@goondocks/myco 0.12.0 → 0.12.1

package/dist/{agent-run-5KYQJQTY.js → agent-run-ECYDEYOJ.js}

@@ -1,14 +1,14 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   connectToDaemon
-} from "./chunk-YRHSTVCZ.js";
+} from "./chunk-YBUXSTBR.js";
 import "./chunk-SAKJMNSR.js";
 import "./chunk-LUQBT2Y4.js";
 import "./chunk-MYX5NCRH.js";
-import "./chunk-DPJVKNNP.js";
+import "./chunk-QUSCGEYI.js";
 import "./chunk-PIRWYDOH.js";
 import "./chunk-S6I62FAH.js";
-import "./chunk-TY7A5OZ5.js";
+import "./chunk-UIGH6TKR.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-PZUWP5VK.js";
 
@@ -31,4 +31,4 @@ async function run(args, vaultDir) {
 export {
   run
 };
-//# sourceMappingURL=agent-run-5KYQJQTY.js.map
+//# sourceMappingURL=agent-run-ECYDEYOJ.js.map

package/dist/{agent-tasks-N7BDYKGB.js → agent-tasks-IH77FIDQ.js}

@@ -1,14 +1,14 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   connectToDaemon
-} from "./chunk-YRHSTVCZ.js";
+} from "./chunk-YBUXSTBR.js";
 import "./chunk-SAKJMNSR.js";
 import "./chunk-LUQBT2Y4.js";
 import "./chunk-MYX5NCRH.js";
-import "./chunk-DPJVKNNP.js";
+import "./chunk-QUSCGEYI.js";
 import "./chunk-PIRWYDOH.js";
 import "./chunk-S6I62FAH.js";
-import "./chunk-TY7A5OZ5.js";
+import "./chunk-UIGH6TKR.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-PZUWP5VK.js";
 
@@ -177,4 +177,4 @@ async function run(args, vaultDir) {
 export {
   run
 };
-//# sourceMappingURL=agent-tasks-N7BDYKGB.js.map
+//# sourceMappingURL=agent-tasks-IH77FIDQ.js.map

package/dist/{chunk-HAG2YDH6.js → chunk-ME3R5B7H.js}

@@ -8,7 +8,7 @@ import {
 } from "./chunk-RR75ZKEV.js";
 import {
   DaemonClient
-} from "./chunk-DPJVKNNP.js";
+} from "./chunk-QUSCGEYI.js";
 import {
   resolveVaultDir
 } from "./chunk-JTYZRPX5.js";
@@ -39,4 +39,4 @@ async function sendEvent(hookName, buildEvent) {
 export {
   sendEvent
 };
-//# sourceMappingURL=chunk-HAG2YDH6.js.map
+//# sourceMappingURL=chunk-ME3R5B7H.js.map

package/dist/{chunk-DPJVKNNP.js → chunk-QUSCGEYI.js}

@@ -7,7 +7,7 @@ import {
 } from "./chunk-PIRWYDOH.js";
 import {
   getPluginVersion
-} from "./chunk-TY7A5OZ5.js";
+} from "./chunk-UIGH6TKR.js";
 
 // src/hooks/client.ts
 import fs from "fs";
@@ -168,4 +168,4 @@ export {
   resolveCliEntryPath,
   DaemonClient
 };
-//# sourceMappingURL=chunk-DPJVKNNP.js.map
+//# sourceMappingURL=chunk-QUSCGEYI.js.map

package/dist/{chunk-TY7A5OZ5.js → chunk-UIGH6TKR.js}

@@ -11,7 +11,7 @@ var cached;
 function getPluginVersion() {
   if (cached) return cached;
   if (true) {
-    cached = "0.12.0";
+    cached = "0.12.1";
     return cached;
   }
   const root = findPackageRoot(path.dirname(fileURLToPath(import.meta.url)));
@@ -32,4 +32,4 @@ function getPluginVersion() {
 export {
   getPluginVersion
 };
-//# sourceMappingURL=chunk-TY7A5OZ5.js.map
+//# sourceMappingURL=chunk-UIGH6TKR.js.map

package/dist/{chunk-YRHSTVCZ.js → chunk-YBUXSTBR.js}

@@ -10,7 +10,7 @@ import {
 } from "./chunk-MYX5NCRH.js";
 import {
   DaemonClient
-} from "./chunk-DPJVKNNP.js";
+} from "./chunk-QUSCGEYI.js";
 
 // src/symbionts/installer.ts
 import fs from "fs";
@@ -185,10 +185,13 @@ var SymbiontInstaller = class {
    * - File doesn't exist: write the full stub template.
    * - File exists without reference: prepend a reference block.
    * - File already has reference: skip (idempotent).
+   *
+   * Also ensures AGENTS.md exists — creates a starter if missing.
    */
   installInstructions() {
     const reg = this.manifest.registration;
     if (!reg?.instructionsFile) return false;
+    ensureAgentsMd(this.projectRoot, this.packageRoot);
     const targetPath = path.join(this.projectRoot, reg.instructionsFile);
     let existing = null;
     try {
@@ -681,6 +684,22 @@ function writeOrDeleteJsonFile(filePath, data) {
     writeJsonFile(filePath, data);
   }
 }
+function ensureAgentsMd(projectRoot, packageRoot) {
+  const agentsMdPath = path.join(projectRoot, "AGENTS.md");
+  if (fs.existsSync(agentsMdPath)) return;
+  const candidates = [
+    path.join(packageRoot, "src/symbionts/templates/agents-starter.md"),
+    path.join(packageRoot, "dist/src/symbionts/templates/agents-starter.md")
+  ];
+  for (const p of candidates) {
+    try {
+      const content = fs.readFileSync(p, "utf-8");
+      fs.writeFileSync(agentsMdPath, content, "utf-8");
+      return;
+    } catch {
+    }
+  }
+}
 function ensureSymlink(linkPath, target) {
   try {
     if (fs.readlinkSync(linkPath) === target) return;
@@ -789,4 +808,4 @@ export {
   VAULT_GITIGNORE,
   registerSymbionts
 };
-//# sourceMappingURL=chunk-YRHSTVCZ.js.map
+//# sourceMappingURL=chunk-YBUXSTBR.js.map

package/dist/chunk-YBUXSTBR.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/symbionts/installer.ts","../src/cli/shared.ts"],"sourcesContent":["import type { SymbiontManifest } from './manifest-schema.js';\nimport fs from 'node:fs';\nimport path from 'node:path';\n\n/** Prefix used to identify Myco-owned hooks in settings files. */\nconst MYCO_HOOK_COMMAND_PREFIX = 'myco-run';\n\n/**\n * Check if a hook group is Myco-owned.\n * Handles both nested format (Claude Code, Codex, etc.) and flat format (Windsurf).\n *\n * Nested: { hooks: [{ command: \"myco-run ...\" }] }\n * Flat:   { command: \"myco-run ...\" }\n */\nfunction isMycoHookGroup(group: Record<string, unknown>): boolean {\n  // Nested format: { hooks: [{ command: \"myco-run ...\" }] }\n  if (Array.isArray(group.hooks) && group.hooks.some((h: { command?: string }) => h.command?.startsWith(MYCO_HOOK_COMMAND_PREFIX))) return true;\n  // Flat format: { command: \"myco-run ...\" }\n  if (typeof group.command === 'string' && group.command.startsWith(MYCO_HOOK_COMMAND_PREFIX)) return true;\n  return false;\n}\n\n/** Comment header for Myco entries in .gitignore. */\nconst GITIGNORE_SKILLS_COMMENT = '# Myco skill symlinks (machine-specific)';\n\n/** Subdirectory within the package where symbiont templates live. */\nconst TEMPLATES_SUBDIR = 'src/symbionts/templates';\n\n/** Subdirectory within the package where skills live. */\nconst SKILLS_SUBDIR = 'skills';\n\n/** Canonical cross-agent skills directory. */\nconst CANONICAL_SKILLS_DIR = '.agents/skills';\n\n/** MCP server name used by Myco in all symbiont configurations. */\nexport const MYCO_MCP_SERVER_NAME = 'myco';\n\n/** Marker text used to identify unmodified instruction stubs. */\nconst INSTRUCTIONS_STUB_MARKER = 'Edit AGENTS.md, not this file';\n\n/** Start/end markers for the reference block prepended to existing instruction files. */\nconst INSTRUCTIONS_REF_START = '<!-- myco:agents-ref:start -->';\nconst INSTRUCTIONS_REF_END = '<!-- myco:agents-ref:end -->';\n\n/** Reference block prepended to existing instruction files. */\nconst INSTRUCTIONS_REF_BLOCK = `${INSTRUCTIONS_REF_START}\n> **Project intelligence:** This project uses [Myco](https://myco.sh). The canonical project rules are in [\\`AGENTS.md\\`](AGENTS.md) — read and follow it alongside this file.\n${INSTRUCTIONS_REF_END}\n\n`;\n\nexport interface InstallResult {\n  hooks: boolean;\n  mcp: boolean;\n  skills: boolean;\n  settings: boolean;\n  instructions: boolean;\n}\n\nexport class SymbiontInstaller {\n  constructor(\n    private manifest: SymbiontManifest,\n    private projectRoot: string,\n    private packageRoot: string,\n  ) {}\n\n  /** Load a JSON template file for this symbiont. Returns null if not found. */\n  loadTemplate(name: string): Record<string, unknown> | null {\n    // Check both source layout and dist layout\n    const candidates = [\n      path.join(this.packageRoot, TEMPLATES_SUBDIR, this.manifest.name, `${name}.json`),\n      // tsup preserves the src/ prefix under dist/, so the same subdir works in both layouts\n      path.join(this.packageRoot, 'dist', TEMPLATES_SUBDIR, this.manifest.name, `${name}.json`),\n    ];\n    for (const filePath of candidates) {\n      try {\n        return JSON.parse(fs.readFileSync(filePath, 'utf-8'));\n      } catch { /* not found or malformed — try next */ }\n    }\n    return null;\n  }\n\n  /** Run all registration steps. */\n  install(): InstallResult {\n    const reg = this.manifest.registration;\n    const result = this.shouldBatchJsonTargets(reg)\n      ? this.installBatchedJson(reg!)\n      : {\n          hooks: this.installHooks(),\n          mcp: this.installMcp(),\n          skills: this.installSkills(),\n          settings: this.installSettings(),\n          instructions: this.installInstructions(),\n        };\n    this.updateGitignore();\n    return result;\n  }\n\n  /**\n   * Check if ALL non-null JSON targets share the same file (e.g., Gemini).\n   * Only batches when every target resolves to one path — partial overlaps\n   * (e.g., Claude Code: hooks+settings share but MCP is separate) use normal path.\n   */\n  private shouldBatchJsonTargets(reg: typeof this.manifest.registration): boolean {\n    if (!reg) return false;\n    const mcpFormat = reg.mcpFormat ?? 'json';\n    if (mcpFormat !== 'json') return false;\n    const targets = [reg.hooksTarget, reg.mcpTarget, reg.settingsTarget].filter(Boolean);\n    return targets.length > 1 && new Set(targets).size === 1;\n  }\n\n  /**\n   * Batched install for agents where hooks, MCP, and settings share one JSON file.\n   * Single read → apply all transforms in memory → single write.\n   */\n  private installBatchedJson(reg: NonNullable<typeof this.manifest.registration>): InstallResult {\n    const targetPath = path.join(this.projectRoot, reg.hooksTarget ?? reg.mcpTarget ?? reg.settingsTarget!);\n    let data = readJsonFile(targetPath);\n    let hooks = false, mcp = false, settings = false;\n\n    // Apply hooks transform\n    const hooksTemplate = reg.hooksTarget ? this.loadTemplate('hooks') : null;\n    if (hooksTemplate) {\n      const existingHooks = (data.hooks ?? {}) as Record<string, unknown[]>;\n      const mergedHooks: Record<string, unknown[]> = {};\n      for (const [event, groups] of Object.entries(existingHooks)) {\n        const nonMyco = (groups as Array<Record<string, unknown>>).filter((g) => !isMycoHookGroup(g));\n        if (nonMyco.length > 0) mergedHooks[event] = nonMyco;\n      }\n      for (const [event, groups] of Object.entries(hooksTemplate)) {\n        mergedHooks[event] = [...(mergedHooks[event] ?? []), ...(groups as unknown[])];\n      }\n      data.hooks = mergedHooks;\n      hooks = true;\n    }\n\n    // Apply MCP transform\n    const mcpTemplate = reg.mcpTarget ? this.loadTemplate('mcp') : null;\n    if (mcpTemplate) {\n      const servers = (data.mcpServers ?? {}) as Record<string, unknown>;\n      for (const [name, def] of Object.entries(mcpTemplate)) {\n        servers[name] = def;\n      }\n      data.mcpServers = servers;\n      mcp = true;\n    }\n\n    // Apply settings transform\n    const settingsTemplate = reg.settingsTarget ? this.loadTemplate('settings') : null;\n    if (settingsTemplate) {\n      data = deepMergeSettings(data, settingsTemplate);\n      settings = true;\n    }\n\n    writeJsonFile(targetPath, data);\n\n    return {\n      hooks,\n      mcp,\n      skills: this.installSkills(),\n      settings,\n      instructions: this.installInstructions(),\n    };\n  }\n\n  /** Remove all Myco registration from this symbiont's project files. */\n  uninstall(): InstallResult {\n    const reg = this.manifest.registration;\n    const result = this.shouldBatchJsonTargets(reg)\n      ? this.uninstallBatchedJson(reg!)\n      : {\n          hooks: this.uninstallHooks(),\n          mcp: this.uninstallMcp(),\n          skills: this.uninstallSkills(),\n          settings: this.uninstallSettings(),\n          instructions: this.uninstallInstructions(),\n        };\n    this.cleanGitignore();\n    return result;\n  }\n\n  /**\n   * Batched uninstall for agents where hooks, MCP, and settings share one JSON file.\n   */\n  private uninstallBatchedJson(reg: NonNullable<typeof this.manifest.registration>): InstallResult {\n    const targetPath = path.join(this.projectRoot, reg.hooksTarget ?? reg.mcpTarget ?? reg.settingsTarget!);\n    const data = readJsonFile(targetPath);\n    if (Object.keys(data).length === 0) {\n      return { hooks: false, mcp: false, skills: this.uninstallSkills(), settings: false, instructions: this.uninstallInstructions() };\n    }\n\n    let hooks = false, mcp = false, settings = false;\n\n    // Remove hooks\n    if (reg.hooksTarget) {\n      const existingHooks = (data.hooks ?? {}) as Record<string, unknown[]>;\n      if (Object.keys(existingHooks).length > 0) {\n        const cleaned: Record<string, unknown[]> = {};\n        for (const [event, groups] of Object.entries(existingHooks)) {\n          const nonMyco = (groups as Array<Record<string, unknown>>).filter((g) => !isMycoHookGroup(g));\n          if (nonMyco.length > 0) cleaned[event] = nonMyco;\n        }\n        if (Object.keys(cleaned).length === 0) {\n          delete data.hooks;\n        } else {\n          data.hooks = cleaned;\n        }\n        hooks = true;\n      }\n    }\n\n    // Remove MCP\n    if (reg.mcpTarget) {\n      const servers = (data.mcpServers ?? {}) as Record<string, unknown>;\n      if (servers[MYCO_MCP_SERVER_NAME]) {\n        delete servers[MYCO_MCP_SERVER_NAME];\n        if (Object.keys(servers).length === 0) delete data.mcpServers;\n        else data.mcpServers = servers;\n        mcp = true;\n      }\n    }\n\n    // Remove settings\n    const settingsTemplate = reg.settingsTarget ? this.loadTemplate('settings') : null;\n    if (settingsTemplate) {\n      settings = deepRemoveSettings(data, settingsTemplate);\n    }\n\n    writeOrDeleteJsonFile(targetPath, data);\n\n    return { hooks, mcp, skills: this.uninstallSkills(), settings, instructions: this.uninstallInstructions() };\n  }\n\n  /**\n   * Ensure the instruction file references AGENTS.md.\n   * - File doesn't exist: write the full stub template.\n   * - File exists without reference: prepend a reference block.\n   * - File already has reference: skip (idempotent).\n   *\n   * Also ensures AGENTS.md exists — creates a starter if missing.\n   */\n  installInstructions(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.instructionsFile) return false;\n\n    // Ensure AGENTS.md exists before creating stubs that reference it\n    ensureAgentsMd(this.projectRoot, this.packageRoot);\n\n    const targetPath = path.join(this.projectRoot, reg.instructionsFile);\n\n    // Check if file already exists\n    let existing: string | null = null;\n    try { existing = fs.readFileSync(targetPath, 'utf-8'); } catch { /* doesn't exist */ }\n\n    if (existing !== null) {\n      // File exists — check if it already has our reference\n      if (existing.includes(INSTRUCTIONS_REF_START) || existing.includes(INSTRUCTIONS_STUB_MARKER)) {\n        return false; // Already has reference — idempotent\n      }\n      // Prepend reference block to existing content\n      fs.writeFileSync(targetPath, INSTRUCTIONS_REF_BLOCK + existing, 'utf-8');\n      return true;\n    }\n\n    // File doesn't exist — write the full stub template\n    const templateCandidates = [\n      path.join(this.packageRoot, 'src/symbionts/templates/instructions-stub.md'),\n      path.join(this.packageRoot, 'dist/src/symbionts/templates/instructions-stub.md'),\n    ];\n    let stub: string | null = null;\n    for (const p of templateCandidates) {\n      try { stub = fs.readFileSync(p, 'utf-8'); break; } catch { /* try next */ }\n    }\n    if (!stub) return false;\n\n    stub = stub.replace('{agentDisplayName}', this.manifest.displayName);\n    fs.mkdirSync(path.dirname(targetPath), { recursive: true });\n    fs.writeFileSync(targetPath, stub, 'utf-8');\n    return true;\n  }\n\n  /**\n   * Remove Myco's instruction file reference.\n   * - If file is the full stub (only Myco content): delete it.\n   * - If file has user content + prepended reference: remove just the reference block.\n   */\n  uninstallInstructions(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.instructionsFile) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.instructionsFile);\n    let content: string;\n    try { content = fs.readFileSync(targetPath, 'utf-8'); } catch { return false; }\n\n    // Case 1: Full stub — delete the file entirely\n    if (content.includes(INSTRUCTIONS_STUB_MARKER)) {\n      fs.unlinkSync(targetPath);\n      return true;\n    }\n\n    // Case 2: Prepended reference block — remove just the block\n    if (content.includes(INSTRUCTIONS_REF_START)) {\n      const startIdx = content.indexOf(INSTRUCTIONS_REF_START);\n      const endIdx = content.indexOf(INSTRUCTIONS_REF_END);\n      if (endIdx > startIdx) {\n        // Remove from start marker through end marker + trailing whitespace\n        const afterEnd = endIdx + INSTRUCTIONS_REF_END.length;\n        const cleaned = (content.slice(0, startIdx) + content.slice(afterEnd)).replace(/^\\n+/, '');\n        fs.writeFileSync(targetPath, cleaned, 'utf-8');\n        return true;\n      }\n    }\n\n    return false;\n  }\n\n  /** List skill directory names from the package root. Returns empty array if not found. */\n  private listSkillDirs(): string[] {\n    try {\n      return fs.readdirSync(path.join(this.packageRoot, SKILLS_SUBDIR), { withFileTypes: true })\n        .filter((d) => d.isDirectory())\n        .map((d) => d.name);\n    } catch { return []; }\n  }\n\n  /** Add skill symlink paths to project .gitignore. */\n  private updateGitignore(): void {\n    const reg = this.manifest.registration;\n    if (!reg?.skillsTarget) return;\n\n    const skillNames = this.listSkillDirs();\n\n    const entries = [\n      `${CANONICAL_SKILLS_DIR}/`,\n      ...(reg.skillsTarget !== CANONICAL_SKILLS_DIR\n        ? skillNames.map((name) => `${reg.skillsTarget}/${name}`)\n        : []\n      ),\n    ];\n\n    const gitignorePath = path.join(this.projectRoot, '.gitignore');\n    let existing = '';\n    try { existing = fs.readFileSync(gitignorePath, 'utf-8'); } catch { /* doesn't exist yet */ }\n\n    const newEntries = entries.filter((e) => !existing.includes(e));\n    if (newEntries.length === 0) return;\n\n    const separator = existing.endsWith('\\n') || existing === '' ? '' : '\\n';\n    const block = `${separator}\\n${GITIGNORE_SKILLS_COMMENT}\\n${newEntries.join('\\n')}\\n`;\n    fs.writeFileSync(gitignorePath, existing + block, 'utf-8');\n  }\n\n  /**\n   * Merge hooks template into the target settings file.\n   * Replaces all Myco-owned hook groups; preserves non-Myco hooks.\n   */\n  installHooks(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.hooksTarget) return false;\n\n    const template = this.loadTemplate('hooks');\n    if (!template) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.hooksTarget);\n    const settings = readJsonFile(targetPath);\n    const existingHooks = (settings.hooks ?? {}) as Record<string, unknown[]>;\n\n    // Build merged hooks: for each event, keep non-Myco groups + add template groups\n    const mergedHooks: Record<string, unknown[]> = {};\n\n    // Preserve non-Myco hooks from existing config\n    for (const [event, groups] of Object.entries(existingHooks)) {\n      const nonMycoGroups = (groups as Array<Record<string, unknown>>).filter(\n        (group) => !isMycoHookGroup(group),\n      );\n      if (nonMycoGroups.length > 0) {\n        mergedHooks[event] = nonMycoGroups;\n      }\n    }\n\n    // Add template hooks\n    for (const [event, groups] of Object.entries(template)) {\n      mergedHooks[event] = [...(mergedHooks[event] ?? []), ...(groups as unknown[])];\n    }\n\n    settings.hooks = mergedHooks;\n    writeJsonFile(targetPath, settings);\n    return true;\n  }\n\n  /**\n   * Merge MCP server template into the target config file.\n   * Replaces the `myco` server entry; preserves other servers.\n   */\n  installMcp(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.mcpTarget) return false;\n\n    const template = this.loadTemplate('mcp');\n    if (!template) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.mcpTarget);\n    const mcpFormat = reg.mcpFormat ?? 'json';\n\n    if (mcpFormat === 'toml') {\n      return this.installMcpToml(targetPath, template);\n    }\n    return this.installMcpJson(targetPath, template);\n  }\n\n  /** Write MCP servers to a JSON config file. */\n  private installMcpJson(targetPath: string, template: Record<string, unknown>): boolean {\n    const config = readJsonFile(targetPath);\n    const servers = (config.mcpServers ?? {}) as Record<string, unknown>;\n\n    for (const [name, def] of Object.entries(template)) {\n      servers[name] = def;\n    }\n\n    config.mcpServers = servers;\n    writeJsonFile(targetPath, config);\n    return true;\n  }\n\n  /** Write MCP servers to a TOML config file. */\n  private installMcpToml(targetPath: string, template: Record<string, unknown>): boolean {\n    let raw = '';\n    try { raw = fs.readFileSync(targetPath, 'utf-8'); } catch { /* doesn't exist */ }\n\n    for (const [name, def] of Object.entries(template)) {\n      raw = buildTomlMcpSection(raw, name, def as Record<string, unknown>);\n    }\n\n    fs.mkdirSync(path.dirname(targetPath), { recursive: true });\n    fs.writeFileSync(targetPath, raw, 'utf-8');\n    return true;\n  }\n\n  /**\n   * Create symlinks for skills through .agents/skills/ canonical layer.\n   * Canonical: .agents/skills/<name> -> <packageRoot>/skills/<name>\n   * Agent-specific: <skillsTarget>/<name> -> ../../.agents/skills/<name>\n   */\n  installSkills(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.skillsTarget) return false;\n\n    const skillNames = this.listSkillDirs();\n    if (skillNames.length === 0) return false;\n\n    const skillsSrc = path.join(this.packageRoot, SKILLS_SUBDIR);\n\n    // Create canonical symlinks: .agents/skills/<name> -> package skills\n    const canonicalDir = path.join(this.projectRoot, CANONICAL_SKILLS_DIR);\n    fs.mkdirSync(canonicalDir, { recursive: true });\n\n    for (const name of skillNames) {\n      const canonicalLink = path.join(canonicalDir, name);\n      const target = path.join(skillsSrc, name);\n      ensureSymlink(canonicalLink, target);\n    }\n\n    // Create agent-specific symlinks if skillsTarget differs from canonical\n    const agentSkillsDir = path.join(this.projectRoot, reg.skillsTarget);\n    const canonicalRel = path.relative(agentSkillsDir, canonicalDir);\n\n    if (reg.skillsTarget !== CANONICAL_SKILLS_DIR) {\n      fs.mkdirSync(agentSkillsDir, { recursive: true });\n      for (const name of skillNames) {\n        const agentLink = path.join(agentSkillsDir, name);\n        const relTarget = path.join(canonicalRel, name);\n        ensureSymlink(agentLink, relTarget);\n      }\n    }\n\n    return true;\n  }\n\n  /**\n   * Merge settings template into the target settings file.\n   * Deep merges objects and deduplicates arrays.\n   */\n  installSettings(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.settingsTarget) return false;\n\n    const template = this.loadTemplate('settings');\n    if (!template) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.settingsTarget);\n    const existing = readJsonFile(targetPath);\n    const merged = deepMergeSettings(existing, template);\n    writeJsonFile(targetPath, merged);\n    return true;\n  }\n\n  /**\n   * Remove Myco entries from the target settings file.\n   * Template-driven: loads the settings template and removes matching values.\n   * Arrays: filter out values present in the template.\n   * Objects: delete keys present in the template.\n   */\n  uninstallSettings(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.settingsTarget) return false;\n\n    const template = this.loadTemplate('settings');\n    if (!template) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.settingsTarget);\n    const settings = readJsonFile(targetPath);\n    if (Object.keys(settings).length === 0) return false;\n\n    const changed = deepRemoveSettings(settings, template);\n    if (!changed) return false;\n\n    writeOrDeleteJsonFile(targetPath, settings);\n    return true;\n  }\n\n  /** Remove Myco hook groups from the target settings file. */\n  uninstallHooks(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.hooksTarget) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.hooksTarget);\n    const settings = readJsonFile(targetPath);\n    const existingHooks = (settings.hooks ?? {}) as Record<string, unknown[]>;\n    if (Object.keys(existingHooks).length === 0) return false;\n\n    const cleaned: Record<string, unknown[]> = {};\n    for (const [event, groups] of Object.entries(existingHooks)) {\n      const nonMyco = (groups as Array<Record<string, unknown>>).filter(\n        (group) => !isMycoHookGroup(group),\n      );\n      if (nonMyco.length > 0) {\n        cleaned[event] = nonMyco;\n      }\n    }\n\n    if (Object.keys(cleaned).length === 0) {\n      delete settings.hooks;\n    } else {\n      settings.hooks = cleaned;\n    }\n\n    writeOrDeleteJsonFile(targetPath, settings);\n    return true;\n  }\n\n  /** Remove Myco MCP server entry from the target config file. */\n  uninstallMcp(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.mcpTarget) return false;\n\n    const targetPath = path.join(this.projectRoot, reg.mcpTarget);\n    const mcpFormat = reg.mcpFormat ?? 'json';\n\n    if (mcpFormat === 'toml') {\n      return this.uninstallMcpToml(targetPath);\n    }\n    return this.uninstallMcpJson(targetPath);\n  }\n\n  private uninstallMcpJson(targetPath: string): boolean {\n    const config = readJsonFile(targetPath);\n    const servers = (config.mcpServers ?? {}) as Record<string, unknown>;\n    if (!servers[MYCO_MCP_SERVER_NAME]) return false;\n\n    delete servers[MYCO_MCP_SERVER_NAME];\n\n    if (Object.keys(servers).length === 0) {\n      delete config.mcpServers;\n    } else {\n      config.mcpServers = servers;\n    }\n\n    writeOrDeleteJsonFile(targetPath, config);\n    return true;\n  }\n\n  private uninstallMcpToml(targetPath: string): boolean {\n    let raw = '';\n    try { raw = fs.readFileSync(targetPath, 'utf-8'); } catch { return false; }\n\n    const sectionHeader = `[mcp_servers.${MYCO_MCP_SERVER_NAME}]`;\n    if (!raw.includes(sectionHeader)) return false;\n\n    const startIdx = raw.indexOf(sectionHeader);\n    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, MYCO_MCP_SERVER_NAME);\n    const before = raw.slice(0, startIdx).trimEnd();\n    const after = raw.slice(endIdx).trimStart();\n    const updated = (before + (before && after ? '\\n\\n' : '') + after).trimEnd();\n\n    if (!updated.trim()) {\n      try { fs.unlinkSync(targetPath); } catch { /* ignore */ }\n    } else {\n      fs.writeFileSync(targetPath, updated + '\\n', 'utf-8');\n    }\n    return true;\n  }\n\n  /** Remove skill symlinks (canonical + agent-specific). */\n  uninstallSkills(): boolean {\n    const reg = this.manifest.registration;\n    if (!reg?.skillsTarget) return false;\n\n    const skillNames = this.listSkillDirs();\n    if (skillNames.length === 0) return false;\n\n    let removed = false;\n\n    // Remove agent-specific symlinks\n    if (reg.skillsTarget !== CANONICAL_SKILLS_DIR) {\n      for (const name of skillNames) {\n        const link = path.join(this.projectRoot, reg.skillsTarget, name);\n        try { fs.unlinkSync(link); removed = true; } catch { /* doesn't exist */ }\n      }\n      // Remove agent skills dir if now empty (rmdirSync fails atomically if non-empty)\n      try { fs.rmdirSync(path.join(this.projectRoot, reg.skillsTarget)); } catch { /* not empty or missing */ }\n    }\n\n    // Remove canonical symlinks\n    const canonicalDir = path.join(this.projectRoot, CANONICAL_SKILLS_DIR);\n    for (const name of skillNames) {\n      const link = path.join(canonicalDir, name);\n      try { fs.unlinkSync(link); removed = true; } catch { /* doesn't exist */ }\n    }\n    // Remove empty dirs (rmdirSync fails atomically if non-empty)\n    try { fs.rmdirSync(canonicalDir); } catch { /* not empty or missing */ }\n    try { fs.rmdirSync(path.join(this.projectRoot, '.agents')); } catch { /* not empty or missing */ }\n\n    return removed;\n  }\n\n  /** Remove Myco entries from project .gitignore. */\n  private cleanGitignore(): void {\n    const gitignorePath = path.join(this.projectRoot, '.gitignore');\n    let content = '';\n    try { content = fs.readFileSync(gitignorePath, 'utf-8'); } catch { return; }\n\n    // Remove the Myco skill symlinks block and individual entries\n    const reg = this.manifest.registration;\n    const skillNames = reg?.skillsTarget && reg.skillsTarget !== CANONICAL_SKILLS_DIR\n      ? this.listSkillDirs()\n      : [];\n    const lines = content.split('\\n');\n    const filtered = lines.filter((line) => {\n      if (line === GITIGNORE_SKILLS_COMMENT) return false;\n      if (line === `${CANONICAL_SKILLS_DIR}/`) return false;\n      if (skillNames.some((name) => line === `${reg!.skillsTarget}/${name}`)) return false;\n      return true;\n    });\n\n    // Clean up consecutive blank lines left by removal\n    const cleaned = filtered.join('\\n').replace(/\\n{3,}/g, '\\n\\n').trim();\n    if (cleaned) {\n      fs.writeFileSync(gitignorePath, cleaned + '\\n', 'utf-8');\n    } else {\n      try { fs.unlinkSync(gitignorePath); } catch { /* ignore */ }\n    }\n  }\n}\n\n// --- TOML helpers ---\n\n/** TOML section header pattern. */\nconst TOML_SECTION_RE = /^\\[([^\\]]+)\\]/;\n\n/** Find where a [mcp_servers.<name>] section ends in a TOML string. */\nfunction findTomlSectionEnd(raw: string, searchStart: number, serverName: string): number {\n  const subsectionPrefix = `mcp_servers.${serverName}.`;\n  const rawLines = raw.slice(searchStart).split('\\n');\n  let offset = searchStart;\n  for (const line of rawLines) {\n    offset += line.length + 1;\n    const m = line.match(TOML_SECTION_RE);\n    if (m && !m[1].startsWith(subsectionPrefix) && m[1] !== `mcp_servers.${serverName}`) {\n      return offset - line.length - 1;\n    }\n  }\n  return raw.length;\n}\n\n/**\n * Build/update a specific mcp_servers entry in a TOML string.\n * Pure transformation — returns updated content without writing to disk.\n */\nfunction buildTomlMcpSection(\n  raw: string,\n  serverName: string,\n  server: Record<string, unknown>,\n): string {\n  const sectionHeader = `[mcp_servers.${serverName}]`;\n\n  // Build the TOML block for this server\n  const lines: string[] = [sectionHeader];\n  for (const [key, val] of Object.entries(server)) {\n    if (key === 'env' && typeof val === 'object' && val !== null) continue; // Handle env as subtable\n    if (typeof val === 'string') {\n      lines.push(`${key} = \"${val}\"`);\n    } else if (Array.isArray(val)) {\n      lines.push(`${key} = [${val.map((v: unknown) => `\"${v}\"`).join(', ')}]`);\n    } else if (typeof val === 'boolean') {\n      lines.push(`${key} = ${val}`);\n    }\n  }\n\n  // Add env subtable if present\n  const env = server.env as Record<string, string> | undefined;\n  if (env && Object.keys(env).length > 0) {\n    lines.push('');\n    lines.push(`[mcp_servers.${serverName}.env]`);\n    for (const [key, val] of Object.entries(env)) {\n      lines.push(`${key} = \"${val}\"`);\n    }\n  }\n\n  const block = lines.join('\\n');\n\n  let updated: string;\n  if (raw.includes(sectionHeader)) {\n    const startIdx = raw.indexOf(sectionHeader);\n    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, serverName);\n    const before = raw.slice(0, startIdx).trimEnd();\n    const after = raw.slice(endIdx);\n    const separator = before ? '\\n\\n' : '';\n    updated = (before + separator + block + after).trimEnd() + '\\n';\n  } else {\n    // Append new section\n    const separator = raw.trim() ? '\\n\\n' : '';\n    updated = (raw.trimEnd() + separator + block).trimEnd() + '\\n';\n  }\n\n  return updated;\n}\n\n// --- Settings merge helpers ---\n\n/** Deep merge two settings objects. Arrays are appended + deduplicated; objects recurse. */\nfunction deepMergeSettings(\n  target: Record<string, unknown>,\n  source: Record<string, unknown>,\n): Record<string, unknown> {\n  const result = { ...target };\n  for (const [key, sourceVal] of Object.entries(source)) {\n    const targetVal = result[key];\n    if (Array.isArray(sourceVal) && Array.isArray(targetVal)) {\n      result[key] = [...new Set([...targetVal, ...sourceVal])];\n    } else if (isPlainObject(sourceVal) && isPlainObject(targetVal)) {\n      result[key] = deepMergeSettings(\n        targetVal as Record<string, unknown>,\n        sourceVal as Record<string, unknown>,\n      );\n    } else {\n      result[key] = sourceVal;\n    }\n  }\n  return result;\n}\n\nfunction isPlainObject(val: unknown): val is Record<string, unknown> {\n  return typeof val === 'object' && val !== null && !Array.isArray(val);\n}\n\n/**\n * Remove values from target that match the template structure.\n * Arrays: filter out values present in the template array.\n * Objects: delete keys present in the template object, recurse into nested objects.\n * Returns true if anything was removed.\n */\nfunction deepRemoveSettings(\n  target: Record<string, unknown>,\n  template: Record<string, unknown>,\n): boolean {\n  let changed = false;\n  for (const [key, templateVal] of Object.entries(template)) {\n    const targetVal = target[key];\n    if (targetVal === undefined) continue;\n\n    if (Array.isArray(templateVal) && Array.isArray(targetVal)) {\n      // Filter out values that appear in the template array\n      const templateSet = new Set(templateVal.map(String));\n      const filtered = targetVal.filter((v) => !templateSet.has(String(v)));\n      if (filtered.length !== targetVal.length) {\n        if (filtered.length > 0) {\n          target[key] = filtered;\n        } else {\n          delete target[key];\n        }\n        changed = true;\n      }\n    } else if (isPlainObject(templateVal) && isPlainObject(targetVal)) {\n      // Recurse into nested objects, then prune if empty\n      if (deepRemoveSettings(targetVal, templateVal)) {\n        if (Object.keys(targetVal).length === 0) {\n          delete target[key];\n        }\n        changed = true;\n      }\n    } else {\n      // Scalar: delete if value matches\n      if (String(targetVal) === String(templateVal)) {\n        delete target[key];\n        changed = true;\n      }\n    }\n  }\n  return changed;\n}\n\n// --- JSON helpers ---\n\nfunction readJsonFile(filePath: string): Record<string, unknown> {\n  try {\n    return JSON.parse(fs.readFileSync(filePath, 'utf-8'));\n  } catch {\n    return {};\n  }\n}\n\nfunction writeJsonFile(filePath: string, data: Record<string, unknown>): void {\n  fs.mkdirSync(path.dirname(filePath), { recursive: true });\n  fs.writeFileSync(filePath, JSON.stringify(data, null, 2) + '\\n', 'utf-8');\n}\n\n/** Write a JSON file, or delete it if the object is empty. */\nfunction writeOrDeleteJsonFile(filePath: string, data: Record<string, unknown>): void {\n  if (Object.keys(data).length === 0) {\n    try { fs.unlinkSync(filePath); } catch { /* ignore */ }\n  } else {\n    writeJsonFile(filePath, data);\n  }\n}\n\n/**\n * Create a starter AGENTS.md if the project doesn't have one.\n * Idempotent — skips if AGENTS.md already exists.\n */\nfunction ensureAgentsMd(projectRoot: string, packageRoot: string): void {\n  const agentsMdPath = path.join(projectRoot, 'AGENTS.md');\n  if (fs.existsSync(agentsMdPath)) return;\n\n  const candidates = [\n    path.join(packageRoot, 'src/symbionts/templates/agents-starter.md'),\n    path.join(packageRoot, 'dist/src/symbionts/templates/agents-starter.md'),\n  ];\n  for (const p of candidates) {\n    try {\n      const content = fs.readFileSync(p, 'utf-8');\n      fs.writeFileSync(agentsMdPath, content, 'utf-8');\n      return;\n    } catch { /* try next */ }\n  }\n}\n\nfunction ensureSymlink(linkPath: string, target: string): void {\n  try {\n    if (fs.readlinkSync(linkPath) === target) return;\n  } catch { /* does not exist or is not a symlink — proceed */ }\n  try { fs.rmSync(linkPath, { recursive: true, force: true }); } catch { /* ignore */ }\n  fs.symlinkSync(target, linkPath);\n}\n","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# Binary attachments — screenshots captured from transcripts\nattachments/\n\n# Team worker deployment — patched wrangler.toml + source copy\n.team-worker/\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      ].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 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package/dist/{chunk-RGRPAKEY.js → chunk-ZI3NGD5O.js}

@@ -1,7 +1,7 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   isProcessAlive
-} from "./chunk-YRHSTVCZ.js";
+} from "./chunk-YBUXSTBR.js";
 import {
   loadConfig
 } from "./chunk-MAZOVVDU.js";
@@ -144,7 +144,7 @@ function gatherStats(vaultDir, options) {
     },
     vault: {
       path: vaultDir,
-      name: path.basename(vaultDir),
+      name: path.basename(path.dirname(vaultDir)),
       session_count,
       batch_count,
       spore_count,
@@ -184,4 +184,4 @@ export {
   getEmbeddingQueueDepth,
   gatherStats
 };
-//# sourceMappingURL=chunk-RGRPAKEY.js.map
+//# sourceMappingURL=chunk-ZI3NGD5O.js.map

package/dist/{chunk-RGRPAKEY.js.map → chunk-ZI3NGD5O.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/db/queries/embeddings.ts","../src/services/stats.ts"],"sourcesContent":["/**\n * Embedded flag management — tracks which rows have been indexed in the external vector store.\n *\n * All vector storage and similarity search is handled by the external VectorStore.\n * This module only manages the `embedded` flag on relational tables.\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Tables that participate in vector embedding. */\nexport const EMBEDDABLE_TABLES = ['sessions', 'spores', 'plans', 'artifacts'] as const;\n\n/** TypeScript type for valid embeddable table names. */\nexport type EmbeddableTable = (typeof EMBEDDABLE_TABLES)[number];\n\n/** Per-table column that holds the text content used for embedding. */\nexport const EMBEDDABLE_TEXT_COLUMNS: Record<EmbeddableTable, string> = {\n  sessions: 'summary',\n  spores: 'content',\n  plans: 'content',\n  artifacts: 'content',\n};\n\n/** Error message for invalid table names. */\nconst INVALID_TABLE_MSG = 'Invalid table name — must be one of: sessions, spores, plans, artifacts';\n\n/** Default number of rows returned by getUnembedded. */\nconst DEFAULT_UNEMBEDDED_LIMIT = 100;\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/**\n * Validate that a table name is in the allowlist.\n *\n * @throws if the table name is not one of the embeddable tables.\n */\nexport function assertValidTable(table: string): asserts table is EmbeddableTable {\n  if (!(EMBEDDABLE_TABLES as readonly string[]).includes(table)) {\n    throw new Error(INVALID_TABLE_MSG);\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/** Mark a row as embedded in the external vector store. */\nexport function markEmbedded(table: string, id: string | number): void {\n  assertValidTable(table);\n  const db = getDatabase();\n  db.prepare(`UPDATE ${table} SET embedded = 1 WHERE id = ?`).run(id);\n}\n\n/** Clear the embedded flag (e.g., when vector is removed or needs re-embedding). */\nexport function clearEmbedded(table: string, id: string | number): void {\n  assertValidTable(table);\n  const db = getDatabase();\n  db.prepare(`UPDATE ${table} SET embedded = 0 WHERE id = ?`).run(id);\n}\n\n/** Find rows that have not yet been embedded, oldest first. */\nexport function getUnembedded(\n  table: string,\n  limit: number = DEFAULT_UNEMBEDDED_LIMIT,\n): Array<{ id: string | number; created_at: number; text: string }> {\n  assertValidTable(table);\n  const db = getDatabase();\n  const textCol = EMBEDDABLE_TEXT_COLUMNS[table as EmbeddableTable];\n  const contentFilter = table === 'sessions' ? ' AND summary IS NOT NULL' : '';\n  const statusFilter = table === 'spores' ? \" AND status = 'active'\" : '';\n\n  return db.prepare(\n    `SELECT id, created_at, ${textCol} AS text\n     FROM ${table}\n     WHERE embedded = 0${contentFilter}${statusFilter}\n     ORDER BY created_at ASC\n     LIMIT ?`\n  ).all(limit) as Array<{ id: string | number; created_at: number; text: string }>;\n}\n\n/** Get aggregated embedding queue depth across all embeddable tables. */\nexport function getEmbeddingQueueDepth(): {\n  queue_depth: number;\n  embedded_count: number;\n  total: number;\n} {\n  const db = getDatabase();\n\n  const queueRow = db.prepare(`\n    SELECT\n      (SELECT COUNT(*) FROM sessions  WHERE embedded = 0 AND summary IS NOT NULL) +\n      (SELECT COUNT(*) FROM spores    WHERE embedded = 0 AND status = 'active') +\n      (SELECT COUNT(*) FROM plans     WHERE embedded = 0 AND content IS NOT NULL) +\n      (SELECT COUNT(*) FROM artifacts WHERE embedded = 0 AND content IS NOT NULL)\n    AS cnt\n  `).get() as { cnt: number };\n\n  const embeddedRow = db.prepare(`\n    SELECT\n      (SELECT COUNT(*) FROM sessions  WHERE embedded = 1) +\n      (SELECT COUNT(*) FROM spores    WHERE embedded = 1) +\n      (SELECT COUNT(*) FROM plans     WHERE embedded = 1) +\n      (SELECT COUNT(*) FROM artifacts WHERE embedded = 1)\n    AS cnt\n  `).get() as { cnt: number };\n\n  const queue_depth = Number(queueRow.cnt ?? 0);\n  const embedded_count = Number(embeddedRow.cnt ?? 0);\n  return { queue_depth, embedded_count, total: queue_depth + embedded_count };\n}\n","/**\n * Vault statistics — gathered from SQLite.\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport { getEmbeddingQueueDepth } from '@myco/db/queries/embeddings.js';\nimport { loadConfig } from '@myco/config/loader.js';\nimport { isProcessAlive } from '@myco/cli/shared.js';\nimport { DIGEST_TIERS } from '@myco/constants.js';\nimport fs from 'node:fs';\nimport path from 'node:path';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Process uptime is available directly from the daemon process via process.uptime(). */\nconst DAEMON_JSON_FILENAME = 'daemon.json';\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\nexport interface V2Stats {\n  daemon: {\n    pid: number;\n    port: number;\n    version: string;\n    uptime_seconds: number;\n    active_sessions: string[];\n  };\n  vault: {\n    path: string;\n    name: string;\n    session_count: number;\n    batch_count: number;\n    spore_count: number;\n    plan_count: number;\n    artifact_count: number;\n    entity_count: number;\n    edge_count: number;\n  };\n  embedding: {\n    provider: string;\n    model: string;\n    queue_depth: number;\n    embedded_count: number;\n    total_embeddable: number;\n  };\n  agent: {\n    last_run_at: number | null;\n    last_run_status: string | null;\n    total_runs: number;\n  };\n  digest: {\n    freshest_tier: number | null;\n    generated_at: number | null;\n    tiers_available: number[];\n  };\n  unprocessed_batches: number;\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Count rows in a table (sync). */\nfunction countTable(db: ReturnType<typeof getDatabase>, table: string): number {\n  const row = db.prepare(`SELECT COUNT(*) AS cnt FROM ${table}`).get() as { cnt: number };\n  return Number(row.cnt);\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\nexport function gatherStats(vaultDir: string, options?: { active_sessions?: string[] }): V2Stats {\n  const db = getDatabase();\n\n  // Load config for embedding provider info (sync — already on disk)\n  const config = loadConfig(vaultDir);\n\n  // All queries are synchronous — no Promise.all needed\n  const session_count = countTable(db, 'sessions');\n  const batch_count = countTable(db, 'prompt_batches');\n  const spore_count = countTable(db, 'spores');\n  const plan_count = countTable(db, 'plans');\n  const artifact_count = countTable(db, 'artifacts');\n  const entity_count = countTable(db, 'entities');\n  const edge_count = countTable(db, 'graph_edges');\n\n  // Shared embedding queue depth helper (consistent filter logic)\n  const embeddingStats = getEmbeddingQueueDepth();\n  const { queue_depth, embedded_count, total: total_embeddable } = embeddingStats;\n\n  // Unprocessed batches\n  const unprocessedRow = db.prepare(\n    'SELECT COUNT(*) AS cnt FROM prompt_batches WHERE processed = 0',\n  ).get() as { cnt: number };\n  const unprocessed_batches = Number(unprocessedRow.cnt ?? 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+{"version":3,"sources":["../src/db/queries/embeddings.ts","../src/services/stats.ts"],"sourcesContent":["/**\n * Embedded flag management — tracks which rows have been indexed in the external vector store.\n *\n * All vector storage and similarity search is handled by the external VectorStore.\n * This module only manages the `embedded` flag on relational tables.\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Tables that participate in vector embedding. */\nexport const EMBEDDABLE_TABLES = ['sessions', 'spores', 'plans', 'artifacts'] as const;\n\n/** TypeScript type for valid embeddable table names. */\nexport type EmbeddableTable = (typeof EMBEDDABLE_TABLES)[number];\n\n/** Per-table column that holds the text content used for embedding. */\nexport const EMBEDDABLE_TEXT_COLUMNS: Record<EmbeddableTable, string> = {\n  sessions: 'summary',\n  spores: 'content',\n  plans: 'content',\n  artifacts: 'content',\n};\n\n/** Error message for invalid table names. */\nconst INVALID_TABLE_MSG = 'Invalid table name — must be one of: sessions, spores, plans, artifacts';\n\n/** Default number of rows returned by getUnembedded. */\nconst DEFAULT_UNEMBEDDED_LIMIT = 100;\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/**\n * Validate that a table name is in the allowlist.\n *\n * @throws if the table name is not one of the embeddable tables.\n */\nexport function assertValidTable(table: string): asserts table is EmbeddableTable {\n  if (!(EMBEDDABLE_TABLES as readonly string[]).includes(table)) {\n    throw new Error(INVALID_TABLE_MSG);\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/** Mark a row as embedded in the external vector store. */\nexport function markEmbedded(table: string, id: string | number): void {\n  assertValidTable(table);\n  const db = getDatabase();\n  db.prepare(`UPDATE ${table} SET embedded = 1 WHERE id = ?`).run(id);\n}\n\n/** Clear the embedded flag (e.g., when vector is removed or needs re-embedding). */\nexport function clearEmbedded(table: string, id: string | number): void {\n  assertValidTable(table);\n  const db = getDatabase();\n  db.prepare(`UPDATE ${table} SET embedded = 0 WHERE id = ?`).run(id);\n}\n\n/** Find rows that have not yet been embedded, oldest first. */\nexport function getUnembedded(\n  table: string,\n  limit: number = DEFAULT_UNEMBEDDED_LIMIT,\n): Array<{ id: string | number; created_at: number; text: string }> {\n  assertValidTable(table);\n  const db = getDatabase();\n  const textCol = EMBEDDABLE_TEXT_COLUMNS[table as EmbeddableTable];\n  const contentFilter = table === 'sessions' ? ' AND summary IS NOT NULL' : '';\n  const statusFilter = table === 'spores' ? \" AND status = 'active'\" : '';\n\n  return db.prepare(\n    `SELECT id, created_at, ${textCol} AS text\n     FROM ${table}\n     WHERE embedded = 0${contentFilter}${statusFilter}\n     ORDER BY created_at ASC\n     LIMIT ?`\n  ).all(limit) as Array<{ id: string | number; created_at: number; text: string }>;\n}\n\n/** Get aggregated embedding queue depth across all embeddable tables. */\nexport function getEmbeddingQueueDepth(): {\n  queue_depth: number;\n  embedded_count: number;\n  total: number;\n} {\n  const db = getDatabase();\n\n  const queueRow = db.prepare(`\n    SELECT\n      (SELECT COUNT(*) FROM sessions  WHERE embedded = 0 AND summary IS NOT NULL) +\n      (SELECT COUNT(*) FROM spores    WHERE embedded = 0 AND status = 'active') +\n      (SELECT COUNT(*) FROM plans     WHERE embedded = 0 AND content IS NOT NULL) +\n      (SELECT COUNT(*) FROM artifacts WHERE embedded = 0 AND content IS NOT NULL)\n    AS cnt\n  `).get() as { cnt: number };\n\n  const embeddedRow = db.prepare(`\n    SELECT\n      (SELECT COUNT(*) FROM sessions  WHERE embedded = 1) +\n      (SELECT COUNT(*) FROM spores    WHERE embedded = 1) +\n      (SELECT COUNT(*) FROM plans     WHERE embedded = 1) +\n      (SELECT COUNT(*) FROM artifacts WHERE embedded = 1)\n    AS cnt\n  `).get() as { cnt: number };\n\n  const queue_depth = Number(queueRow.cnt ?? 0);\n  const embedded_count = Number(embeddedRow.cnt ?? 0);\n  return { queue_depth, embedded_count, total: queue_depth + embedded_count };\n}\n","/**\n * Vault statistics — gathered from SQLite.\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport { getEmbeddingQueueDepth } from '@myco/db/queries/embeddings.js';\nimport { loadConfig } from '@myco/config/loader.js';\nimport { isProcessAlive } from '@myco/cli/shared.js';\nimport { DIGEST_TIERS } from '@myco/constants.js';\nimport fs from 'node:fs';\nimport path from 'node:path';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Process uptime is available directly from the daemon process via process.uptime(). */\nconst DAEMON_JSON_FILENAME = 'daemon.json';\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\nexport interface V2Stats {\n  daemon: {\n    pid: number;\n    port: number;\n    version: string;\n    uptime_seconds: number;\n    active_sessions: string[];\n  };\n  vault: {\n    path: string;\n    name: string;\n    session_count: number;\n    batch_count: number;\n    spore_count: number;\n    plan_count: number;\n    artifact_count: number;\n    entity_count: number;\n    edge_count: number;\n  };\n  embedding: {\n    provider: string;\n    model: string;\n    queue_depth: number;\n    embedded_count: number;\n    total_embeddable: number;\n  };\n  agent: {\n    last_run_at: number | null;\n    last_run_status: string | null;\n    total_runs: number;\n  };\n  digest: {\n    freshest_tier: number | null;\n    generated_at: number | null;\n    tiers_available: number[];\n  };\n  unprocessed_batches: number;\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Count rows in a table (sync). */\nfunction countTable(db: ReturnType<typeof getDatabase>, table: string): number {\n  const row = db.prepare(`SELECT COUNT(*) AS cnt FROM ${table}`).get() as { cnt: number };\n  return Number(row.cnt);\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\nexport function gatherStats(vaultDir: string, options?: { active_sessions?: string[] }): V2Stats {\n  const db = getDatabase();\n\n  // Load config for embedding provider info (sync — already on disk)\n  const config = loadConfig(vaultDir);\n\n  // All queries are synchronous — no Promise.all needed\n  const session_count = countTable(db, 'sessions');\n  const batch_count = countTable(db, 'prompt_batches');\n  const spore_count = countTable(db, 'spores');\n  const plan_count = countTable(db, 'plans');\n  const artifact_count = countTable(db, 'artifacts');\n  const entity_count = countTable(db, 'entities');\n  const edge_count = countTable(db, 'graph_edges');\n\n  // Shared embedding queue depth helper (consistent filter logic)\n  const embeddingStats = getEmbeddingQueueDepth();\n  const { queue_depth, embedded_count, total: total_embeddable } = embeddingStats;\n\n  // Unprocessed batches\n  const unprocessedRow = db.prepare(\n    'SELECT COUNT(*) AS cnt FROM prompt_batches WHERE processed = 0',\n  ).get() as { cnt: number };\n  const unprocessed_batches = Number(unprocessedRow.cnt ?? 0);\n\n  // Agent: most recent run\n  const lastRun = db.prepare(\n    'SELECT started_at, status FROM agent_runs ORDER BY started_at DESC LIMIT 1',\n  ).get() as { started_at: number; status: string } | undefined;\n  const last_run_at = lastRun ? lastRun.started_at : null;\n  const last_run_status = lastRun ? lastRun.status : null;\n\n  // Total agent runs\n  const agentTotalRow = db.prepare(\n    'SELECT COUNT(*) AS cnt FROM agent_runs',\n  ).get() as { cnt: number };\n  const total_runs = Number(agentTotalRow.cnt ?? 0);\n\n  // Digest extracts: only report tiers that are currently configured\n  const digestRows = db.prepare(\n    'SELECT tier, generated_at FROM digest_extracts ORDER BY tier ASC',\n  ).all() as Array<{ tier: number; generated_at: number }>;\n  const configuredTiers = new Set<number>(DIGEST_TIERS);\n  const activeDigestRows = digestRows.filter((r) => configuredTiers.has(r.tier));\n  const tiers_available = activeDigestRows.map((r) => r.tier);\n  const freshest_tier = tiers_available.length > 0 ? Math.max(...tiers_available) : null;\n  const freshestRow = activeDigestRows.find((r) => r.tier === freshest_tier);\n  const generated_at = freshestRow ? freshestRow.generated_at : null;\n\n  // Daemon info from daemon.json\n  let daemonPid = 0;\n  let daemonPort = 0;\n  let daemonVersion = '';\n  let daemonUptimeSeconds = 0;\n  const daemonPath = path.join(vaultDir, DAEMON_JSON_FILENAME);\n  if (fs.existsSync(daemonPath)) {\n    try {\n      const info = JSON.parse(fs.readFileSync(daemonPath, 'utf-8')) as Record<string, unknown>;\n      daemonPid = (info.pid as number) ?? 0;\n      daemonPort = (info.port as number) ?? 0;\n      daemonVersion = (info.version as string) ?? 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package/dist/{cli-Y5QZJAHX.js → cli-VPKNXU2Q.js}

@@ -2,14 +2,14 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   loadEnv
-} from "./chunk-YRHSTVCZ.js";
+} from "./chunk-YBUXSTBR.js";
 import "./chunk-SAKJMNSR.js";
 import "./chunk-LUQBT2Y4.js";
 import "./chunk-MYX5NCRH.js";
-import "./chunk-DPJVKNNP.js";
+import "./chunk-QUSCGEYI.js";
 import "./chunk-PIRWYDOH.js";
 import "./chunk-S6I62FAH.js";
-import "./chunk-TY7A5OZ5.js";
+import "./chunk-UIGH6TKR.js";
 import "./chunk-LPUQPDC2.js";
 import {
   resolveVaultDir
@@ -52,29 +52,29 @@ async function main() {
     process.stdout.write(USAGE);
     return;
   }
-  if (cmd === "init") return (await import("./init-NMSG24BY.js")).run(args);
+  if (cmd === "init") return (await import("./init-7YSOIIGM.js")).run(args);
   if (cmd === "detect-providers") return (await import("./detect-providers-JFE3QLJI.js")).run(args);
   if (cmd === "version" || cmd === "--version" || cmd === "-v") {
-    const { getPluginVersion } = await import("./version-GTFCEIJ2.js");
+    const { getPluginVersion } = await import("./version-ORVUUFGG.js");
     console.log(getPluginVersion());
     return;
   }
-  if (cmd === "mcp") return (await import("./server-GMRVF2PB.js")).main();
+  if (cmd === "mcp") return (await import("./server-7LQPO5WY.js")).main();
   if (cmd === "hook") {
     const hookName = args[0];
     const HOOK_DISPATCH = {
-      "session-start": () => import("./session-start-OH7SBUIA.js"),
-      "session-end": () => import("./session-end-V3V3GMP2.js"),
-      "stop": () => import("./stop-D6L2KRHZ.js"),
-      "user-prompt-submit": () => import("./user-prompt-submit-X4BCPMZ4.js"),
-      "post-tool-use": () => import("./post-tool-use-LSG6N3W5.js"),
-      "post-tool-use-failure": () => import("./post-tool-use-failure-5V3OCLI6.js"),
-      "subagent-start": () => import("./subagent-start-MKL5I54S.js"),
-      "subagent-stop": () => import("./subagent-stop-2E7VKZW2.js"),
-      "stop-failure": () => import("./stop-failure-7OM2AYRX.js"),
-      "task-completed": () => import("./task-completed-5QHIT773.js"),
-      "pre-compact": () => import("./pre-compact-F7Y7SDSZ.js"),
-      "post-compact": () => import("./post-compact-3DDK3OVZ.js")
+      "session-start": () => import("./session-start-M33PWCJD.js"),
+      "session-end": () => import("./session-end-PXS5ACST.js"),
+      "stop": () => import("./stop-RCBDSSPO.js"),
+      "user-prompt-submit": () => import("./user-prompt-submit-DIZJ7QPB.js"),
+      "post-tool-use": () => import("./post-tool-use-BGTDDWAO.js"),
+      "post-tool-use-failure": () => import("./post-tool-use-failure-E3J3MDVD.js"),
+      "subagent-start": () => import("./subagent-start-PZHS5UDO.js"),
+      "subagent-stop": () => import("./subagent-stop-D2YKWNG4.js"),
+      "stop-failure": () => import("./stop-failure-7GSAM3RS.js"),
+      "task-completed": () => import("./task-completed-ADUANOQI.js"),
+      "pre-compact": () => import("./pre-compact-2E6H57AT.js"),
+      "post-compact": () => import("./post-compact-3PIKQGFQ.js")
     };
     const loader = HOOK_DISPATCH[hookName];
     if (!loader) {
@@ -83,13 +83,13 @@ async function main() {
     }
     return (await loader()).main();
   }
-  if (cmd === "daemon") return (await import("./main-3NTAT7ZD.js")).main();
+  if (cmd === "daemon") return (await import("./main-TDE4T4MX.js")).main();
   if (cmd === "doctor") {
     const vaultDir2 = resolveVaultDir();
-    return (await import("./doctor-NFWPX75B.js")).run(args, vaultDir2);
+    return (await import("./doctor-4KHMJYMF.js")).run(args, vaultDir2);
   }
-  if (cmd === "update") return (await import("./update-4NVFET56.js")).run(args);
-  if (cmd === "remove") return (await import("./remove-VCWRNG54.js")).run(args);
+  if (cmd === "update") return (await import("./update-L35DSYQL.js")).run(args);
+  if (cmd === "remove") return (await import("./remove-PVWK3CHQ.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.`);
@@ -101,21 +101,21 @@ async function main() {
     case "verify":
       return (await import("./verify-D7EDVXO5.js")).run(args, vaultDir);
     case "stats":
-      return (await import("./stats-B2V7P45Y.js")).run(args, vaultDir);
+      return (await import("./stats-GAG6QBZL.js")).run(args, vaultDir);
     case "search":
-      return (await import("./search-L7KTBURJ.js")).run(args, vaultDir);
+      return (await import("./search-QZVYVKAE.js")).run(args, vaultDir);
     case "vectors":
-      return (await import("./search-L7KTBURJ.js")).runVectors(args, vaultDir);
+      return (await import("./search-QZVYVKAE.js")).runVectors(args, vaultDir);
     case "session":
-      return (await import("./session-V3SNFG7J.js")).run(args, vaultDir);
+      return (await import("./session-UKCZ7T4P.js")).run(args, vaultDir);
     case "setup-llm":
-      return (await import("./setup-llm-5AMWEAJ5.js")).run(args, vaultDir);
+      return (await import("./setup-llm-WNSUUNXA.js")).run(args, vaultDir);
     case "setup-digest":
       return (await import("./setup-digest-4KDSXAIV.js")).run(args, vaultDir);
     case "agent":
-      return (await import("./agent-run-5KYQJQTY.js")).run(args, vaultDir);
+      return (await import("./agent-run-ECYDEYOJ.js")).run(args, vaultDir);
     case "task":
-      return (await import("./agent-tasks-N7BDYKGB.js")).run(args, vaultDir);
+      return (await import("./agent-tasks-IH77FIDQ.js")).run(args, vaultDir);
     case "team": {
       const sub = args[0];
       if (sub === "init") return (await import("./team-TBS5OILG.js")).teamInit(vaultDir);
@@ -125,7 +125,7 @@ async function main() {
       break;
     }
     case "restart":
-      return (await import("./restart-YYJ7SH4K.js")).run(args, vaultDir);
+      return (await import("./restart-FKPX2TJ2.js")).run(args, vaultDir);
     case "logs":
       return (await import("./logs-LXHPDKUA.js")).run(args, vaultDir);
     default:
@@ -138,4 +138,4 @@ main().catch((err) => {
   console.error(`myco: ${err.message}`);
   process.exit(1);
 });
-//# sourceMappingURL=cli-Y5QZJAHX.js.map
+//# sourceMappingURL=cli-VPKNXU2Q.js.map

package/dist/{client-UGM6MG55.js → client-3TCFLWWW.js}

@@ -2,14 +2,14 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   DaemonClient,
   resolveCliEntryPath
-} from "./chunk-DPJVKNNP.js";
+} from "./chunk-QUSCGEYI.js";
 import "./chunk-PIRWYDOH.js";
 import "./chunk-S6I62FAH.js";
-import "./chunk-TY7A5OZ5.js";
+import "./chunk-UIGH6TKR.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-PZUWP5VK.js";
 export {
   DaemonClient,
   resolveCliEntryPath
 };
-//# sourceMappingURL=client-UGM6MG55.js.map
+//# sourceMappingURL=client-3TCFLWWW.js.map

package/dist/{doctor-NFWPX75B.js → doctor-4KHMJYMF.js}

@@ -2,14 +2,14 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   MYCO_MCP_SERVER_NAME,
   isProcessAlive
-} from "./chunk-YRHSTVCZ.js";
+} from "./chunk-YBUXSTBR.js";
 import "./chunk-SAKJMNSR.js";
 import "./chunk-LUQBT2Y4.js";
 import "./chunk-MYX5NCRH.js";
-import "./chunk-DPJVKNNP.js";
+import "./chunk-QUSCGEYI.js";
 import "./chunk-PIRWYDOH.js";
 import "./chunk-S6I62FAH.js";
-import "./chunk-TY7A5OZ5.js";
+import "./chunk-UIGH6TKR.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-PZUWP5VK.js";
 
@@ -249,4 +249,4 @@ export {
   run,
   runChecks
 };
-//# sourceMappingURL=doctor-NFWPX75B.js.map
+//# sourceMappingURL=doctor-4KHMJYMF.js.map

package/dist/{executor-ESRLUCGU.js → executor-2BZMDCYN.js}

@@ -71,7 +71,7 @@ import {
 import "./chunk-S6I62FAH.js";
 import {
   getPluginVersion
-} from "./chunk-TY7A5OZ5.js";
+} from "./chunk-UIGH6TKR.js";
 import {
   findPackageRoot
 } from "./chunk-LPUQPDC2.js";
@@ -1451,4 +1451,4 @@ export {
   computeWaves,
   runAgent
 };
-//# sourceMappingURL=executor-ESRLUCGU.js.map
+//# sourceMappingURL=executor-2BZMDCYN.js.map