@goondocks/myco 0.16.2 → 0.17.1

package/dist/{chunk-RPILIIYT.js → chunk-Y7QCKCEJ.js}

@@ -1,7 +1,7 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   CloudEmbeddingBase
-} from "./chunk-DZWSHCAC.js";
+} from "./chunk-KGL5QSDN.js";
 
 // src/cli/providers/openai-embeddings.ts
 var OPENAI_API_KEY_ENV = "MYCO_OPENAI_API_KEY";
@@ -23,4 +23,4 @@ export {
   OPENAI_API_KEY_ENV,
   OpenAIEmbeddingProvider
 };
-//# sourceMappingURL=chunk-RPILIIYT.js.map
+//# sourceMappingURL=chunk-Y7QCKCEJ.js.map

package/dist/{chunk-D63XTGBV.js → chunk-YTOD6L6N.js}

@@ -2,17 +2,17 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   getSpore,
   listSporeIdsSince
-} from "./chunk-IRSNOBGD.js";
+} from "./chunk-UDBCAFXS.js";
 import {
   getSession
-} from "./chunk-SGYYOTNM.js";
+} from "./chunk-VGVRBSLC.js";
 import {
   getTeamMachineId,
   syncRow
-} from "./chunk-4JVHWBZF.js";
+} from "./chunk-KKEMVH6D.js";
 import {
   loadConfig
-} from "./chunk-XAXQ72L3.js";
+} from "./chunk-FEX6ALLH.js";
 import {
   getDatabase
 } from "./chunk-MYX5NCRH.js";
@@ -26,7 +26,7 @@ import {
   GRAPH_EDGE_DEFAULT_CONFIDENCE,
   QUERY_DEFAULT_LIST_LIMIT,
   epochSeconds
-} from "./chunk-34NHDRWI.js";
+} from "./chunk-6SDC6V3N.js";
 
 // src/utils/error-message.ts
 function errorMessage(err) {
@@ -1579,4 +1579,4 @@ export {
   insertReport,
   listReports
 };
-//# sourceMappingURL=chunk-D63XTGBV.js.map
+//# sourceMappingURL=chunk-YTOD6L6N.js.map

package/dist/{chunk-D2NTFSVO.js → chunk-ZUSTCXHT.js}

@@ -3,14 +3,14 @@ import {
   AgentTaskSchema,
   loadAgentTasks,
   taskFromParsed
-} from "./chunk-W7ZOOZMK.js";
+} from "./chunk-VQQ57UPG.js";
 import {
   BUILT_IN_SOURCE,
   MAX_TASK_NAME_LENGTH,
   TASK_NAME_PATTERN,
   USER_TASKS_DIR,
   USER_TASK_SOURCE
-} from "./chunk-34NHDRWI.js";
+} from "./chunk-6SDC6V3N.js";
 import {
   require_dist
 } from "./chunk-D7TYRPRM.js";
@@ -100,4 +100,4 @@ export {
   deleteUserTask,
   copyTaskToUser
 };
-//# sourceMappingURL=chunk-D2NTFSVO.js.map
+//# sourceMappingURL=chunk-ZUSTCXHT.js.map

package/dist/{cli-RYYABF2X.js → cli-353VNZIY.js}

@@ -2,18 +2,18 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   loadEnv
-} from "./chunk-BNAYBGPH.js";
+} from "./chunk-XQHL4GMO.js";
 import "./chunk-SAKJMNSR.js";
-import "./chunk-TIAYBVSI.js";
-import "./chunk-VWXDSDJU.js";
+import "./chunk-VVGZL2HX.js";
+import "./chunk-DKSQMH5X.js";
 import "./chunk-MYX5NCRH.js";
 import {
   resolveVaultDir
 } from "./chunk-5ZT2Q6P5.js";
-import "./chunk-RJRRHTAA.js";
-import "./chunk-2E7YGLLN.js";
+import "./chunk-N6JNOSBQ.js";
+import "./chunk-LA7NDX3J.js";
 import "./chunk-LPUQPDC2.js";
-import "./chunk-34NHDRWI.js";
+import "./chunk-6SDC6V3N.js";
 import "./chunk-E7NUADTQ.js";
 import "./chunk-PZUWP5VK.js";
 
@@ -55,29 +55,29 @@ async function main() {
     process.stdout.write(USAGE);
     return;
   }
-  if (cmd === "init") return (await import("./init-AEHAQFPK.js")).run(args);
-  if (cmd === "detect-providers") return (await import("./detect-providers-R7QOB3H6.js")).run(args);
+  if (cmd === "init") return (await import("./init-XR2JZWY2.js")).run(args);
+  if (cmd === "detect-providers") return (await import("./detect-providers-OE6HWW3M.js")).run(args);
   if (cmd === "version" || cmd === "--version" || cmd === "-v") {
-    const { getPluginVersion } = await import("./version-VS2EDHBG.js");
+    const { getPluginVersion } = await import("./version-OHJ5ZLHX.js");
     console.log(getPluginVersion());
     return;
   }
-  if (cmd === "mcp") return (await import("./server-OFRKA6N7.js")).main();
+  if (cmd === "mcp") return (await import("./server-LXUA7XUQ.js")).main();
   if (cmd === "hook") {
     const hookName = args[0];
     const HOOK_DISPATCH = {
-      "session-start": () => import("./session-start-OL2ICLED.js"),
-      "session-end": () => import("./session-end-5EIVRCPS.js"),
-      "stop": () => import("./stop-YUZNQBRQ.js"),
-      "user-prompt-submit": () => import("./user-prompt-submit-FSYEPW7W.js"),
-      "post-tool-use": () => import("./post-tool-use-B3KOEOIM.js"),
-      "post-tool-use-failure": () => import("./post-tool-use-failure-2I5ELTTN.js"),
-      "subagent-start": () => import("./subagent-start-GWJXAAH3.js"),
-      "subagent-stop": () => import("./subagent-stop-B44SMV2R.js"),
-      "stop-failure": () => import("./stop-failure-6WFAKH2U.js"),
-      "task-completed": () => import("./task-completed-GIUFSRTP.js"),
-      "pre-compact": () => import("./pre-compact-NOXNJ5EV.js"),
-      "post-compact": () => import("./post-compact-OAWEBEDK.js")
+      "session-start": () => import("./session-start-3STH4HFL.js"),
+      "session-end": () => import("./session-end-4Y5VY4OI.js"),
+      "stop": () => import("./stop-L7BLMHUD.js"),
+      "user-prompt-submit": () => import("./user-prompt-submit-4J7ZW6X3.js"),
+      "post-tool-use": () => import("./post-tool-use-5WLLRGZ5.js"),
+      "post-tool-use-failure": () => import("./post-tool-use-failure-6C6HSBHI.js"),
+      "subagent-start": () => import("./subagent-start-AIEFG4HA.js"),
+      "subagent-stop": () => import("./subagent-stop-TZ62BSNI.js"),
+      "stop-failure": () => import("./stop-failure-P5MYHGAZ.js"),
+      "task-completed": () => import("./task-completed-ZKVCUBCP.js"),
+      "pre-compact": () => import("./pre-compact-Z4E4JLAK.js"),
+      "post-compact": () => import("./post-compact-WPS4SONO.js")
     };
     const loader = HOOK_DISPATCH[hookName];
     if (!loader) {
@@ -86,13 +86,13 @@ async function main() {
     }
     return (await loader()).main();
   }
-  if (cmd === "daemon") return (await import("./main-GAGOE6XB.js")).main();
+  if (cmd === "daemon") return (await import("./main-6DGPZXRF.js")).main();
   if (cmd === "doctor") {
     const vaultDir2 = resolveVaultDir();
-    return (await import("./doctor-M4Q7VCDO.js")).run(args, vaultDir2);
+    return (await import("./doctor-RYFP7ABA.js")).run(args, vaultDir2);
   }
-  if (cmd === "update") return (await import("./update-QPRTLGYU.js")).run(args);
-  if (cmd === "remove") return (await import("./remove-LX4G6KP7.js")).run(args);
+  if (cmd === "update") return (await import("./update-P7GIQLIV.js")).run(args);
+  if (cmd === "remove") return (await import("./remove-B2PFVQXK.js")).run(args);
   const vaultDir = resolveVaultDir();
   if (!fs.existsSync(path.join(vaultDir, "myco.yaml"))) {
     console.error(`No myco.yaml found in ${vaultDir}. Run 'myco init' first.`);
@@ -100,37 +100,37 @@ async function main() {
   }
   switch (cmd) {
     case "config":
-      return (await import("./config-VHHCGE4F.js")).run(args, vaultDir);
+      return (await import("./config-K3CJEFFO.js")).run(args, vaultDir);
     case "verify":
-      return (await import("./verify-ITBMLK67.js")).run(args, vaultDir);
+      return (await import("./verify-PSERIZPF.js")).run(args, vaultDir);
     case "stats":
-      return (await import("./stats-U5FHDIR7.js")).run(args, vaultDir);
+      return (await import("./stats-3NW7PGQK.js")).run(args, vaultDir);
     case "search":
-      return (await import("./search-Q6N3SHKP.js")).run(args, vaultDir);
+      return (await import("./search-ERTCTAQ3.js")).run(args, vaultDir);
     case "vectors":
-      return (await import("./search-Q6N3SHKP.js")).runVectors(args, vaultDir);
+      return (await import("./search-ERTCTAQ3.js")).runVectors(args, vaultDir);
     case "session":
-      return (await import("./session-SKXJLJYH.js")).run(args, vaultDir);
+      return (await import("./session-433T6V3C.js")).run(args, vaultDir);
     case "setup-llm":
-      return (await import("./setup-llm-BRNQW7K2.js")).run(args, vaultDir);
+      return (await import("./setup-llm-UBBSQWX5.js")).run(args, vaultDir);
     case "setup-digest":
       return (await import("./setup-digest-4KDSXAIV.js")).run(args, vaultDir);
     case "agent":
-      return (await import("./agent-run-MNU2QWHR.js")).run(args, vaultDir);
+      return (await import("./agent-run-BGW4TY3D.js")).run(args, vaultDir);
     case "task":
-      return (await import("./agent-tasks-NCRKUU6E.js")).run(args, vaultDir);
+      return (await import("./agent-tasks-XUJ6FTPL.js")).run(args, vaultDir);
     case "team": {
       const sub = args[0];
-      if (sub === "init") return (await import("./team-3YI3UWB3.js")).teamInit(vaultDir);
-      if (sub === "upgrade") return (await import("./team-3YI3UWB3.js")).teamUpgrade(vaultDir);
+      if (sub === "init") return (await import("./team-WHZW6IFU.js")).teamInit(vaultDir);
+      if (sub === "upgrade") return (await import("./team-WHZW6IFU.js")).teamUpgrade(vaultDir);
       console.error("Usage: myco team <init|upgrade>");
       process.exit(1);
       break;
     }
     case "open":
-      return (await import("./open-4QMAL32X.js")).run(args, vaultDir);
+      return (await import("./open-P7YEH7UJ.js")).run(args, vaultDir);
     case "restart":
-      return (await import("./restart-WSNBSALP.js")).run(args, vaultDir);
+      return (await import("./restart-XAJDOL3E.js")).run(args, vaultDir);
     case "logs":
       return (await import("./logs-TMKNLSJY.js")).run(args, vaultDir);
     default:
@@ -143,4 +143,4 @@ main().catch((err) => {
   console.error(`myco: ${err.message}`);
   process.exit(1);
 });
-//# sourceMappingURL=cli-RYYABF2X.js.map
+//# sourceMappingURL=cli-353VNZIY.js.map

package/dist/{client-5VXKGNN2.js → client-7KJ453V4.js}

@@ -2,14 +2,14 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   DaemonClient,
   resolveCliEntryPath
-} from "./chunk-RJRRHTAA.js";
-import "./chunk-2E7YGLLN.js";
+} from "./chunk-N6JNOSBQ.js";
+import "./chunk-LA7NDX3J.js";
 import "./chunk-LPUQPDC2.js";
-import "./chunk-34NHDRWI.js";
+import "./chunk-6SDC6V3N.js";
 import "./chunk-E7NUADTQ.js";
 import "./chunk-PZUWP5VK.js";
 export {
   DaemonClient,
   resolveCliEntryPath
 };
-//# sourceMappingURL=client-5VXKGNN2.js.map
+//# sourceMappingURL=client-7KJ453V4.js.map

package/dist/{config-VHHCGE4F.js → config-K3CJEFFO.js}

@@ -5,8 +5,8 @@ import {
 import {
   loadConfig,
   updateConfig
-} from "./chunk-XAXQ72L3.js";
-import "./chunk-34NHDRWI.js";
+} from "./chunk-FEX6ALLH.js";
+import "./chunk-6SDC6V3N.js";
 import "./chunk-E7NUADTQ.js";
 import "./chunk-D7TYRPRM.js";
 import "./chunk-E4VLWIJC.js";
@@ -87,4 +87,4 @@ function parseValue(raw) {
 export {
   run
 };
-//# sourceMappingURL=config-VHHCGE4F.js.map
+//# sourceMappingURL=config-K3CJEFFO.js.map

package/dist/{detect-6FNYONJF.js → detect-NJ2OREDP.js}

@@ -3,7 +3,7 @@ import {
   detectSymbionts,
   loadManifests,
   resolvePackageRoot
-} from "./chunk-GSKXOCFG.js";
+} from "./chunk-EBIYONNZ.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-D7TYRPRM.js";
 import "./chunk-E4VLWIJC.js";
@@ -14,4 +14,4 @@ export {
   loadManifests,
   resolvePackageRoot
 };
-//# sourceMappingURL=detect-6FNYONJF.js.map
+//# sourceMappingURL=detect-NJ2OREDP.js.map

package/dist/{detect-providers-R7QOB3H6.js → detect-providers-OE6HWW3M.js}

@@ -1,9 +1,9 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   checkLocalProvider
-} from "./chunk-6JZEAOLG.js";
-import "./chunk-VWXDSDJU.js";
-import "./chunk-34NHDRWI.js";
+} from "./chunk-CPL76CYD.js";
+import "./chunk-DKSQMH5X.js";
+import "./chunk-6SDC6V3N.js";
 import "./chunk-E7NUADTQ.js";
 import "./chunk-PZUWP5VK.js";
 
@@ -23,4 +23,4 @@ async function run(_args) {
 export {
   run
 };
-//# sourceMappingURL=detect-providers-R7QOB3H6.js.map
+//# sourceMappingURL=detect-providers-OE6HWW3M.js.map

package/dist/{doctor-M4Q7VCDO.js → doctor-RYFP7ABA.js}

@@ -1,17 +1,17 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   isProcessAlive
-} from "./chunk-BNAYBGPH.js";
+} from "./chunk-XQHL4GMO.js";
 import "./chunk-SAKJMNSR.js";
 import {
   MYCO_MCP_SERVER_NAME
-} from "./chunk-TIAYBVSI.js";
-import "./chunk-VWXDSDJU.js";
+} from "./chunk-VVGZL2HX.js";
+import "./chunk-DKSQMH5X.js";
 import "./chunk-MYX5NCRH.js";
-import "./chunk-RJRRHTAA.js";
-import "./chunk-2E7YGLLN.js";
+import "./chunk-N6JNOSBQ.js";
+import "./chunk-LA7NDX3J.js";
 import "./chunk-LPUQPDC2.js";
-import "./chunk-34NHDRWI.js";
+import "./chunk-6SDC6V3N.js";
 import "./chunk-E7NUADTQ.js";
 import "./chunk-PZUWP5VK.js";
 
@@ -29,7 +29,7 @@ async function checkVault(vaultDir) {
     return { check: { name: "Vault", status: "fail", detail: `${CONFIG_FILENAME} not found in ${vaultDir}`, fixable: false }, config: null };
   }
   try {
-    const { loadConfig } = await import("./loader-QDWQTBX4.js");
+    const { loadConfig } = await import("./loader-AVWL7PNO.js");
     const config = loadConfig(vaultDir);
     return { check: { name: "Vault", status: "ok", detail: `.myco/ (v${config.version})`, fixable: false }, config };
   } catch (err) {
@@ -68,7 +68,7 @@ async function checkIntelligence(config) {
       return { name: "Intelligence", status: "ok", detail: `${label} (SDK handles auth)`, fixable: false };
     }
     if (provider.type === "ollama" || provider.type === "lmstudio") {
-      const { checkLocalProvider } = await import("./provider-check-VEYONGNU.js");
+      const { checkLocalProvider } = await import("./provider-check-CESRPIY5.js");
       const status = await checkLocalProvider(provider.type, provider.base_url);
       if (!status.available) {
         return { name: "Intelligence", status: "warn", detail: `${label} (not reachable)`, fixable: false };
@@ -82,7 +82,7 @@ async function checkIntelligence(config) {
 }
 async function checkEmbeddings(config) {
   try {
-    const { createEmbeddingProvider } = await import("./llm-LS7U7BHC.js");
+    const { createEmbeddingProvider } = await import("./llm-PGETQHZ2.js");
     const provider = createEmbeddingProvider(config.embedding);
     const available = await provider.isAvailable();
     const label = `${config.embedding.provider} / ${config.embedding.model}`;
@@ -96,8 +96,8 @@ async function checkEmbeddings(config) {
 }
 async function checkAgents(vaultDir, config) {
   try {
-    const { detectSymbionts } = await import("./detect-6FNYONJF.js");
-    const { getEnabledSymbiontNames } = await import("./loader-QDWQTBX4.js");
+    const { detectSymbionts } = await import("./detect-NJ2OREDP.js");
+    const { getEnabledSymbiontNames } = await import("./loader-AVWL7PNO.js");
     const projectRoot = path.dirname(vaultDir);
     const detected = detectSymbionts(projectRoot);
     const enabledNames = config ? getEnabledSymbiontNames(config) : null;
@@ -156,7 +156,8 @@ function isSymbiontRegistered(d, projectRoot) {
       return raw.includes(`[mcp_servers.${MYCO_MCP_SERVER_NAME}]`);
     }
     const config = JSON.parse(raw);
-    const servers = config.mcpServers;
+    const serversKey = d.manifest.registration?.mcpServersKey ?? "mcpServers";
+    const servers = config[serversKey];
     return !!servers?.[MYCO_MCP_SERVER_NAME];
   } catch {
   }
@@ -270,4 +271,4 @@ export {
   run,
   runChecks
 };
-//# sourceMappingURL=doctor-M4Q7VCDO.js.map
+//# sourceMappingURL=doctor-RYFP7ABA.js.map

package/dist/doctor-RYFP7ABA.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';\nimport { MYCO_MCP_SERVER_NAME } from '../symbionts/installer.js';\n\n// --- Named constants (no magic literals) ---\n\n\n/** Filename of the vault config file. */\nconst CONFIG_FILENAME = 'myco.yaml';\n\n/** Filename of the daemon state file. */\nconst DAEMON_STATE_FILENAME = 'daemon.json';\n\n/** Filename of the SQLite database. */\nconst DB_FILENAME = 'myco.db';\n\n/** Column width for the check name in output. */\nconst NAME_COL_WIDTH = 17;\n\n/** Prefix for indented continuation lines (e.g. multi-line agent output). */\nconst CONTINUATION_INDENT = ' '.repeat(NAME_COL_WIDTH);\n\n// --- Types ---\n\nexport interface DoctorCheck {\n  name: string;\n  status: 'ok' | 'fail' | 'warn';\n  detail: string;\n  fixable: boolean;\n}\n\n// --- Checks ---\n\n/** Check that myco.yaml exists and parses. Returns the parsed config on success. */\nasync function checkVault(vaultDir: string): Promise<{ check: DoctorCheck; config: import('../config/schema.js').MycoConfig | null }> {\n  const configPath = path.join(vaultDir, CONFIG_FILENAME);\n  if (!fs.existsSync(configPath)) {\n    return { check: { name: 'Vault', status: 'fail', detail: `${CONFIG_FILENAME} not found in ${vaultDir}`, fixable: false }, config: null };\n  }\n  try {\n    const { loadConfig } = await import('../config/loader.js');\n    const config = loadConfig(vaultDir);\n    return { check: { name: 'Vault', status: 'ok', detail: `.myco/ (v${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: ${(err as Error).message}`, fixable: false };\n  }\n}\n\n/** Check symbiont detection and registration status. */\nasync function checkAgents(vaultDir: string, config: import('../config/schema.js').MycoConfig | null): Promise<DoctorCheck[]> {\n  try {\n    const { detectSymbionts } = await import('../symbionts/detect.js');\n    const { getEnabledSymbiontNames } = await import('../config/loader.js');\n    const projectRoot = path.dirname(vaultDir);\n    const detected = detectSymbionts(projectRoot);\n\n    const enabledNames = config ? getEnabledSymbiontNames(config) : null;\n\n    if (detected.length === 0 && !enabledNames) {\n      return [{ name: 'Agents', status: 'warn', detail: 'No symbionts detected', fixable: false }];\n    }\n\n    const checks: DoctorCheck[] = [];\n    for (const d of detected) {\n      const registered = isSymbiontRegistered(d, projectRoot);\n      const enabled = enabledNames ? enabledNames.has(d.manifest.name) : registered;\n\n      if (enabled && registered) {\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'ok',\n          detail: `${d.manifest.displayName} (enabled, registered)`,\n          fixable: false,\n        });\n      } else if (enabled && !registered) {\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'warn',\n          detail: `${d.manifest.displayName} (enabled but not registered — run \\`myco update\\`)`,\n          fixable: false,\n        });\n      } else if (!enabled && registered) {\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'warn',\n          detail: `${d.manifest.displayName} (registered but not enabled — run \\`myco remove --symbiont ${d.manifest.name}\\`)`,\n          fixable: false,\n        });\n      } else {\n        // Detected but neither enabled nor registered\n        checks.push({\n          name: checks.length === 0 ? 'Agents' : '',\n          status: 'ok',\n          detail: `${d.manifest.displayName} (detected, not enabled)`,\n          fixable: false,\n        });\n      }\n    }\n\n    if (checks.length === 0) {\n      return [{ name: 'Agents', status: 'warn', detail: 'No symbionts detected or enabled', fixable: false }];\n    }\n\n    return checks;\n  } catch (err) {\n    return [{ name: 'Agents', status: 'fail', detail: `Agent check failed: ${(err as Error).message}`, fixable: false }];\n  }\n}\n\n/** Check if a symbiont has the Myco MCP server registered. */\nfunction isSymbiontRegistered(\n  d: import('../symbionts/detect.js').DetectedSymbiont,\n  projectRoot: string,\n): boolean {\n  try {\n    const mcpTarget = d.manifest.registration?.mcpTarget;\n    if (!mcpTarget) return false;\n\n    const mcpFile = path.join(projectRoot, mcpTarget);\n    const raw = fs.readFileSync(mcpFile, 'utf-8');\n\n    // TOML: check for section header\n    if (mcpTarget.endsWith('.toml')) {\n      return raw.includes(`[mcp_servers.${MYCO_MCP_SERVER_NAME}]`);\n    }\n\n    // JSON: check for server entry under the configured key (defaults to 'mcpServers').\n    // opencode uses 'mcp' — without the manifest lookup, doctor reports opencode as\n    // unregistered even after a successful install.\n    const config = JSON.parse(raw) as Record<string, unknown>;\n    const serversKey = d.manifest.registration?.mcpServersKey ?? 'mcpServers';\n    const servers = config[serversKey] as Record<string, unknown> | undefined;\n    return !!servers?.[MYCO_MCP_SERVER_NAME];\n  } catch { /* config missing or malformed */ }\n  return false;\n}\n\n/** Check the daemon state file and process liveness. */\nasync function checkDaemon(vaultDir: string): Promise<DoctorCheck> {\n  const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);\n  if (!fs.existsSync(daemonFile)) {\n    return { name: 'Daemon', status: 'warn', detail: 'Not running (no daemon.json)', fixable: false };\n  }\n  try {\n    const state = JSON.parse(fs.readFileSync(daemonFile, 'utf-8')) as { pid?: number; port?: number };\n    if (!state.pid) {\n      return { name: 'Daemon', status: 'warn', detail: 'daemon.json exists but no PID', fixable: true };\n    }\n    if (isProcessAlive(state.pid)) {\n      return { name: 'Daemon', status: 'ok', detail: `PID ${state.pid}, port ${state.port ?? 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Returns descriptions of actions taken. */\nexport async function fix(vaultDir: string, checks: DoctorCheck[]): Promise<string[]> {\n  const actions: string[] = [];\n\n  for (const check of checks) {\n    if (!check.fixable || check.status === 'ok') continue;\n\n    // Fix stale daemon.json\n    if (check.name === 'Daemon' && check.detail.includes('Stale')) {\n      const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);\n      fs.unlinkSync(daemonFile);\n      actions.push('Removed stale daemon.json');\n    }\n\n    // Fix malformed daemon.json\n    if (check.name === 'Daemon' && check.detail.includes('parse error')) {\n      const daemonFile = path.join(vaultDir, DAEMON_STATE_FILENAME);\n      fs.unlinkSync(daemonFile);\n      actions.push('Removed malformed daemon.json');\n    }\n\n    // Advise on database issues\n    if (check.name === 'Database' && check.status === 'fail') {\n      actions.push('Run `myco init` to initialize the database');\n    }\n  }\n\n  return actions;\n}\n\n// --- Output formatting ---\n\n/** Status label width (visible characters). */\nconst STATUS_COL_WIDTH = 6;\n\nconst STATUS_LABELS: Record<DoctorCheck['status'], { text: string; color: string }> = {\n  ok: { text: 'ok', color: '\\x1b[32m' },\n  fail: { text: 'FAIL', color: '\\x1b[31m' },\n  warn: { text: '!!', color: '\\x1b[33m' },\n};\n\nfunction formatCheck(check: DoctorCheck): string {\n  const name = check.name ? check.name.padEnd(NAME_COL_WIDTH) : CONTINUATION_INDENT;\n  const { text, color } = STATUS_LABELS[check.status];\n  const paddedText = text.padEnd(STATUS_COL_WIDTH);\n  return `  ${name}${color}${paddedText}\\x1b[0m${check.detail}`;\n}\n\n// --- CLI entry point ---\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const shouldFix = args.includes('--fix');\n\n  console.log('\\nmyco doctor\\n');\n\n  const checks = await runChecks(vaultDir);\n\n  for (const check of checks) {\n    console.log(formatCheck(check));\n  }\n\n  const issues = checks.filter(c => c.status !== 'ok');\n  const fixable = issues.filter(c => c.fixable);\n\n  console.log('');\n\n  if (issues.length === 0) {\n    console.log('  All checks passed.\\n');\n    return;\n  }\n\n  console.log(`  ${issues.length} issue(s) found.`);\n\n  if (shouldFix) {\n    const actions = await fix(vaultDir, checks);\n    if (actions.length > 0) {\n      console.log('');\n      for (const action of actions) {\n        console.log(`  Fixed: ${action}`);\n      }\n      console.log('');\n    } else {\n      console.log('  No auto-fixable issues.\\n');\n    }\n  } else if (fixable.length > 0) {\n    console.log(`  Run \\`myco doctor --fix\\` to repair ${fixable.length} fixable issue(s).\\n`);\n  } else {\n    console.log('');\n  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package/dist/{executor-ULRFWJCH.js → executor-YOKYS7OT.js}

@@ -31,10 +31,10 @@ import {
   updateRunStatus,
   updateSkillRecord,
   upsertDigestExtract
-} from "./chunk-D63XTGBV.js";
+} from "./chunk-YTOD6L6N.js";
 import {
   fullTextSearch
-} from "./chunk-UILSK6DK.js";
+} from "./chunk-GBYLHPML.js";
 import {
   cleanupStagedSkill,
   readStagedManifest,
@@ -44,7 +44,7 @@ import {
 } from "./chunk-U5EW2VIQ.js";
 import {
   loadAllTasks
-} from "./chunk-D2NTFSVO.js";
+} from "./chunk-ZUSTCXHT.js";
 import {
   getAgent,
   getDefaultTask,
@@ -53,33 +53,33 @@ import {
   loadSystemPrompt,
   resolveDefinitionsDir,
   resolveEffectiveConfig
-} from "./chunk-W7ZOOZMK.js";
+} from "./chunk-VQQ57UPG.js";
 import {
   insertTurn
 } from "./chunk-QLCD77AN.js";
 import {
   insertResolutionEvent
-} from "./chunk-P6C6ADBU.js";
+} from "./chunk-2IJ6C63F.js";
 import "./chunk-IB76KGBY.js";
 import {
   DEFAULT_IMPORTANCE,
   insertSpore,
   listSpores,
   updateSporeStatus
-} from "./chunk-IRSNOBGD.js";
+} from "./chunk-UDBCAFXS.js";
 import {
   listSessions,
   updateSession
-} from "./chunk-SGYYOTNM.js";
-import "./chunk-4JVHWBZF.js";
+} from "./chunk-VGVRBSLC.js";
+import "./chunk-KKEMVH6D.js";
 import {
   AGENT_SETTABLE_STATUSES,
   CANDIDATE_STATUS,
   createSchema
-} from "./chunk-CJ2KTRWI.js";
+} from "./chunk-OGNEW5CN.js";
 import {
   loadConfig
-} from "./chunk-XAXQ72L3.js";
+} from "./chunk-FEX6ALLH.js";
 import {
   getDatabase,
   initDatabase,
@@ -87,7 +87,7 @@ import {
 } from "./chunk-MYX5NCRH.js";
 import {
   getPluginVersion
-} from "./chunk-2E7YGLLN.js";
+} from "./chunk-LA7NDX3J.js";
 import {
   findPackageRoot
 } from "./chunk-LPUQPDC2.js";
@@ -99,7 +99,7 @@ import {
   SEARCH_SIMILARITY_THRESHOLD,
   TEAM_SOURCE_PREFIX,
   epochSeconds
-} from "./chunk-34NHDRWI.js";
+} from "./chunk-6SDC6V3N.js";
 import "./chunk-E7NUADTQ.js";
 import "./chunk-D7TYRPRM.js";
 import "./chunk-E4VLWIJC.js";
@@ -985,7 +985,7 @@ function createSkillTools(deps) {
         );
       }
       try {
-        const { syncSkillSymlinks } = await import("./installer-AARSFXI6.js");
+        const { syncSkillSymlinks } = await import("./installer-45ZLP2RP.js");
         syncSkillSymlinks(root, params.name, { remove: true });
       } catch (rollbackErr) {
         console.warn(
@@ -1003,7 +1003,7 @@ function createSkillTools(deps) {
       };
     }
     try {
-      const { syncSkillSymlinks } = await import("./installer-AARSFXI6.js");
+      const { syncSkillSymlinks } = await import("./installer-45ZLP2RP.js");
       syncSkillSymlinks(root, params.name);
     } catch (err) {
       console.warn(
@@ -1236,7 +1236,7 @@ function createSkillTools(deps) {
               console.warn("[vault_skill_records] Failed to remove skill directory:", err instanceof Error ? err.message : err);
             }
             try {
-              const { syncSkillSymlinks } = await import("./installer-AARSFXI6.js");
+              const { syncSkillSymlinks } = await import("./installer-45ZLP2RP.js");
               syncSkillSymlinks(root, result.name, { remove: true });
             } catch (err) {
               console.warn("[vault_skill_records] Failed to remove symlinks:", err instanceof Error ? err.message : err);
@@ -1355,7 +1355,7 @@ function createSkillTools(deps) {
         return textResult({ error: `Failed to write skill file: ${err instanceof Error ? err.message : String(err)}` });
       }
       try {
-        const { syncSkillSymlinks } = await import("./installer-AARSFXI6.js");
+        const { syncSkillSymlinks } = await import("./installer-45ZLP2RP.js");
         syncSkillSymlinks(root, args.name);
       } catch (err) {
         console.warn("[vault_write_skill] syncSkillSymlinks failed:", err instanceof Error ? err.message : err);
@@ -2676,4 +2676,4 @@ export {
   computeWaves,
   runAgent
 };
-//# sourceMappingURL=executor-ULRFWJCH.js.map
+//# sourceMappingURL=executor-YOKYS7OT.js.map

package/dist/{init-AEHAQFPK.js → init-XR2JZWY2.js}

@@ -2,23 +2,23 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   VAULT_GITIGNORE,
   registerSymbionts
-} from "./chunk-BNAYBGPH.js";
+} from "./chunk-XQHL4GMO.js";
 import {
   parseStringFlag
 } from "./chunk-SAKJMNSR.js";
 import {
   writeSecret
 } from "./chunk-RJMXDUMA.js";
-import "./chunk-TIAYBVSI.js";
-import "./chunk-VWXDSDJU.js";
+import "./chunk-VVGZL2HX.js";
+import "./chunk-DKSQMH5X.js";
 import {
   createSchema
-} from "./chunk-CJ2KTRWI.js";
+} from "./chunk-OGNEW5CN.js";
 import {
   MycoConfigSchema,
   saveConfig,
   updateConfig
-} from "./chunk-XAXQ72L3.js";
+} from "./chunk-FEX6ALLH.js";
 import {
   closeDatabase,
   initDatabase,
@@ -27,15 +27,15 @@ import {
 import {
   resolveVaultDir
 } from "./chunk-5ZT2Q6P5.js";
-import "./chunk-RJRRHTAA.js";
-import "./chunk-2E7YGLLN.js";
+import "./chunk-N6JNOSBQ.js";
+import "./chunk-LA7NDX3J.js";
 import {
   detectSymbionts,
   loadManifests,
   resolvePackageRoot
-} from "./chunk-GSKXOCFG.js";
+} from "./chunk-EBIYONNZ.js";
 import "./chunk-LPUQPDC2.js";
-import "./chunk-34NHDRWI.js";
+import "./chunk-6SDC6V3N.js";
 import "./chunk-E7NUADTQ.js";
 import "./chunk-D7TYRPRM.js";
 import "./chunk-E4VLWIJC.js";
@@ -52,7 +52,7 @@ async function run(args) {
   const nonInteractive = args.includes("--non-interactive");
   const isInteractive = !nonInteractive && !!process.stdin.isTTY;
   if (isInteractive) {
-    const { printBanner } = await import("./init-wizard-SVKDS3LR.js");
+    const { printBanner } = await import("./init-wizard-5CH2FD76.js");
     printBanner();
   }
   const vaultDir = vaultPath ? vaultPath.startsWith("~/") ? path.join(os.homedir(), vaultPath.slice(2)) : path.resolve(vaultPath) : path.join(resolveVaultDir());
@@ -67,7 +67,7 @@ async function run(args) {
   let shouldRunWizard = false;
   if (isInteractive && !hasEmbeddingFlags) {
     if (alreadyInitialized) {
-      const { loadConfig } = await import("./loader-QDWQTBX4.js");
+      const { loadConfig } = await import("./loader-AVWL7PNO.js");
       const config = loadConfig(vaultDir);
       const agentProvider = config.agent.provider;
       const embConfig = config.embedding;
@@ -82,7 +82,7 @@ async function run(args) {
     }
   }
   if (shouldRunWizard) {
-    const { runWizard, buildEmbeddingConfig, buildAgentConfig } = await import("./init-wizard-SVKDS3LR.js");
+    const { runWizard, buildEmbeddingConfig, buildAgentConfig } = await import("./init-wizard-5CH2FD76.js");
     const answers = await runWizard();
     wizardAnswers = answers;
     if (answers.embeddingProvider !== "skip") {
@@ -127,8 +127,8 @@ async function run(args) {
     console.log("  Updated myco.yaml");
   }
   if (wizardAnswers?.embeddingApiKey) {
-    const { OPENROUTER_API_KEY_ENV } = await import("./openrouter-YSIUSUQL.js");
-    const { OPENAI_API_KEY_ENV } = await import("./openai-embeddings-FUW6CSN2.js");
+    const { OPENROUTER_API_KEY_ENV } = await import("./openrouter-UTOZG6Z5.js");
+    const { OPENAI_API_KEY_ENV } = await import("./openai-embeddings-LZKY6RV5.js");
     const envVarName = wizardAnswers.embeddingProvider === "openrouter" ? OPENROUTER_API_KEY_ENV : OPENAI_API_KEY_ENV;
     writeSecret(vaultDir, envVarName, wizardAnswers.embeddingApiKey);
   }
@@ -139,7 +139,7 @@ async function run(args) {
   let existingSymbionts;
   if (alreadyInitialized && isInteractive) {
     try {
-      const { loadConfig } = await import("./loader-QDWQTBX4.js");
+      const { loadConfig } = await import("./loader-AVWL7PNO.js");
       const existing = loadConfig(vaultDir);
       existingSymbionts = existing.symbionts;
     } catch {
@@ -181,7 +181,7 @@ async function run(args) {
       registerSymbionts(selectedManifests, projectRoot, pkgRoot, "Registered");
     }
   }
-  const { DaemonClient } = await import("./client-5VXKGNN2.js");
+  const { DaemonClient } = await import("./client-7KJ453V4.js");
   const client = new DaemonClient(vaultDir);
   const daemonHealthy = await client.ensureRunning();
   let daemonUrl = "";
@@ -211,4 +211,4 @@ async function run(args) {
 export {
   run
 };
-//# sourceMappingURL=init-AEHAQFPK.js.map
+//# sourceMappingURL=init-XR2JZWY2.js.map