@goondocks/myco 0.6.4 → 0.9.0

package/dist/cli-ODLFRIYS.js

@@ -0,0 +1,128 @@
+#!/usr/bin/env node
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  loadEnv
+} from "./chunk-KB4DGYIY.js";
+import "./chunk-SAKJMNSR.js";
+import "./chunk-UBZPD4HN.js";
+import "./chunk-MYX5NCRH.js";
+import "./chunk-TRUJLI6K.js";
+import "./chunk-5VZ52A4T.js";
+import "./chunk-WGTCA2NU.js";
+import "./chunk-PB6TOLRQ.js";
+import "./chunk-LPUQPDC2.js";
+import {
+  resolveVaultDir
+} from "./chunk-JTYZRPX5.js";
+import "./chunk-PZUWP5VK.js";
+
+// src/cli.ts
+import fs from "fs";
+import path from "path";
+loadEnv();
+var USAGE = `Usage: myco <command> [args]
+
+Commands:
+  init [options]           Initialize a new vault
+  config <get|set> [args]  Get or set vault config values
+  detect-providers         Detect available LLM/embedding providers (JSON)
+  verify                   Test LLM and embedding connectivity
+  stats                    Vault health, index counts, vector count
+  search <query>           Combined FTS + vector search with scores
+  vectors <query>          Raw vector search with similarity scores
+  session [id|latest]      Show a session
+  logs [options]           View daemon logs
+  setup-llm [options]      Configure LLM and embedding providers
+  setup-digest [options]   Configure digest and capture settings
+  agent [options]          Run the intelligence agent
+  task <subcommand>        Manage agent task definitions
+  doctor [--fix]          Check vault health and repair issues
+  restart                  Restart the daemon
+  version                  Show plugin version
+  mcp                     Start the MCP stdio server
+  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)
+  daemon --vault <dir>    Start the daemon process
+`;
+async function main() {
+  const [cmd, ...args] = process.argv.slice(2);
+  if (!cmd || cmd === "--help" || cmd === "-h") {
+    process.stdout.write(USAGE);
+    return;
+  }
+  if (cmd === "init") return (await import("./init-6GWY345B.js")).run(args);
+  if (cmd === "detect-providers") return (await import("./detect-providers-Q42OD4OS.js")).run(args);
+  if (cmd === "version" || cmd === "--version" || cmd === "-v") {
+    const { getPluginVersion } = await import("./version-KLBN4HZT.js");
+    console.log(getPluginVersion());
+    return;
+  }
+  if (cmd === "mcp") return (await import("./server-6KMBJCHZ.js")).main();
+  if (cmd === "hook") {
+    const hookName = args[0];
+    const HOOK_DISPATCH = {
+      "session-start": () => import("./session-start-UCLK7PXE.js"),
+      "session-end": () => import("./session-end-FLVX32LE.js"),
+      "stop": () => import("./stop-XRQLLXST.js"),
+      "user-prompt-submit": () => import("./user-prompt-submit-KSM3AR6P.js"),
+      "post-tool-use": () => import("./post-tool-use-DOUM7CGQ.js"),
+      "post-tool-use-failure": () => import("./post-tool-use-failure-SG3C7PE6.js"),
+      "subagent-start": () => import("./subagent-start-MWWQTZMQ.js"),
+      "subagent-stop": () => import("./subagent-stop-PJXYGRXB.js"),
+      "stop-failure": () => import("./stop-failure-2CAJJKRG.js"),
+      "task-completed": () => import("./task-completed-4LFRJVGI.js"),
+      "pre-compact": () => import("./pre-compact-3J33CHXQ.js"),
+      "post-compact": () => import("./post-compact-OWFSOITU.js")
+    };
+    const loader = HOOK_DISPATCH[hookName];
+    if (!loader) {
+      console.error(`Unknown hook: ${hookName}. Available: ${Object.keys(HOOK_DISPATCH).join(", ")}`);
+      process.exit(1);
+    }
+    return (await loader()).main();
+  }
+  if (cmd === "daemon") return (await import("./main-BMCL7CPO.js")).main();
+  if (cmd === "doctor") {
+    const vaultDir2 = resolveVaultDir();
+    return (await import("./doctor-JLKTXDEH.js")).run(args, vaultDir2);
+  }
+  const vaultDir = resolveVaultDir();
+  if (!fs.existsSync(path.join(vaultDir, "myco.yaml"))) {
+    console.error(`No myco.yaml found in ${vaultDir}. Run 'myco init' first.`);
+    process.exit(1);
+  }
+  switch (cmd) {
+    case "config":
+      return (await import("./config-UR5BSGVX.js")).run(args, vaultDir);
+    case "verify":
+      return (await import("./verify-UDAYVX37.js")).run(args, vaultDir);
+    case "stats":
+      return (await import("./stats-IUJPZSVZ.js")).run(args, vaultDir);
+    case "search":
+      return (await import("./search-ZGQR5MDE.js")).run(args, vaultDir);
+    case "vectors":
+      return (await import("./search-ZGQR5MDE.js")).runVectors(args, vaultDir);
+    case "session":
+      return (await import("./session-Z2FXDDG6.js")).run(args, vaultDir);
+    case "setup-llm":
+      return (await import("./setup-llm-GKMCHURK.js")).run(args, vaultDir);
+    case "setup-digest":
+      return (await import("./setup-digest-4KDSXAIV.js")).run(args, vaultDir);
+    case "agent":
+      return (await import("./agent-run-EFICNTAU.js")).run(args, vaultDir);
+    case "task":
+      return (await import("./agent-tasks-RXJ7Z5NG.js")).run(args, vaultDir);
+    case "restart":
+      return (await import("./restart-2VM33WOB.js")).run(args, vaultDir);
+    case "logs":
+      return (await import("./logs-QZVYF6FP.js")).run(args, vaultDir);
+    default:
+      console.error(`Unknown command: ${cmd}`);
+      process.stdout.write(USAGE);
+      process.exit(1);
+  }
+}
+main().catch((err) => {
+  console.error(`myco: ${err.message}`);
+  process.exit(1);
+});
+//# sourceMappingURL=cli-ODLFRIYS.js.map

package/dist/cli-ODLFRIYS.js.map

@@ -0,0 +1 @@
+{"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  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  doctor [--fix]          Check vault health and repair issues\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}. Available: ${Object.keys(HOOK_DISPATCH).join(', ')}`);\n      process.exit(1);\n    }\n    return (await loader()).main();\n  }\n  if (cmd === 'daemon') return (await import('./daemon/main.js')).main();\n\n  if (cmd === 'doctor') {\n    const vaultDir = resolveVaultDir();\n    return (await import('./cli/doctor.js')).run(args, vaultDir);\n  }\n\n  const vaultDir = resolveVaultDir();\n  if (!fs.existsSync(path.join(vaultDir, 'myco.yaml'))) {\n    console.error(`No myco.yaml found in ${vaultDir}. Run 'myco init' first.`);\n    process.exit(1);\n  }\n\n  switch (cmd) {\n    case 'config': return (await import('./cli/config.js')).run(args, vaultDir);\n    case 'verify': return (await import('./cli/verify.js')).run(args, vaultDir);\n    case 'stats': return (await import('./cli/stats.js')).run(args, vaultDir);\n    case 'search': return (await import('./cli/search.js')).run(args, vaultDir);\n    case 'vectors': return (await import('./cli/search.js')).runVectors(args, vaultDir);\n    case 'session': return (await import('./cli/session.js')).run(args, vaultDir);\n    case 'setup-llm': return (await import('./cli/setup-llm.js')).run(args, vaultDir);\n    case 'setup-digest': return (await import('./cli/setup-digest.js')).run(args, vaultDir);\n    case 'agent': return (await import('./cli/agent-run.js')).run(args, vaultDir);\n    case 'task': return (await import('./cli/agent-tasks.js')).run(args, vaultDir);\n    case 'restart': return (await import('./cli/restart.js')).run(args, vaultDir);\n    case 'logs': return (await import('./cli/logs.js')).run(args, vaultDir);\n    default:\n      console.error(`Unknown command: ${cmd}`);\n      process.stdout.write(USAGE);\n      process.exit(1);\n  }\n}\n\nmain().catch((err) => {\n  console.error(`myco: ${(err as Error).message}`);\n  process.exit(1);\n});\n"],"mappings":";;;;;;;;;;;;;;;;;;;AAGA,OAAO,QAAQ;AACf,OAAO,UAAU;AAEjB,QAAQ;AAER,IAAM,QAAQ;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAwBd,eAAe,OAAsB;AACnC,QAAM,CAAC,KAAK,GAAG,IAAI,IAAI,QAAQ,KAAK,MAAM,CAAC;AAC3C,MAAI,CAAC,OAAO,QAAQ,YAAY,QAAQ,MAAM;AAC5C,YAAQ,OAAO,MAAM,KAAK;AAC1B;AAAA,EACF;AAEA,MAAI,QAAQ,OAAQ,SAAQ,MAAM,OAAO,oBAAe,GAAG,IAAI,IAAI;AACnE,MAAI,QAAQ,mBAAoB,SAAQ,MAAM,OAAO,gCAA2B,GAAG,IAAI,IAAI;AAC3F,MAAI,QAAQ,aAAa,QAAQ,eAAe,QAAQ,MAAM;AAC5D,UAAM,EAAE,iBAAiB,IAAI,MAAM,OAAO,uBAAc;AACxD,YAAQ,IAAI,iBAAiB,CAAC;AAC9B;AAAA,EACF;AACA,MAAI,QAAQ,MAAO,SAAQ,MAAM,OAAO,sBAAiB,GAAG,KAAK;AACjE,MAAI,QAAQ,QAAQ;AAClB,UAAM,WAAW,KAAK,CAAC;AACvB,UAAM,gBAA8E;AAAA,MAClF,iBAAiB,MAAM,OAAO,6BAA0B;AAAA,MACxD,eAAe,MAAM,OAAO,2BAAwB;AAAA,MACpD,QAAQ,MAAM,OAAO,oBAAiB;AAAA,MACtC,sBAAsB,MAAM,OAAO,kCAA+B;AAAA,MAClE,iBAAiB,MAAM,OAAO,6BAA0B;AAAA,MACxD,yBAAyB,MAAM,OAAO,qCAAkC;AAAA,MACxE,kBAAkB,MAAM,OAAO,8BAA2B;AAAA,MAC1D,iBAAiB,MAAM,OAAO,6BAA0B;AAAA,MACxD,gBAAgB,MAAM,OAAO,4BAAyB;AAAA,MACtD,kBAAkB,MAAM,OAAO,8BAA2B;AAAA,MAC1D,eAAe,MAAM,OAAO,2BAAwB;AAAA,MACpD,gBAAgB,MAAM,OAAO,4BAAyB;AAAA,IACxD;AACA,UAAM,SAAS,cAAc,QAAQ;AACrC,QAAI,CAAC,QAAQ;AACX,cAAQ,MAAM,iBAAiB,QAAQ,gBAAgB,OAAO,KAAK,aAAa,EAAE,KAAK,IAAI,CAAC,EAAE;AAC9F,cAAQ,KAAK,CAAC;AAAA,IAChB;AACA,YAAQ,MAAM,OAAO,GAAG,KAAK;AAAA,EAC/B;AACA,MAAI,QAAQ,SAAU,SAAQ,MAAM,OAAO,oBAAkB,GAAG,KAAK;AAErE,MAAI,QAAQ,UAAU;AACpB,UAAMA,YAAW,gBAAgB;AACjC,YAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAMA,SAAQ;AAAA,EAC7D;AAEA,QAAM,WAAW,gBAAgB;AACjC,MAAI,CAAC,GAAG,WAAW,KAAK,KAAK,UAAU,WAAW,CAAC,GAAG;AACpD,YAAQ,MAAM,yBAAyB,QAAQ,0BAA0B;AACzE,YAAQ,KAAK,CAAC;AAAA,EAChB;AAEA,UAAQ,KAAK;AAAA,IACX,KAAK;AAAU,cAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC1E,KAAK;AAAU,cAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC1E,KAAK;AAAS,cAAQ,MAAM,OAAO,qBAAgB,GAAG,IAAI,MAAM,QAAQ;AAAA,IACxE,KAAK;AAAU,cAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC1E,KAAK;AAAW,cAAQ,MAAM,OAAO,sBAAiB,GAAG,WAAW,MAAM,QAAQ;AAAA,IAClF,KAAK;AAAW,cAAQ,MAAM,OAAO,uBAAkB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC5E,KAAK;AAAa,cAAQ,MAAM,OAAO,yBAAoB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAChF,KAAK;AAAgB,cAAQ,MAAM,OAAO,4BAAuB,GAAG,IAAI,MAAM,QAAQ;AAAA,IACtF,KAAK;AAAS,cAAQ,MAAM,OAAO,yBAAoB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC5E,KAAK;AAAQ,cAAQ,MAAM,OAAO,2BAAsB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC7E,KAAK;AAAW,cAAQ,MAAM,OAAO,uBAAkB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC5E,KAAK;AAAQ,cAAQ,MAAM,OAAO,oBAAe,GAAG,IAAI,MAAM,QAAQ;AAAA,IACtE;AACE,cAAQ,MAAM,oBAAoB,GAAG,EAAE;AACvC,cAAQ,OAAO,MAAM,KAAK;AAC1B,cAAQ,KAAK,CAAC;AAAA,EAClB;AACF;AAEA,KAAK,EAAE,MAAM,CAAC,QAAQ;AACpB,UAAQ,MAAM,SAAU,IAAc,OAAO,EAAE;AAC/C,UAAQ,KAAK,CAAC;AAChB,CAAC;","names":["vaultDir"]}

package/dist/client-EYOTW3JU.js

@@ -0,0 +1,19 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  SQLITE_DB_FILE,
+  closeDatabase,
+  getDatabase,
+  initDatabase,
+  openReadonly,
+  vaultDbPath
+} from "./chunk-MYX5NCRH.js";
+import "./chunk-PZUWP5VK.js";
+export {
+  SQLITE_DB_FILE,
+  closeDatabase,
+  getDatabase,
+  initDatabase,
+  openReadonly,
+  vaultDbPath
+};
+//# sourceMappingURL=client-EYOTW3JU.js.map

package/dist/client-MXRNQ5FI.js

@@ -0,0 +1,13 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  DaemonClient
+} from "./chunk-TRUJLI6K.js";
+import "./chunk-5VZ52A4T.js";
+import "./chunk-WGTCA2NU.js";
+import "./chunk-PB6TOLRQ.js";
+import "./chunk-LPUQPDC2.js";
+import "./chunk-PZUWP5VK.js";
+export {
+  DaemonClient
+};
+//# sourceMappingURL=client-MXRNQ5FI.js.map

package/dist/{config-IBS6KOLQ.js → config-UR5BSGVX.js}

@@ -1,20 +1,19 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
-  loadConfig
-} from "./chunk-HYVT345Y.js";
+  withValue
+} from "./chunk-M5XWW7UI.js";
 import {
-  MycoConfigSchema,
-  require_dist
-} from "./chunk-ERG2IEWX.js";
-import {
-  __toESM
-} from "./chunk-PZUWP5VK.js";
+  loadConfig,
+  updateConfig
+} from "./chunk-MHSCMET3.js";
+import "./chunk-D7TYRPRM.js";
+import "./chunk-E4VLWIJC.js";
+import "./chunk-KH64DHOY.js";
+import "./chunk-PZUWP5VK.js";
 
 // src/cli/config.ts
-var import_yaml = __toESM(require_dist(), 1);
 import fs from "fs";
 import path from "path";
-var CONFIG_FILENAME = "myco.yaml";
 var DAEMON_STATE_FILENAME = "daemon.json";
 async function run(args, vaultDir) {
   const [subcommand, key, ...rest] = args;
@@ -46,20 +45,20 @@ function configGet(dotPath, vaultDir) {
   console.log(typeof value === "object" ? JSON.stringify(value, null, 2) : String(value));
 }
 function configSet(dotPath, rawValue, vaultDir) {
-  const configPath = path.join(vaultDir, CONFIG_FILENAME);
-  const raw = fs.readFileSync(configPath, "utf-8");
-  const doc = import_yaml.default.parse(raw);
   const value = parseValue(rawValue);
-  setPath(doc, dotPath, value);
-  const result = MycoConfigSchema.safeParse(doc);
-  if (!result.success) {
-    console.error("Validation error:");
-    for (const issue of result.error.issues) {
-      console.error(`  ${issue.path.join(".")}: ${issue.message}`);
+  try {
+    updateConfig(vaultDir, (config) => withValue(config, dotPath, value));
+  } catch (err) {
+    if (err instanceof Error && "issues" in err) {
+      const issues = err.issues;
+      console.error("Validation error:");
+      for (const issue of issues) {
+        console.error(`  ${issue.path.join(".")}: ${issue.message}`);
+      }
+      process.exit(1);
     }
-    process.exit(1);
+    throw err;
   }
-  fs.writeFileSync(configPath, import_yaml.default.stringify(doc), "utf-8");
   console.log(`Set ${dotPath} = ${JSON.stringify(value)}`);
   if (fs.existsSync(path.join(vaultDir, DAEMON_STATE_FILENAME))) {
     console.log("Note: restart the daemon for changes to take effect (myco restart)");
@@ -76,18 +75,6 @@ function walkPath(obj, dotPath) {
   }
   return current;
 }
-function setPath(obj, dotPath, value) {
-  const segments = dotPath.split(".");
-  let current = obj;
-  for (let i = 0; i < segments.length - 1; i++) {
-    const segment = segments[i];
-    if (current[segment] === void 0 || current[segment] === null || typeof current[segment] !== "object") {
-      current[segment] = {};
-    }
-    current = current[segment];
-  }
-  current[segments[segments.length - 1]] = value;
-}
 function parseValue(raw) {
   try {
     return JSON.parse(raw);
@@ -98,4 +85,4 @@ function parseValue(raw) {
 export {
   run
 };
-//# sourceMappingURL=config-IBS6KOLQ.js.map
+//# sourceMappingURL=config-UR5BSGVX.js.map

package/dist/config-UR5BSGVX.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/config.ts"],"sourcesContent":["import fs from 'node:fs';\nimport path from 'node:path';\nimport { loadConfig, updateConfig } from '../config/loader.js';\nimport { withValue } from '../config/updates.js';\n\nconst DAEMON_STATE_FILENAME = 'daemon.json';\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const [subcommand, key, ...rest] = args;\n\n  if (subcommand === 'get') {\n    if (!key) {\n      console.error('Usage: myco config get <dot.path.key>');\n      process.exit(1);\n    }\n    return configGet(key, vaultDir);\n  }\n\n  if (subcommand === 'set') {\n    const value = rest[0];\n    if (!key || value === undefined) {\n      console.error('Usage: myco config set <dot.path.key> <value>');\n      process.exit(1);\n    }\n    return configSet(key, value, vaultDir);\n  }\n\n  console.error('Usage: myco config <get|set> <dot.path.key> [value]');\n  process.exit(1);\n}\n\nfunction configGet(dotPath: string, vaultDir: string): void {\n  const config = loadConfig(vaultDir);\n  const value = walkPath(config as Record<string, unknown>, dotPath);\n  if (value === undefined) {\n    console.error(`Key not found: ${dotPath}`);\n    process.exit(1);\n  }\n  console.log(typeof value === 'object' ? JSON.stringify(value, null, 2) : String(value));\n}\n\nfunction configSet(dotPath: string, rawValue: string, vaultDir: string): void {\n  const value = parseValue(rawValue);\n\n  try {\n    updateConfig(vaultDir, (config) => withValue(config, dotPath, value));\n  } catch (err) {\n    if (err instanceof Error && 'issues' in err) {\n      const issues = (err as { issues: Array<{ path: (string | number)[]; message: string }> }).issues;\n      console.error('Validation error:');\n      for (const issue of issues) {\n        console.error(`  ${issue.path.join('.')}: ${issue.message}`);\n      }\n      process.exit(1);\n    }\n    throw err;\n  }\n\n  console.log(`Set ${dotPath} = ${JSON.stringify(value)}`);\n\n  if (fs.existsSync(path.join(vaultDir, DAEMON_STATE_FILENAME))) {\n    console.log('Note: restart the daemon for changes to take effect (myco restart)');\n  }\n}\n\n/** Walk a dot-separated path to retrieve a nested value. */\nfunction walkPath(obj: Record<string, unknown>, dotPath: string): unknown {\n  const segments = dotPath.split('.');\n  let current: unknown = obj;\n  for (const segment of segments) {\n    if (current === null || current === undefined || typeof current !== 'object') {\n      return undefined;\n    }\n    current = (current as Record<string, unknown>)[segment];\n  }\n  return current;\n}\n\n/** Parse a string value as JSON (number, boolean, array, object), falling back to raw string. */\nfunction parseValue(raw: string): unknown {\n  try {\n    return JSON.parse(raw);\n  } catch {\n    return raw;\n  }\n}\n"],"mappings":";;;;;;;;;;;;;;AAAA,OAAO,QAAQ;AACf,OAAO,UAAU;AAIjB,IAAM,wBAAwB;AAE9B,eAAsB,IAAI,MAAgB,UAAiC;AACzE,QAAM,CAAC,YAAY,KAAK,GAAG,IAAI,IAAI;AAEnC,MAAI,eAAe,OAAO;AACxB,QAAI,CAAC,KAAK;AACR,cAAQ,MAAM,uCAAuC;AACrD,cAAQ,KAAK,CAAC;AAAA,IAChB;AACA,WAAO,UAAU,KAAK,QAAQ;AAAA,EAChC;AAEA,MAAI,eAAe,OAAO;AACxB,UAAM,QAAQ,KAAK,CAAC;AACpB,QAAI,CAAC,OAAO,UAAU,QAAW;AAC/B,cAAQ,MAAM,+CAA+C;AAC7D,cAAQ,KAAK,CAAC;AAAA,IAChB;AACA,WAAO,UAAU,KAAK,OAAO,QAAQ;AAAA,EACvC;AAEA,UAAQ,MAAM,qDAAqD;AACnE,UAAQ,KAAK,CAAC;AAChB;AAEA,SAAS,UAAU,SAAiB,UAAwB;AAC1D,QAAM,SAAS,WAAW,QAAQ;AAClC,QAAM,QAAQ,SAAS,QAAmC,OAAO;AACjE,MAAI,UAAU,QAAW;AACvB,YAAQ,MAAM,kBAAkB,OAAO,EAAE;AACzC,YAAQ,KAAK,CAAC;AAAA,EAChB;AACA,UAAQ,IAAI,OAAO,UAAU,WAAW,KAAK,UAAU,OAAO,MAAM,CAAC,IAAI,OAAO,KAAK,CAAC;AACxF;AAEA,SAAS,UAAU,SAAiB,UAAkB,UAAwB;AAC5E,QAAM,QAAQ,WAAW,QAAQ;AAEjC,MAAI;AACF,iBAAa,UAAU,CAAC,WAAW,UAAU,QAAQ,SAAS,KAAK,CAAC;AAAA,EACtE,SAAS,KAAK;AACZ,QAAI,eAAe,SAAS,YAAY,KAAK;AAC3C,YAAM,SAAU,IAA0E;AAC1F,cAAQ,MAAM,mBAAmB;AACjC,iBAAW,SAAS,QAAQ;AAC1B,gBAAQ,MAAM,KAAK,MAAM,KAAK,KAAK,GAAG,CAAC,KAAK,MAAM,OAAO,EAAE;AAAA,MAC7D;AACA,cAAQ,KAAK,CAAC;AAAA,IAChB;AACA,UAAM;AAAA,EACR;AAEA,UAAQ,IAAI,OAAO,OAAO,MAAM,KAAK,UAAU,KAAK,CAAC,EAAE;AAEvD,MAAI,GAAG,WAAW,KAAK,KAAK,UAAU,qBAAqB,CAAC,GAAG;AAC7D,YAAQ,IAAI,oEAAoE;AAAA,EAClF;AACF;AAGA,SAAS,SAAS,KAA8B,SAA0B;AACxE,QAAM,WAAW,QAAQ,MAAM,GAAG;AAClC,MAAI,UAAmB;AACvB,aAAW,WAAW,UAAU;AAC9B,QAAI,YAAY,QAAQ,YAAY,UAAa,OAAO,YAAY,UAAU;AAC5E,aAAO;AAAA,IACT;AACA,cAAW,QAAoC,OAAO;AAAA,EACxD;AACA,SAAO;AACT;AAGA,SAAS,WAAW,KAAsB;AACxC,MAAI;AACF,WAAO,KAAK,MAAM,GAAG;AAAA,EACvB,QAAQ;AACN,WAAO;AAAA,EACT;AACF;","names":[]}

package/dist/detect-H5OPI7GD.js

@@ -0,0 +1,17 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  detectSymbionts,
+  loadManifests,
+  resolvePackageRoot
+} from "./chunk-5PEUFJ6U.js";
+import "./chunk-D7TYRPRM.js";
+import "./chunk-E4VLWIJC.js";
+import "./chunk-KH64DHOY.js";
+import "./chunk-LPUQPDC2.js";
+import "./chunk-PZUWP5VK.js";
+export {
+  detectSymbionts,
+  loadManifests,
+  resolvePackageRoot
+};
+//# sourceMappingURL=detect-H5OPI7GD.js.map

package/dist/detect-H5OPI7GD.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/dist/detect-providers-Q42OD4OS.js

@@ -0,0 +1,26 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  checkLocalProvider
+} from "./chunk-DCXRSSBP.js";
+import "./chunk-UBZPD4HN.js";
+import "./chunk-5VZ52A4T.js";
+import "./chunk-WGTCA2NU.js";
+import "./chunk-PZUWP5VK.js";
+
+// src/cli/detect-providers.ts
+async function run(_args) {
+  const [ollamaResult, lmStudioResult] = await Promise.all([
+    checkLocalProvider("ollama"),
+    checkLocalProvider("lmstudio")
+  ]);
+  const result = {
+    ollama: ollamaResult,
+    "lm-studio": lmStudioResult,
+    anthropic: { available: !!process.env.ANTHROPIC_API_KEY, models: [] }
+  };
+  console.log(JSON.stringify(result, null, 2));
+}
+export {
+  run
+};
+//# sourceMappingURL=detect-providers-Q42OD4OS.js.map

package/dist/detect-providers-Q42OD4OS.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/detect-providers.ts"],"sourcesContent":["import { checkLocalProvider } from '../intelligence/provider-check.js';\n\ninterface ProviderResult {\n  available: boolean;\n  models: string[];\n}\n\ninterface DetectResult {\n  ollama: ProviderResult;\n  'lm-studio': ProviderResult;\n  anthropic: ProviderResult;\n}\n\nexport async function run(_args: string[]): Promise<void> {\n  const [ollamaResult, lmStudioResult] = await Promise.all([\n    checkLocalProvider('ollama'),\n    checkLocalProvider('lmstudio'),\n  ]);\n\n  const result: DetectResult = {\n    ollama: ollamaResult,\n    'lm-studio': lmStudioResult,\n    anthropic: { available: !!process.env.ANTHROPIC_API_KEY, models: [] },\n  };\n\n  console.log(JSON.stringify(result, null, 2));\n}\n"],"mappings":";;;;;;;;;;AAaA,eAAsB,IAAI,OAAgC;AACxD,QAAM,CAAC,cAAc,cAAc,IAAI,MAAM,QAAQ,IAAI;AAAA,IACvD,mBAAmB,QAAQ;AAAA,IAC3B,mBAAmB,UAAU;AAAA,EAC/B,CAAC;AAED,QAAM,SAAuB;AAAA,IAC3B,QAAQ;AAAA,IACR,aAAa;AAAA,IACb,WAAW,EAAE,WAAW,CAAC,CAAC,QAAQ,IAAI,mBAAmB,QAAQ,CAAC,EAAE;AAAA,EACtE;AAEA,UAAQ,IAAI,KAAK,UAAU,QAAQ,MAAM,CAAC,CAAC;AAC7C;","names":[]}

package/dist/doctor-JLKTXDEH.js

@@ -0,0 +1,258 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  isProcessAlive
+} from "./chunk-KB4DGYIY.js";
+import "./chunk-SAKJMNSR.js";
+import "./chunk-UBZPD4HN.js";
+import "./chunk-MYX5NCRH.js";
+import "./chunk-TRUJLI6K.js";
+import "./chunk-5VZ52A4T.js";
+import "./chunk-WGTCA2NU.js";
+import "./chunk-PB6TOLRQ.js";
+import "./chunk-LPUQPDC2.js";
+import "./chunk-PZUWP5VK.js";
+
+// src/cli/doctor.ts
+import fs from "fs";
+import path from "path";
+var CONFIG_FILENAME = "myco.yaml";
+var DAEMON_STATE_FILENAME = "daemon.json";
+var DB_FILENAME = "myco.db";
+var NAME_COL_WIDTH = 17;
+var CONTINUATION_INDENT = " ".repeat(NAME_COL_WIDTH);
+async function checkVault(vaultDir) {
+  const configPath = path.join(vaultDir, CONFIG_FILENAME);
+  if (!fs.existsSync(configPath)) {
+    return { check: { name: "Vault", status: "fail", detail: `${CONFIG_FILENAME} not found in ${vaultDir}`, fixable: false }, config: null };
+  }
+  try {
+    const { loadConfig } = await import("./loader-XVXKZZDH.js");
+    const config = loadConfig(vaultDir);
+    return { check: { name: "Vault", status: "ok", detail: `.myco/ (v${config.version})`, fixable: false }, config };
+  } catch (err) {
+    return { check: { name: "Vault", status: "fail", detail: `${CONFIG_FILENAME} parse error: ${err.message}`, fixable: false }, config: null };
+  }
+}
+async function checkDatabase(vaultDir) {
+  const dbPath = path.join(vaultDir, DB_FILENAME);
+  if (!fs.existsSync(dbPath)) {
+    return { name: "Database", status: "fail", detail: `${DB_FILENAME} not found \u2014 run \`myco init\``, fixable: false };
+  }
+  try {
+    const { initDatabase, closeDatabase, vaultDbPath } = await import("./client-EYOTW3JU.js");
+    const db = initDatabase(vaultDbPath(vaultDir));
+    const row = db.prepare("SELECT count(*) AS cnt FROM sessions").get();
+    const count = row?.cnt ?? 0;
+    closeDatabase();
+    return { name: "Database", status: "ok", detail: `${DB_FILENAME} (${count.toLocaleString()} sessions)`, fixable: false };
+  } catch (err) {
+    try {
+      const { closeDatabase } = await import("./client-EYOTW3JU.js");
+      closeDatabase();
+    } catch {
+    }
+    return { name: "Database", status: "fail", detail: `Database error: ${err.message}`, fixable: false };
+  }
+}
+async function checkIntelligence(config) {
+  try {
+    const provider = config.agent.provider;
+    if (!provider) {
+      return { name: "Intelligence", status: "warn", detail: "No agent provider configured \u2014 run `myco init` to set up", fixable: false };
+    }
+    const label = `${provider.type}${provider.model ? ` / ${provider.model}` : ""}`;
+    if (provider.type === "cloud") {
+      return { name: "Intelligence", status: "ok", detail: `${label} (SDK handles auth)`, fixable: false };
+    }
+    if (provider.type === "ollama" || provider.type === "lmstudio") {
+      const { checkLocalProvider } = await import("./provider-check-3WBPZADE.js");
+      const status = await checkLocalProvider(provider.type, provider.base_url);
+      if (!status.available) {
+        return { name: "Intelligence", status: "warn", detail: `${label} (not reachable)`, fixable: false };
+      }
+      return { name: "Intelligence", status: "ok", detail: label, fixable: false };
+    }
+    return { name: "Intelligence", status: "ok", detail: label, fixable: false };
+  } catch (err) {
+    return { name: "Intelligence", status: "fail", detail: `Intelligence check failed: ${err.message}`, fixable: false };
+  }
+}
+async function checkEmbeddings(config) {
+  try {
+    const { createEmbeddingProvider } = await import("./llm-BV3QNVRD.js");
+    const provider = createEmbeddingProvider(config.embedding);
+    const available = await provider.isAvailable();
+    const label = `${config.embedding.provider} / ${config.embedding.model}`;
+    if (available) {
+      return { name: "Embeddings", status: "ok", detail: label, fixable: false };
+    }
+    return { name: "Embeddings", status: "warn", detail: `${label} (not reachable)`, fixable: false };
+  } catch (err) {
+    return { name: "Embeddings", status: "fail", detail: `Embedding check failed: ${err.message}`, fixable: false };
+  }
+}
+async function checkAgents(vaultDir) {
+  try {
+    const { detectSymbionts } = await import("./detect-H5OPI7GD.js");
+    const { resolveVaultDir } = await import("./resolve-3FEUV462.js");
+    const projectRoot = path.dirname(resolveVaultDir());
+    const detected = detectSymbionts(projectRoot);
+    if (detected.length === 0) {
+      return [{ name: "Agents", status: "warn", detail: "No symbionts detected", fixable: false }];
+    }
+    const checks = [];
+    for (const d of detected) {
+      const registered = isSymbiontRegistered(d, projectRoot);
+      if (registered) {
+        checks.push({
+          name: checks.length === 0 ? "Agents" : "",
+          status: "ok",
+          detail: `${d.manifest.displayName} (registered)`,
+          fixable: false
+        });
+      } else {
+        checks.push({
+          name: checks.length === 0 ? "Agents" : "",
+          status: "warn",
+          detail: `${d.manifest.displayName} (detected but not registered)`,
+          fixable: true
+        });
+      }
+    }
+    return checks;
+  } catch (err) {
+    return [{ name: "Agents", status: "fail", detail: `Agent check failed: ${err.message}`, fixable: false }];
+  }
+}
+function isSymbiontRegistered(d, projectRoot) {
+  try {
+    if (d.manifest.settingsPath) {
+      const settingsFile = path.join(projectRoot, d.manifest.settingsPath);
+      if (!fs.existsSync(settingsFile)) return false;
+      const settings = JSON.parse(fs.readFileSync(settingsFile, "utf-8"));
+      const env = settings.env;
+      return !!env?.MYCO_VAULT_DIR;
+    }
+    if (d.manifest.mcpConfigPath) {
+      const mcpFile = path.join(projectRoot, d.manifest.mcpConfigPath);
+      if (!fs.existsSync(mcpFile)) return false;
+      const config = JSON.parse(fs.readFileSync(mcpFile, "utf-8"));
+      const servers = config.mcpServers;
+      return !!servers?.myco?.env?.MYCO_VAULT_DIR;
+    }
+  } catch {
+  }
+  return false;
+}
+async function checkDaemon(vaultDir) {
+  const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);
+  if (!fs.existsSync(daemonFile)) {
+    return { name: "Daemon", status: "warn", detail: "Not running (no daemon.json)", fixable: false };
+  }
+  try {
+    const state = JSON.parse(fs.readFileSync(daemonFile, "utf-8"));
+    if (!state.pid) {
+      return { name: "Daemon", status: "warn", detail: "daemon.json exists but no PID", fixable: true };
+    }
+    if (isProcessAlive(state.pid)) {
+      return { name: "Daemon", status: "ok", detail: `PID ${state.pid}, port ${state.port ?? "unknown"}`, fixable: false };
+    }
+    return { name: "Daemon", status: "warn", detail: `Stale daemon.json (PID ${state.pid} not running)`, fixable: true };
+  } catch (err) {
+    return { name: "Daemon", status: "fail", detail: `daemon.json parse error: ${err.message}`, fixable: true };
+  }
+}
+async function runChecks(vaultDir) {
+  const { check: vaultCheck, config } = await checkVault(vaultDir);
+  const checks = [vaultCheck];
+  if (!config) {
+    checks.push(
+      { name: "Database", status: "fail", detail: "Skipped (vault check failed)", fixable: false },
+      { name: "Intelligence", status: "fail", detail: "Skipped (vault check failed)", fixable: false },
+      { name: "Embeddings", status: "fail", detail: "Skipped (vault check failed)", fixable: false },
+      { name: "Agents", status: "fail", detail: "Skipped (vault check failed)", fixable: false },
+      await checkDaemon(vaultDir)
+    );
+    return checks;
+  }
+  checks.push(await checkDatabase(vaultDir));
+  checks.push(await checkIntelligence(config));
+  checks.push(await checkEmbeddings(config));
+  checks.push(...await checkAgents(vaultDir));
+  checks.push(await checkDaemon(vaultDir));
+  return checks;
+}
+async function fix(vaultDir, checks) {
+  const actions = [];
+  for (const check of checks) {
+    if (!check.fixable || check.status === "ok") continue;
+    if (check.name === "Daemon" && check.detail.includes("Stale")) {
+      const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);
+      fs.unlinkSync(daemonFile);
+      actions.push("Removed stale daemon.json");
+    }
+    if (check.name === "Daemon" && check.detail.includes("parse error")) {
+      const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);
+      fs.unlinkSync(daemonFile);
+      actions.push("Removed malformed daemon.json");
+    }
+    if ((check.name === "Agents" || check.name === "") && check.detail.includes("not registered")) {
+      actions.push("Run `myco init` to register detected agents");
+    }
+    if (check.name === "Database" && check.status === "fail") {
+      actions.push("Run `myco init` to initialize the database");
+    }
+  }
+  return actions;
+}
+var STATUS_COL_WIDTH = 6;
+var STATUS_LABELS = {
+  ok: { text: "ok", color: "\x1B[32m" },
+  fail: { text: "FAIL", color: "\x1B[31m" },
+  warn: { text: "!!", color: "\x1B[33m" }
+};
+function formatCheck(check) {
+  const name = check.name ? check.name.padEnd(NAME_COL_WIDTH) : CONTINUATION_INDENT;
+  const { text, color } = STATUS_LABELS[check.status];
+  const paddedText = text.padEnd(STATUS_COL_WIDTH);
+  return `  ${name}${color}${paddedText}\x1B[0m${check.detail}`;
+}
+async function run(args, vaultDir) {
+  const shouldFix = args.includes("--fix");
+  console.log("\nmyco doctor\n");
+  const checks = await runChecks(vaultDir);
+  for (const check of checks) {
+    console.log(formatCheck(check));
+  }
+  const issues = checks.filter((c) => c.status !== "ok");
+  const fixable = issues.filter((c) => c.fixable);
+  console.log("");
+  if (issues.length === 0) {
+    console.log("  All checks passed.\n");
+    return;
+  }
+  console.log(`  ${issues.length} issue(s) found.`);
+  if (shouldFix) {
+    const actions = await fix(vaultDir, checks);
+    if (actions.length > 0) {
+      console.log("");
+      for (const action of actions) {
+        console.log(`  Fixed: ${action}`);
+      }
+      console.log("");
+    } else {
+      console.log("  No auto-fixable issues.\n");
+    }
+  } else if (fixable.length > 0) {
+    console.log(`  Run \`myco doctor --fix\` to repair ${fixable.length} fixable issue(s).
+`);
+  } else {
+    console.log("");
+  }
+}
+export {
+  fix,
+  run,
+  runChecks
+};
+//# sourceMappingURL=doctor-JLKTXDEH.js.map

package/dist/doctor-JLKTXDEH.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/doctor.ts"],"sourcesContent":["/**\n * CLI: myco doctor — check vault health and auto-repair fixable issues.\n *\n * Runs a series of health checks against the vault directory and reports\n * status. 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';\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 ${vaultDir}`, fixable: false }, config: null };\n  }\n  try {\n    const { loadConfig } = await import('../config/loader.js');\n    const config = loadConfig(vaultDir);\n    return { check: { name: 'Vault', status: 'ok', detail: `.myco/ (v${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 ? ` / ${provider.model}` : ''}`;\n\n    if (provider.type === 'cloud') {\n      return { name: 'Intelligence', status: 'ok', detail: `${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: ${(err as Error).message}`, fixable: false };\n  }\n}\n\n/** Check symbiont detection and registration status. */\nasync function checkAgents(vaultDir: string): Promise<DoctorCheck[]> {\n  try {\n    const { detectSymbionts } = await import('../symbionts/detect.js');\n    const { resolveVaultDir } = await import('../vault/resolve.js');\n    const projectRoot = path.dirname(resolveVaultDir());\n    const detected = detectSymbionts(projectRoot);\n\n    if (detected.length === 0) {\n      return [{ name: 'Agents', status: 'warn', detail: 'No symbionts detected', fixable: false }];\n    }\n\n    const checks: DoctorCheck[] = [];\n    for (const d of detected) {\n      const registered = isSymbiontRegistered(d, projectRoot);\n      if (registered) {\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'ok',\n          detail: `${d.manifest.displayName} (registered)`,\n          fixable: false,\n        });\n      } else {\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'warn',\n          detail: `${d.manifest.displayName} (detected but not registered)`,\n          fixable: true,\n        });\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 MYCO_VAULT_DIR configured in its settings/MCP config. */\nfunction isSymbiontRegistered(\n  d: import('../symbionts/detect.js').DetectedSymbiont,\n  projectRoot: string,\n): boolean {\n  try {\n    if (d.manifest.settingsPath) {\n      const settingsFile = path.join(projectRoot, d.manifest.settingsPath);\n      if (!fs.existsSync(settingsFile)) return false;\n      const settings = JSON.parse(fs.readFileSync(settingsFile, 'utf-8')) as Record<string, unknown>;\n      const env = settings.env as Record<string, string> | undefined;\n      return !!env?.MYCO_VAULT_DIR;\n    }\n\n    if (d.manifest.mcpConfigPath) {\n      const mcpFile = path.join(projectRoot, d.manifest.mcpConfigPath);\n      if (!fs.existsSync(mcpFile)) return false;\n      const config = JSON.parse(fs.readFileSync(mcpFile, 'utf-8')) as Record<string, unknown>;\n      const servers = config.mcpServers as Record<string, { env?: Record<string, string> }> | undefined;\n      return !!servers?.myco?.env?.MYCO_VAULT_DIR;\n    }\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 ?? 'unknown'}`, fixable: false };\n    }\n    return { name: 'Daemon', status: 'warn', detail: `Stale daemon.json (PID ${state.pid} not running)`, fixable: true };\n  } catch (err) {\n    return { name: 'Daemon', status: 'fail', detail: `daemon.json parse error: ${(err as Error).message}`, fixable: true };\n  }\n}\n\n\n// --- Public API ---\n\n/** Run all health checks against a vault directory. */\nexport async function runChecks(vaultDir: string): Promise<DoctorCheck[]> {\n  const { check: vaultCheck, config } = await checkVault(vaultDir);\n  const checks: DoctorCheck[] = [vaultCheck];\n\n  if (!config) {\n    checks.push(\n      { name: 'Database', status: 'fail', detail: 'Skipped (vault check failed)', fixable: false },\n      { name: 'Intelligence', status: 'fail', detail: 'Skipped (vault check failed)', fixable: false },\n      { name: 'Embeddings', status: 'fail', detail: 'Skipped (vault check failed)', fixable: false },\n      { name: 'Agents', status: 'fail', detail: 'Skipped (vault check failed)', fixable: false },\n      await checkDaemon(vaultDir),\n    );\n    return checks;\n  }\n\n  checks.push(await checkDatabase(vaultDir));\n  checks.push(await checkIntelligence(config));\n  checks.push(await checkEmbeddings(config));\n  checks.push(...await checkAgents(vaultDir));\n  checks.push(await checkDaemon(vaultDir));\n\n  return checks;\n}\n\n/** Auto-repair fixable issues. 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 agent registration\n    if ((check.name === 'Agents' || check.name === '') && check.detail.includes('not registered')) {\n      actions.push('Run `myco init` to register detected agents');\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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