a single type. */\n  type?: string;\n  /** Maximum number of results to return (default: SEARCH_RESULTS_DEFAULT_LIMIT). */\n  limit?: number;\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Full-text search across capture tables using SQLite FTS5.\n *\n * Searches prompt_batches (indexed on user_prompt) and activities (indexed\n * on tool_name, tool_input, file_path). The raw query string is passed\n * directly to FTS5 MATCH — callers should sanitize if needed.\n *\n * FTS5 `rank` values are negative (lower = better match). This function\n * converts them to positive scores via `Math.abs()` so higher = better\n * in the returned results.\n *\n * When `options.type` is specified, only the matching table branch is queried.\n *\n * @param query — search string (FTS5 MATCH syntax)\n * @param options — optional type filter and result limit\n * @returns SearchResult[] ordered by score DESC\n */\nexport function fullTextSearch(\n  query: string,\n  options: SearchOptions = {},\n): SearchResult[] {\n  const db = getDatabase();\n  const limit = options.limit ?? SEARCH_RESULTS_DEFAULT_LIMIT;\n  const typeFilter = options.type;\n\n  const results: SearchResult[] = [];\n\n  // -- prompt_batches branch ------------------------------------------------\n  if (typeFilter === undefined || typeFilter === 'prompt_batch') {\n    const batchRows = db.prepare(\n      `SELECT pb.id, pb.prompt_number, pb.session_id,\n              substr(COALESCE(pb.user_prompt, '') || ' ' || COALESCE(pb.response_summary, ''), 1, ?) AS preview,\n              fts.rank\n       FROM prompt_batches_fts fts\n       JOIN prompt_batches pb ON pb.id = fts.rowid\n       WHERE prompt_batches_fts MATCH ?\n       ORDER BY fts.rank\n       LIMIT ?`\n    ).all(SEARCH_PREVIEW_CHARS, query, limit) as Array<{\n      id: number;\n      prompt_number: number | null;\n      session_id: string | null;\n      preview: string;\n      rank: number;\n    }>;\n\n    for (const row of batchRows) {\n      results.push({\n        id: String(row.id),\n        type: 'prompt_batch',\n        title: row.prompt_number != null\n          ? `Batch #${row.prompt_number}`\n          : `Batch ${row.id}`,\n        preview: row.preview,\n        score: Math.abs(row.rank),\n        ...(row.session_id != null ? { session_id: row.session_id } : {}),\n      });\n    }\n  }\n\n  // -- activities branch ----------------------------------------------------\n  if (typeFilter === undefined || typeFilter === 'activity') {\n    const activityRows = db.prepare(\n      `SELECT a.id, a.tool_name, a.tool_input, a.file_path, a.session_id,\n              fts.rank\n       FROM activities_fts fts\n       JOIN activities a ON a.id = fts.rowid\n       WHERE activities_fts MATCH ?\n       ORDER BY fts.rank\n       LIMIT ?`\n    ).all(query, limit) as Array<{\n      id: number;\n      tool_name: string;\n      tool_input: string | null;\n      file_path: string | null;\n      session_id: string | null;\n      rank: number;\n    }>;\n\n    for (const row of activityRows) {\n      const preview = (row.tool_input ?? row.file_path ?? '').slice(0, SEARCH_PREVIEW_CHARS);\n      results.push({\n        id: String(row.id),\n        type: 'activity',\n        title: row.tool_name,\n        preview,\n        score: Math.abs(row.rank),\n        ...(row.session_id != null ? { session_id: row.session_id } : {}),\n      });\n    }\n  }\n\n  // -- spores branch --------------------------------------------------------\n  if (typeFilter === undefined || typeFilter === 'spore') {\n    const sporeRows = db.prepare(\n      `SELECT s.id, s.observation_type, s.session_id,\n              substr(COALESCE(s.content, ''), 1, ?) AS preview,\n              fts.rank\n       FROM spores_fts fts\n       JOIN spores s ON s.rowid = fts.rowid\n       WHERE spores_fts MATCH ?\n       ORDER BY fts.rank\n       LIMIT ?`\n    ).all(SEARCH_PREVIEW_CHARS, query, limit) as Array<{\n      id: string;\n      observation_type: string;\n      session_id: string | null;\n      preview: string;\n      rank: number;\n    }>;\n\n    for (const row of sporeRows) {\n      results.push({\n        id: String(row.id),\n        type: 'spore',\n        title: row.observation_type,\n        preview: row.preview,\n        score: Math.abs(row.rank),\n        ...(row.session_id != null ? { session_id: row.session_id } : {}),\n      });\n    }\n  }\n\n  // -- sessions branch ------------------------------------------------------\n  if (typeFilter === undefined || typeFilter === 'session') {\n    const sessionRows = db.prepare(\n      `SELECT s.id, s.title,\n              substr(COALESCE(s.summary, s.title, ''), 1, ?) AS preview,\n              fts.rank\n       FROM sessions_fts fts\n       JOIN sessions s ON s.rowid = fts.rowid\n       WHERE sessions_fts MATCH ?\n       ORDER BY fts.rank\n       LIMIT ?`\n    ).all(SEARCH_PREVIEW_CHARS, query, limit) as Array<{\n      id: string;\n      title: string | null;\n      preview: string;\n      rank: number;\n    }>;\n\n    for (const row of sessionRows) {\n      results.push({\n        id: String(row.id),\n        type: 'session',\n        title: row.title ?? `Session ${row.id.slice(-6)}`,\n        preview: row.preview,\n        score: Math.abs(row.rank),\n      });\n    }\n  }\n\n  // Sort combined results by score DESC and apply limit.\n  results.sort((a, b) => b.score - a.score);\n  return results.slice(0, limit);\n}\n\n// ---------------------------------------------------------------------------\n// Hydration — convert VectorSearchResults into SearchResults\n// ---------------------------------------------------------------------------\n\n/** Row shape returned from sessions table for hydration. */\ninterface SessionRow {\n  id: string;\n  title: string | null;\n  summary: string | null;\n  session_id?: undefined;\n}\n\n/** Row shape returned from spores table for hydration. */\ninterface SporeRow {\n  id: string;\n  observation_type: string;\n  content: string;\n  session_id: string | null;\n}\n\n/** Row shape returned from plans table for hydration. */\ninterface PlanRow {\n  id: string;\n  title: string | null;\n  content: string | null;\n  session_id: string | null;\n}\n\n/** Row shape returned from artifacts table for hydration. */\ninterface ArtifactRow {\n  id: string;\n  title: string;\n  content: string | null;\n}\n\n/**\n * Hydrate vector search results into SearchResults by fetching full records\n * from the record store.\n *\n * Groups results by namespace, queries each table for the relevant IDs, then\n * maps them into SearchResult format with titles and previews.\n */\nexport function hydrateSearchResults(\n  vectorResults: VectorSearchResult[],\n): SearchResult[] {\n  if (vectorResults.length === 0) return [];\n\n  const db = getDatabase();\n  const results: SearchResult[] = [];\n\n  // Group result IDs by namespace\n  const byNamespace = new Map<string, VectorSearchResult[]>();\n  for (const vr of vectorResults) {\n    const group = byNamespace.get(vr.namespace) ?? [];\n    group.push(vr);\n    byNamespace.set(vr.namespace, group);\n  }\n\n  // Use json_each so the statement text is stable and SQLite can cache the plan.\n  const sessionStmt = db.prepare(\n    `SELECT id, title, summary FROM sessions WHERE id IN (SELECT value FROM json_each(?))`,\n  );\n  const sporeStmt = db.prepare(\n    `SELECT id, observation_type, content, session_id FROM spores WHERE id IN (SELECT value FROM json_each(?))`,\n  );\n  const planStmt = db.prepare(\n    `SELECT id, title, content, session_id FROM plans WHERE id IN (SELECT value FROM json_each(?))`,\n  );\n  const artifactStmt = db.prepare(\n    `SELECT id, title, content FROM artifacts WHERE id IN (SELECT value FROM json_each(?))`,\n  );\n  const skillStmt = db.prepare(\n    `SELECT id, name, display_name, description FROM skill_records WHERE id IN (SELECT value FROM json_each(?))`,\n  );\n\n  // --- sessions ---\n  const sessionResults = byNamespace.get('sessions');\n  if (sessionResults && sessionResults.length > 0) {\n    const ids = sessionResults.map((r) => r.id);\n    const rows = sessionStmt.all(JSON.stringify(ids)) as SessionRow[];\n\n    const rowMap = new Map(rows.map((r) => [r.id, r]));\n    for (const vr of sessionResults) {\n      const row = rowMap.get(vr.id);\n      if (!row) continue;\n      results.push({\n        id: row.id,\n        type: 'session',\n        title: row.title ?? `Session ${row.id.slice(-6)}`,\n        preview: (row.summary ?? '').slice(0, SEARCH_PREVIEW_CHARS),\n        score: vr.similarity,\n      });\n    }\n  }\n\n  // --- spores ---\n  const sporeResults = byNamespace.get('spores');\n  if (sporeResults && sporeResults.length > 0) {\n    const ids = sporeResults.map((r) => r.id);\n    const rows = sporeStmt.all(JSON.stringify(ids)) as SporeRow[];\n\n    const rowMap = new Map(rows.map((r) => [r.id, r]));\n    for (const vr of sporeResults) {\n      const row = rowMap.get(vr.id);\n      if (!row) continue;\n      results.push({\n        id: row.id,\n        type: 'spore',\n        title: row.observation_type,\n        preview: row.content.slice(0, SEARCH_PREVIEW_CHARS),\n        score: vr.similarity,\n        ...(row.session_id != null ? { session_id: row.session_id } : {}),\n      });\n    }\n  }\n\n  // --- plans ---\n  const planResults = byNamespace.get('plans');\n  if (planResults && planResults.length > 0) {\n    const ids = planResults.map((r) => r.id);\n    const rows = planStmt.all(JSON.stringify(ids)) as PlanRow[];\n\n    const rowMap = new Map(rows.map((r) => [r.id, r]));\n    for (const vr of planResults) {\n      const row = rowMap.get(vr.id);\n      if (!row) continue;\n      results.push({\n        id: row.id,\n        type: 'plan',\n        title: row.title ?? `Plan ${row.id.slice(-6)}`,\n        preview: (row.content ?? '').slice(0, SEARCH_PREVIEW_CHARS),\n        score: vr.similarity,\n        ...(row.session_id != null ? { session_id: row.session_id } : {}),\n      });\n    }\n  }\n\n  // --- artifacts ---\n  const artifactResults = byNamespace.get('artifacts');\n  if (artifactResults && artifactResults.length > 0) {\n    const ids = artifactResults.map((r) => r.id);\n    const rows = artifactStmt.all(JSON.stringify(ids)) as ArtifactRow[];\n\n    const rowMap = new Map(rows.map((r) => [r.id, r]));\n    for (const vr of artifactResults) {\n      const row = rowMap.get(vr.id);\n      if (!row) continue;\n      results.push({\n        id: row.id,\n        type: 'artifact',\n        title: row.title,\n        preview: (row.content ?? '').slice(0, SEARCH_PREVIEW_CHARS),\n        score: vr.similarity,\n      });\n    }\n  }\n\n  // --- skill_records ---\n  const skillResults = byNamespace.get('skill_records');\n  if (skillResults && skillResults.length > 0) {\n    const ids = skillResults.map((r) => r.id);\n    const rows = skillStmt.all(JSON.stringify(ids)) as Array<{ id: string; name: string; display_name: string; description: string }>;\n\n    const rowMap = new Map(rows.map((r) => [r.id, r]));\n    for (const vr of skillResults) {\n      const row = rowMap.get(vr.id);\n      if (!row) continue;\n      results.push({\n        id: row.id,\n        type: 'skill',\n        title: row.display_name || row.name,\n        preview: row.description.slice(0, SEARCH_PREVIEW_CHARS),\n        score: vr.similarity,\n      });\n    }\n  }\n\n  // Preserve the original similarity-based ordering from vector search\n  results.sort((a, b) => b.score - a.score);\n  return 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package/dist/{chunk-ZSJPI5MS.js → chunk-TZAXQKO6.js}

@@ -2,7 +2,7 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   getTeamMachineId,
   syncRow
-} from "./chunk-C3C5QVLK.js";
+} from "./chunk-O3TRN3RC.js";
 import {
   getDatabase
 } from "./chunk-MYX5NCRH.js";
@@ -124,6 +124,10 @@ function buildSporeWhere(options) {
     const pattern = `%${options.search}%`;
     params.push(pattern, pattern);
   }
+  if (options.since !== void 0) {
+    conditions.push("created_at > ?");
+    params.push(options.since);
+  }
   return {
     where: conditions.length > 0 ? `WHERE ${conditions.join(" AND ")}` : "",
     params
@@ -183,4 +187,4 @@ export {
   listSporeIdsSince,
   updateSporeStatus
 };
-//# sourceMappingURL=chunk-ZSJPI5MS.js.map
+//# sourceMappingURL=chunk-TZAXQKO6.js.map

package/dist/chunk-TZAXQKO6.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/db/queries/spores.ts"],"sourcesContent":["/**\n * Spore CRUD query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport { getTeamMachineId } from '@myco/daemon/team-context.js';\nimport { syncRow } from '@myco/db/queries/team-outbox.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default number of spores returned by listSpores when no limit given. */\nconst DEFAULT_LIST_LIMIT = 100;\n\n/** Default spore status for new spores. */\nconst DEFAULT_STATUS = 'active';\n\n/** Default importance score for new spores. */\nexport const DEFAULT_IMPORTANCE = 5;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Fields required (or optional) when inserting a spore. */\nexport interface SporeInsert {\n  id: string;\n  agent_id: string;\n  observation_type: string;\n  content: string;\n  created_at: number;\n  session_id?: string | null;\n  prompt_batch_id?: number | null;\n  status?: string;\n  context?: string | null;\n  importance?: number;\n  file_path?: string | null;\n  tags?: string | null;\n  content_hash?: string | null;\n  properties?: string | null;\n  updated_at?: number | null;\n  machine_id?: string;\n}\n\n/** Row shape returned from spore queries (all columns). */\nexport interface SporeRow {\n  id: string;\n  agent_id: string;\n  session_id: string | null;\n  prompt_batch_id: number | null;\n  observation_type: string;\n  status: string;\n  content: string;\n  context: string | null;\n  importance: number;\n  file_path: string | null;\n  tags: string | null;\n  content_hash: string | null;\n  properties: string | null;\n  embedded: number;\n  created_at: number;\n  updated_at: number | null;\n  machine_id: string;\n  synced_at: number | null;\n}\n\n/** Filter options for `listSpores`. */\nexport interface ListSporesOptions {\n  agent_id?: string;\n  observation_type?: string;\n  status?: string;\n  session_id?: string;\n  search?: string;\n  /** Only return spores created after this epoch-seconds timestamp. */\n  since?: number;\n  limit?: number;\n  offset?: number;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst SPORE_COLUMNS = [\n  'id',\n  'agent_id',\n  'session_id',\n  'prompt_batch_id',\n  'observation_type',\n  'status',\n  'content',\n  'context',\n  'importance',\n  'file_path',\n  'tags',\n  'content_hash',\n  'properties',\n  'embedded',\n  'created_at',\n  'updated_at',\n  'machine_id',\n  'synced_at',\n] as const;\n\nconst SELECT_COLUMNS = SPORE_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed SporeRow. */\nfunction toSporeRow(row: Record<string, unknown>): SporeRow {\n  return {\n    id: row.id as string,\n    agent_id: row.agent_id as string,\n    session_id: (row.session_id as string) ?? null,\n    prompt_batch_id: (row.prompt_batch_id as number) ?? null,\n    observation_type: row.observation_type as string,\n    status: row.status as string,\n    content: row.content as string,\n    context: (row.context as string) ?? null,\n    importance: row.importance as number,\n    file_path: (row.file_path as string) ?? null,\n    tags: (row.tags as string) ?? null,\n    content_hash: (row.content_hash as string) ?? null,\n    properties: (row.properties as string) ?? null,\n    embedded: (row.embedded as number) ?? 0,\n    created_at: row.created_at as number,\n    updated_at: (row.updated_at as number) ?? null,\n    machine_id: (row.machine_id as string) ?? 'local',\n    synced_at: (row.synced_at as number) ?? null,\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Insert a new spore.\n *\n * Requires a valid `agent_id` (foreign key to agents table).\n */\nexport function insertSpore(data: SporeInsert): SporeRow {\n  const db = getDatabase();\n\n  db.prepare(\n    `INSERT INTO spores (\n       id, agent_id, session_id, prompt_batch_id,\n       observation_type, status, content, context,\n       importance, file_path, tags, content_hash,\n       properties, created_at, updated_at, machine_id\n     ) VALUES (\n       ?, ?, ?, ?,\n       ?, ?, ?, ?,\n       ?, ?, ?, ?,\n       ?, ?, ?, ?\n     )`,\n  ).run(\n    data.id,\n    data.agent_id,\n    data.session_id ?? null,\n    data.prompt_batch_id ?? null,\n    data.observation_type,\n    data.status ?? DEFAULT_STATUS,\n    data.content,\n    data.context ?? null,\n    data.importance ?? DEFAULT_IMPORTANCE,\n    data.file_path ?? null,\n    data.tags ?? null,\n    data.content_hash ?? null,\n    data.properties ?? null,\n    data.created_at,\n    data.updated_at ?? null,\n    data.machine_id ?? getTeamMachineId(),\n  );\n\n  const row = toSporeRow(\n    db.prepare(`SELECT ${SELECT_COLUMNS} FROM spores WHERE id = ?`).get(data.id) as Record<string, unknown>,\n  );\n\n  syncRow('spores', row);\n\n  return row;\n}\n\n/**\n * Retrieve a single spore by id.\n *\n * @returns the spore row, or null if not found.\n */\nexport function getSpore(id: string): SporeRow | null {\n  const db = getDatabase();\n\n  const row = db.prepare(\n    `SELECT ${SELECT_COLUMNS} FROM spores WHERE id = ?`,\n  ).get(id) as Record<string, unknown> | undefined;\n\n  if (!row) return null;\n  return toSporeRow(row);\n}\n\n/**\n * List spores with optional filters, ordered by created_at DESC.\n */\n/** Build WHERE clause and bound params from spore filter options. */\nfunction buildSporeWhere(\n  options: Omit<ListSporesOptions, 'limit' | 'offset'>,\n): { where: string; params: unknown[] } {\n  const conditions: string[] = [];\n  const params: unknown[] = [];\n\n  if (options.agent_id !== undefined) {\n    conditions.push(`agent_id = ?`);\n    params.push(options.agent_id);\n  }\n  if (options.observation_type !== undefined) {\n    conditions.push(`observation_type = ?`);\n    params.push(options.observation_type);\n  }\n  if (options.status !== undefined) {\n    conditions.push(`status = ?`);\n    params.push(options.status);\n  }\n  if (options.session_id !== undefined) {\n    conditions.push(`session_id = ?`);\n    params.push(options.session_id);\n  }\n  if (options.search !== undefined && options.search.length > 0) {\n    conditions.push(`(content LIKE ? OR observation_type LIKE ?)`);\n    const pattern = `%${options.search}%`;\n    params.push(pattern, pattern);\n  }\n  if (options.since !== undefined) {\n    conditions.push('created_at > ?');\n    params.push(options.since);\n  }\n\n  return {\n    where: conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '',\n    params,\n  };\n}\n\n/**\n * List spores with optional filters, ordered by created_at DESC.\n */\nexport function listSpores(\n  options: ListSporesOptions = {},\n): SporeRow[] {\n  const db = getDatabase();\n  const { where, params } = buildSporeWhere(options);\n  const limit = options.limit ?? DEFAULT_LIST_LIMIT;\n  const offset = options.offset ?? 0;\n\n  const rows = db.prepare(\n    `SELECT ${SELECT_COLUMNS}\n     FROM spores\n     ${where}\n     ORDER BY created_at DESC\n     LIMIT ?\n     OFFSET ?`,\n  ).all(...params, limit, offset) as Record<string, unknown>[];\n\n  return rows.map(toSporeRow);\n}\n\n/**\n * Count spores matching optional filters (for pagination totals).\n */\nexport function countSpores(\n  options: Omit<ListSporesOptions, 'limit' | 'offset'> = {},\n): number {\n  const db = getDatabase();\n  const { where, params } = buildSporeWhere(options);\n\n  const row = db.prepare(\n    `SELECT COUNT(*) as count FROM spores ${where}`,\n  ).get(...params) as { count: number };\n\n  return row.count;\n}\n\n/**\n * Count active spores created after a given timestamp.\n * Used by skill-evolve to detect new knowledge since last assessment.\n */\nexport function countSporesSince(sinceEpoch: number): number {\n  const db = getDatabase();\n  const row = db.prepare(\n    `SELECT COUNT(*) as count FROM spores WHERE created_at > ? AND status = 'active'`,\n  ).get(sinceEpoch) as { count: number };\n  return row.count;\n}\n\n/**\n * List active spore IDs created after a given timestamp, ordered newest first.\n */\nexport function listSporeIdsSince(sinceEpoch: number, limit = 20): string[] {\n  const db = getDatabase();\n  const rows = db.prepare(\n    `SELECT id FROM spores WHERE created_at > ? AND status = 'active' ORDER BY created_at DESC LIMIT ?`,\n  ).all(sinceEpoch, limit) as Array<{ id: string }>;\n  return rows.map(r => r.id);\n}\n\n/**\n * Update the status and updated_at timestamp of a spore.\n *\n * @returns the updated row, or null if the spore does not exist.\n */\nexport function updateSporeStatus(\n  id: string,\n  status: string,\n  updatedAt: number,\n): SporeRow | null {\n  const db = getDatabase();\n\n  const info = db.prepare(\n    `UPDATE spores\n     SET status = ?, updated_at = ?\n     WHERE id = ?`,\n  ).run(status, updatedAt, id);\n\n  if (info.changes === 0) return null;\n\n  const row = toSporeRow(\n    db.prepare(`SELECT ${SELECT_COLUMNS} FROM spores WHERE id = ?`).get(id) as Record<string, unknown>,\n  );\n\n  syncRow('spores', row);\n\n  return row;\n}\n"],"mappings":";;;;;;;;;;AAgBA,IAAM,qBAAqB;AAG3B,IAAM,iBAAiB;AAGhB,IAAM,qBAAqB;AAiElC,IAAM,gBAAgB;AAAA,EACpB;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;AAEA,IAAM,iBAAiB,cAAc,KAAK,IAAI;AAO9C,SAAS,WAAW,KAAwC;AAC1D,SAAO;AAAA,IACL,IAAI,IAAI;AAAA,IACR,UAAU,IAAI;AAAA,IACd,YAAa,IAAI,cAAyB;AAAA,IAC1C,iBAAkB,IAAI,mBAA8B;AAAA,IACpD,kBAAkB,IAAI;AAAA,IACtB,QAAQ,IAAI;AAAA,IACZ,SAAS,IAAI;AAAA,IACb,SAAU,IAAI,WAAsB;AAAA,IACpC,YAAY,IAAI;AAAA,IAChB,WAAY,IAAI,aAAwB;AAAA,IACxC,MAAO,IAAI,QAAmB;AAAA,IAC9B,cAAe,IAAI,gBAA2B;AAAA,IAC9C,YAAa,IAAI,cAAyB;AAAA,IAC1C,UAAW,IAAI,YAAuB;AAAA,IACtC,YAAY,IAAI;AAAA,IAChB,YAAa,IAAI,cAAyB;AAAA,IAC1C,YAAa,IAAI,cAAyB;AAAA,IAC1C,WAAY,IAAI,aAAwB;AAAA,EAC1C;AACF;AAWO,SAAS,YAAY,MAA6B;AACvD,QAAM,KAAK,YAAY;AAEvB,KAAG;AAAA,IACD;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,EAWF,EAAE;AAAA,IACA,KAAK;AAAA,IACL,KAAK;AAAA,IACL,KAAK,cAAc;AAAA,IACnB,KAAK,mBAAmB;AAAA,IACxB,KAAK;AAAA,IACL,KAAK,UAAU;AAAA,IACf,KAAK;AAAA,IACL,KAAK,WAAW;AAAA,IAChB,KAAK,cAAc;AAAA,IACnB,KAAK,aAAa;AAAA,IAClB,KAAK,QAAQ;AAAA,IACb,KAAK,gBAAgB;AAAA,IACrB,KAAK,cAAc;AAAA,IACnB,KAAK;AAAA,IACL,KAAK,cAAc;AAAA,IACnB,KAAK,cAAc,iBAAiB;AAAA,EACtC;AAEA,QAAM,MAAM;AAAA,IACV,GAAG,QAAQ,UAAU,cAAc,2BAA2B,EAAE,IAAI,KAAK,EAAE;AAAA,EAC7E;AAEA,UAAQ,UAAU,GAAG;AAErB,SAAO;AACT;AAOO,SAAS,SAAS,IAA6B;AACpD,QAAM,KAAK,YAAY;AAEvB,QAAM,MAAM,GAAG;AAAA,IACb,UAAU,cAAc;AAAA,EAC1B,EAAE,IAAI,EAAE;AAER,MAAI,CAAC,IAAK,QAAO;AACjB,SAAO,WAAW,GAAG;AACvB;AAMA,SAAS,gBACP,SACsC;AACtC,QAAM,aAAuB,CAAC;AAC9B,QAAM,SAAoB,CAAC;AAE3B,MAAI,QAAQ,aAAa,QAAW;AAClC,eAAW,KAAK,cAAc;AAC9B,WAAO,KAAK,QAAQ,QAAQ;AAAA,EAC9B;AACA,MAAI,QAAQ,qBAAqB,QAAW;AAC1C,eAAW,KAAK,sBAAsB;AACtC,WAAO,KAAK,QAAQ,gBAAgB;AAAA,EACtC;AACA,MAAI,QAAQ,WAAW,QAAW;AAChC,eAAW,KAAK,YAAY;AAC5B,WAAO,KAAK,QAAQ,MAAM;AAAA,EAC5B;AACA,MAAI,QAAQ,eAAe,QAAW;AACpC,eAAW,KAAK,gBAAgB;AAChC,WAAO,KAAK,QAAQ,UAAU;AAAA,EAChC;AACA,MAAI,QAAQ,WAAW,UAAa,QAAQ,OAAO,SAAS,GAAG;AAC7D,eAAW,KAAK,6CAA6C;AAC7D,UAAM,UAAU,IAAI,QAAQ,MAAM;AAClC,WAAO,KAAK,SAAS,OAAO;AAAA,EAC9B;AACA,MAAI,QAAQ,UAAU,QAAW;AAC/B,eAAW,KAAK,gBAAgB;AAChC,WAAO,KAAK,QAAQ,KAAK;AAAA,EAC3B;AAEA,SAAO;AAAA,IACL,OAAO,WAAW,SAAS,IAAI,SAAS,WAAW,KAAK,OAAO,CAAC,KAAK;AAAA,IACrE;AAAA,EACF;AACF;AAKO,SAAS,WACd,UAA6B,CAAC,GAClB;AACZ,QAAM,KAAK,YAAY;AACvB,QAAM,EAAE,OAAO,OAAO,IAAI,gBAAgB,OAAO;AACjD,QAAM,QAAQ,QAAQ,SAAS;AAC/B,QAAM,SAAS,QAAQ,UAAU;AAEjC,QAAM,OAAO,GAAG;AAAA,IACd,UAAU,cAAc;AAAA;AAAA,OAErB,KAAK;AAAA;AAAA;AAAA;AAAA,EAIV,EAAE,IAAI,GAAG,QAAQ,OAAO,MAAM;AAE9B,SAAO,KAAK,IAAI,UAAU;AAC5B;AAKO,SAAS,YACd,UAAuD,CAAC,GAChD;AACR,QAAM,KAAK,YAAY;AACvB,QAAM,EAAE,OAAO,OAAO,IAAI,gBAAgB,OAAO;AAEjD,QAAM,MAAM,GAAG;AAAA,IACb,wCAAwC,KAAK;AAAA,EAC/C,EAAE,IAAI,GAAG,MAAM;AAEf,SAAO,IAAI;AACb;AAiBO,SAAS,kBAAkB,YAAoB,QAAQ,IAAc;AAC1E,QAAM,KAAK,YAAY;AACvB,QAAM,OAAO,GAAG;AAAA,IACd;AAAA,EACF,EAAE,IAAI,YAAY,KAAK;AACvB,SAAO,KAAK,IAAI,OAAK,EAAE,EAAE;AAC3B;AAOO,SAAS,kBACd,IACA,QACA,WACiB;AACjB,QAAM,KAAK,YAAY;AAEvB,QAAM,OAAO,GAAG;AAAA,IACd;AAAA;AAAA;AAAA,EAGF,EAAE,IAAI,QAAQ,WAAW,EAAE;AAE3B,MAAI,KAAK,YAAY,EAAG,QAAO;AAE/B,QAAM,MAAM;AAAA,IACV,GAAG,QAAQ,UAAU,cAAc,2BAA2B,EAAE,IAAI,EAAE;AAAA,EACxE;AAEA,UAAQ,UAAU,GAAG;AAErB,SAAO;AACT;","names":[]}

package/dist/{chunk-RKPTMHED.js → chunk-U3J2DDSR.js}

@@ -2,7 +2,7 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   getTeamMachineId,
   syncRow
-} from "./chunk-C3C5QVLK.js";
+} from "./chunk-O3TRN3RC.js";
 import {
   getDatabase
 } from "./chunk-MYX5NCRH.js";
@@ -88,4 +88,4 @@ export {
   insertResolutionEvent,
   listResolutionEvents
 };
-//# sourceMappingURL=chunk-RKPTMHED.js.map
+//# sourceMappingURL=chunk-U3J2DDSR.js.map

package/dist/{chunk-SI5BBQAT.js → chunk-W7WENJ6F.js}

@@ -11,7 +11,7 @@ var cached;
 function getPluginVersion() {
   if (cached) return cached;
   if (true) {
-    cached = "0.17.2";
+    cached = "0.18.1";
     return cached;
   }
   const root = findPackageRoot(path.dirname(fileURLToPath(import.meta.url)));
@@ -32,4 +32,4 @@ function getPluginVersion() {
 export {
   getPluginVersion
 };
-//# sourceMappingURL=chunk-SI5BBQAT.js.map
+//# sourceMappingURL=chunk-W7WENJ6F.js.map

package/dist/{chunk-VVGZL2HX.js → chunk-WYOE4IAX.js}

@@ -208,9 +208,8 @@ function writeOrDeleteJsonFile(filePath, data) {
 // src/symbionts/install-helpers.ts
 import fs2 from "fs";
 import path2 from "path";
-var MYCO_HOOK_COMMAND_PREFIX = "myco-run";
 function isMycoHookCommand(command) {
-  return command.startsWith(MYCO_HOOK_COMMAND_PREFIX) || command.includes(".agents/myco-hook.cjs");
+  return command.includes(".agents/myco-run.cjs") || command.includes(".agents/myco-hook.cjs") || command.startsWith("myco-run");
 }
 function isMycoHookGroup(group) {
   if (Array.isArray(group.hooks) && group.hooks.some((h) => h.command && isMycoHookCommand(h.command))) return true;
@@ -250,9 +249,10 @@ var GITIGNORE_COMMENT = "# Myco managed (machine-specific)";
 var GITIGNORE_SKILLS_COMMENT_LEGACY = "# Myco skill symlinks (machine-specific)";
 var WRANGLER_CACHE_DIR = ".wrangler/";
 var TEMPLATES_SUBDIR = "src/symbionts/templates";
-var HOOK_GUARD_TEMPLATE_FILENAME = "hook-guard.cjs";
-var HOOK_GUARD_INSTALLED_FILENAME = "myco-hook.cjs";
+var HOOK_GUARD_TEMPLATE_FILENAME = "myco-run.cjs";
+var HOOK_GUARD_INSTALLED_FILENAME = "myco-run.cjs";
 var HOOK_GUARD_PROJECT_PATH = `.agents/${HOOK_GUARD_INSTALLED_FILENAME}`;
+var LEGACY_HOOK_GUARD_PATH = ".agents/myco-hook.cjs";
 var SKILLS_SUBDIR = "skills";
 var CANONICAL_SKILLS_DIR = ".agents/skills";
 var MYCO_MCP_SERVER_NAME = "myco";
@@ -306,33 +306,47 @@ var SymbiontInstaller = class {
     return true;
   }
   /**
-   * Copy the hook-guard script into .agents/myco-hook.cjs.
-   * Returns true if the file was written (or updated); false if skipped or N/A.
+   * Copy the hook guard script into .agents/myco-run.cjs and delete the
+   * legacy .agents/myco-hook.cjs if present.
+   *
+   * The guard is the cross-platform entry point for lifecycle hooks.
+   * Hook commands invoke `node .agents/myco-run.cjs …`, and the guard
+   * resolves which myco binary to exec via `.myco/runtime.command`.
+   * MCP server spawn continues to use the published `myco-run` binary.
+   * Returns true if the file was written (or updated); false if skipped
+   * or N/A.
    */
   installHookGuard() {
     const reg = this.manifest.registration;
     if (!reg?.hooksTarget) return false;
     const guardTemplate = this.readTemplateFile(HOOK_GUARD_TEMPLATE_FILENAME);
     if (!guardTemplate) return false;
+    try {
+      fs3.unlinkSync(path3.join(this.projectRoot, LEGACY_HOOK_GUARD_PATH));
+    } catch {
+    }
     return this.writeManagedFile(
       path3.join(this.projectRoot, HOOK_GUARD_PROJECT_PATH),
       guardTemplate
     );
   }
   /**
-   * Remove the hook-guard script from .agents/myco-hook.cjs.
-   * Returns true if the file was removed; false otherwise.
+   * Remove the hook guard script from .agents/myco-run.cjs.
+   * Also deletes the legacy .agents/myco-hook.cjs if present.
+   * Returns true if any file was removed; false otherwise.
    */
   uninstallHookGuard() {
     const reg = this.manifest.registration;
     if (!reg?.hooksTarget) return false;
-    const targetPath = path3.join(this.projectRoot, HOOK_GUARD_PROJECT_PATH);
-    try {
-      fs3.unlinkSync(targetPath);
-      return true;
-    } catch {
-      return false;
+    let removed = false;
+    for (const relPath of [HOOK_GUARD_PROJECT_PATH, LEGACY_HOOK_GUARD_PATH]) {
+      try {
+        fs3.unlinkSync(path3.join(this.projectRoot, relPath));
+        removed = true;
+      } catch {
+      }
     }
+    return removed;
   }
   /** Load a JSON template file for this symbiont. Returns null if not found. */
   loadTemplate(name) {
@@ -356,6 +370,7 @@ var SymbiontInstaller = class {
   install() {
     const reg = this.manifest.registration;
     this.installHookGuard();
+    this.cleanupLegacyMycoCmdEntries();
     const result = this.shouldBatchJsonTargets(reg) ? this.installBatchedJson(reg) : {
       hooks: this.installHooks(),
       mcp: this.installMcp(),
@@ -367,6 +382,129 @@ var SymbiontInstaller = class {
     this.updateGitignore();
     return result;
   }
+  /**
+   * Sweep legacy `MYCO_CMD` env-var writes and `myco-run` command-name
+   * entries from this symbiont's installed config files.
+   *
+   * Background: prior to the `.myco/runtime.command` refactor, `make
+   * dev-link` injected `MYCO_CMD=myco-dev` into each symbiont's env
+   * block (`.claude/settings.json` → `env`, `.cursor/mcp.json` →
+   * `mcp.myco.env`, `.codex/config.toml` →
+   * `[shell_environment_policy.set]`), and each symbiont's template
+   * permission allowlist listed `myco-run` as a callable command. The
+   * env-var pattern is now obsolete — `.myco/runtime.command` is the
+   * hook-side source of truth — while the old allowlist entries remain
+   * legacy noise after the permissions refactor.
+   *
+   * This cleanup runs automatically on every install/update pass so
+   * contributors upgrading across this refactor don't need to manually
+   * edit any config file. Idempotent: a second run after cleanup is a
+   * no-op. Safe to remove from the install pipeline once every known
+   * contributor has updated at least once.
+   */
+  cleanupLegacyMycoCmdEntries() {
+    const reg = this.manifest.registration;
+    if (!reg) return;
+    if (reg.settingsTarget) {
+      const settingsPath = path3.join(this.projectRoot, reg.settingsTarget);
+      const format = reg.settingsFormat ?? "json";
+      if (format === "toml") {
+        this.stripLegacyFromToml(settingsPath);
+      } else {
+        this.stripLegacyFromJson(settingsPath);
+      }
+    }
+    if (reg.mcpTarget && reg.mcpFormat !== "toml") {
+      this.stripLegacyFromJson(path3.join(this.projectRoot, reg.mcpTarget));
+    }
+  }
+  /**
+   * Walk a JSON settings/MCP file and delete legacy MYCO_CMD + myco-run
+   * entries. Writes back only if something changed.
+   *
+   * Removes:
+   * - `MYCO_CMD` key from any object named `env` anywhere in the tree
+   * - `myco-run` / `myco-run *` / `myco-run:*` / `Bash(myco-run *)` /
+   *   `Bash(myco-run:*)` / `ShellTool(myco-run *)` from string arrays
+   * - `myco-run` / `myco-run *` keys from object-boolean maps like
+   *   `chat.tools.terminal.autoApprove`
+   */
+  stripLegacyFromJson(filePath) {
+    let raw;
+    try {
+      raw = fs3.readFileSync(filePath, "utf-8");
+    } catch {
+      return;
+    }
+    let data;
+    try {
+      data = JSON.parse(raw);
+    } catch {
+      return;
+    }
+    let changed = false;
+    const LEGACY_STRINGS = /* @__PURE__ */ new Set([
+      "myco-run",
+      "myco-run *",
+      "myco-run:*",
+      "Bash(myco-run *)",
+      "Bash(myco-run:*)",
+      "ShellTool(myco-run *)"
+    ]);
+    const LEGACY_OBJECT_KEYS = ["myco-run", "myco-run *"];
+    const EXEC_ARGV_KEYS = /* @__PURE__ */ new Set(["command", "args"]);
+    const walk = (node, parentKey) => {
+      if (node === null || typeof node !== "object") return;
+      if (Array.isArray(node)) {
+        if (parentKey !== void 0 && EXEC_ARGV_KEYS.has(parentKey)) return;
+        for (let i = node.length - 1; i >= 0; i--) {
+          if (typeof node[i] === "string" && LEGACY_STRINGS.has(node[i])) {
+            node.splice(i, 1);
+            changed = true;
+          } else {
+            walk(node[i]);
+          }
+        }
+        return;
+      }
+      const obj = node;
+      if (parentKey === "env" && "MYCO_CMD" in obj) {
+        delete obj.MYCO_CMD;
+        changed = true;
+      }
+      for (const key of LEGACY_OBJECT_KEYS) {
+        if (key in obj) {
+          delete obj[key];
+          changed = true;
+        }
+      }
+      for (const [k, v] of Object.entries(obj)) {
+        walk(v, k);
+      }
+    };
+    walk(data);
+    if (changed) {
+      fs3.writeFileSync(filePath, JSON.stringify(data, null, 2) + "\n", "utf-8");
+    }
+  }
+  /**
+   * Strip `MYCO_CMD = "..."` from the `[shell_environment_policy.set]`
+   * section of a TOML settings file. Leaves the rest of the file
+   * untouched. Drops the `[shell_environment_policy.set]` header entirely
+   * when the section becomes empty.
+   */
+  stripLegacyFromToml(filePath) {
+    let raw;
+    try {
+      raw = fs3.readFileSync(filePath, "utf-8");
+    } catch {
+      return;
+    }
+    const next = removeTomlSectionKeys(raw, "shell_environment_policy.set", ["MYCO_CMD"]);
+    if (next !== raw) {
+      fs3.writeFileSync(filePath, next, "utf-8");
+    }
+  }
   /**
    * Check if ALL non-null JSON targets share the same file (e.g., Gemini).
    * Only batches when every target resolves to one path — partial overlaps
@@ -1102,4 +1240,4 @@ export {
   SymbiontInstaller,
   syncSkillSymlinks
 };
-//# sourceMappingURL=chunk-VVGZL2HX.js.map
+//# sourceMappingURL=chunk-WYOE4IAX.js.map