@theglitchking/semantic-memory 1.2.1 → 1.5.0

package/dist/cli/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/cli/index.ts","../../src/cli/skills.ts","../../src/cli/migrate-state.ts"],"sourcesContent":["#!/usr/bin/env node\n\nimport { program } from \"commander\";\nimport { resolve, join, dirname, relative } from \"node:path\";\nimport { existsSync, readFileSync, writeFileSync, rmSync } from \"node:fs\";\nimport { createRequire } from \"node:module\";\nimport { spawnSync } from \"node:child_process\";\nimport { registerUpdateCommands } from \"@theglitchking/claude-plugin-runtime\";\nimport {\n  resolveTarget,\n  installSkills,\n  uninstallSkills,\n  listShippedSkills,\n  SKILL_BUNDLER_AGENTS,\n  type AgentName,\n  type Scope,\n} from \"./skills.js\";\nimport { migrateState } from \"./migrate-state.js\";\n\nconst require_ = createRequire(import.meta.url);\nconst { version } = require_(\"../../package.json\") as { version: string };\n\nconst PKG_NAME = \"@theglitchking/semantic-memory\";\nconst LEGACY_PKG_NAME = \"@theglitchking/semantic-sidekick\";\n\nfunction runRelink(cwd: string) {\n  const candidates = [\n    join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-memory\", \"scripts\", \"link-skills.js\"),\n    join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-sidekick\", \"scripts\", \"link-skills.js\"),\n    resolve(process.cwd(), \"scripts\", \"link-skills.js\"),\n  ];\n  const script = candidates.find((p) => existsSync(p));\n  if (!script) {\n    console.error(\"link-skills.js not found — is the package installed?\");\n    return;\n  }\n  spawnSync(process.execPath, [script], {\n    cwd,\n    env: { ...process.env, INIT_CWD: cwd },\n    stdio: \"inherit\",\n  });\n}\n\nfunction findLocalBin(cwd: string): string | null {\n  const candidates = [\n    join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-memory\", \"bin\", \"semantic-memory\"),\n    join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-sidekick\", \"bin\", \"semantic-sidekick\"),\n  ];\n  for (const p of candidates) {\n    if (existsSync(p)) return p;\n  }\n  return null;\n}\n\nfunction localBinArg(cwd: string): string | null {\n  const abs = findLocalBin(cwd);\n  if (!abs) return null;\n  const rel = relative(cwd, abs);\n  return rel.startsWith(\"..\") ? abs : `./${rel}`;\n}\n\nfunction readJsonSafe(path: string): any {\n  try {\n    const raw = readFileSync(path, \"utf8\");\n    return raw.trim() ? JSON.parse(raw) : null;\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Returns the fragile npx-form pattern we used to write in pre-0.10.0\n * SessionStart hooks, so normalize-config can detect and rewrite it.\n */\nfunction isNpxForm(entry: any): boolean {\n  if (!entry || typeof entry !== \"object\") return false;\n  const cmd = entry.command;\n  const args = Array.isArray(entry.args) ? entry.args : [];\n  return (\n    cmd === \"npx\" &&\n    args.some(\n      (a: unknown) => typeof a === \"string\" && (a.includes(PKG_NAME) || a.includes(LEGACY_PKG_NAME))\n    )\n  );\n}\n\nfunction isLocalForm(entry: any): boolean {\n  if (!entry || typeof entry !== \"object\") return false;\n  const cmd = entry.command;\n  const args = Array.isArray(entry.args) ? entry.args : [];\n  return (\n    cmd === \"node\" &&\n    args.some(\n      (a: unknown) =>\n        typeof a === \"string\" &&\n        (a.includes(\"node_modules/@theglitchking/semantic-memory\") ||\n          a.includes(\"node_modules/@theglitchking/semantic-sidekick\"))\n    )\n  );\n}\n\nfunction extractNotesPath(entry: any): string | null {\n  const args = Array.isArray(entry?.args) ? entry.args : [];\n  const i = args.indexOf(\"--notes\");\n  if (i === -1 || i + 1 >= args.length) return null;\n  return String(args[i + 1]);\n}\n\nfunction extractExtraFlags(entry: any): string[] {\n  const args = Array.isArray(entry?.args) ? entry.args : [];\n  return args.filter((a: unknown): a is string => typeof a === \"string\" && a.startsWith(\"--\") && a !== \"--notes\");\n}\n\nconst TOOL_HELP: Record<string, { description: string; args: string; examples: string[] }> = {\n  // Search\n  search_semantic: {\n    description: \"Vector similarity search — find notes by meaning, not just keywords\",\n    args: '{ \"query\": \"string\", \"limit?\": 10 }',\n    examples: [\n      '{ \"query\": \"microservices architecture\", \"limit\": 5 }',\n      '{ \"query\": \"how to deploy to production\" }',\n    ],\n  },\n  search_text: {\n    description: \"Full-text keyword or regex search with optional filters\",\n    args: '{ \"pattern\": \"string\", \"regex?\": false, \"caseSensitive?\": false, \"pathGlob?\": \"string\", \"tagFilter?\": [\"string\"], \"limit?\": 20 }',\n    examples: [\n      '{ \"pattern\": \"RabbitMQ\" }',\n      '{ \"pattern\": \"OAuth\\\\\\\\d\", \"regex\": true }',\n      '{ \"pattern\": \"deploy\", \"pathGlob\": \"devops/**\", \"tagFilter\": [\"kubernetes\"] }',\n    ],\n  },\n  search_graph: {\n    description: \"Graph traversal — find notes connected to a concept via wikilinks and tags\",\n    args: '{ \"concept\": \"string\", \"maxDepth?\": 2 }',\n    examples: [\n      '{ \"concept\": \"microservices\" }',\n      '{ \"concept\": \"auth\", \"maxDepth\": 3 }',\n    ],\n  },\n  search_hybrid: {\n    description: \"Combined semantic + graph search — vector results re-ranked by graph proximity\",\n    args: '{ \"query\": \"string\", \"limit?\": 10 }',\n    examples: [\n      '{ \"query\": \"event driven architecture\", \"limit\": 5 }',\n    ],\n  },\n\n  // Read\n  read_note: {\n    description: \"Read the full content of a specific note by path\",\n    args: '{ \"path\": \"string\" }',\n    examples: [\n      '{ \"path\": \"project-overview.md\" }',\n      '{ \"path\": \"notes/meeting-2024-01-15.md\" }',\n    ],\n  },\n  read_multiple_notes: {\n    description: \"Batch read multiple notes in one call\",\n    args: '{ \"paths\": [\"string\"] }',\n    examples: [\n      '{ \"paths\": [\"overview.md\", \"architecture.md\", \"deployment.md\"] }',\n    ],\n  },\n  list_notes: {\n    description: \"List all indexed notes with metadata (title, tags, link count)\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n\n  // Write\n  create_note: {\n    description: \"Create a new markdown note with optional YAML frontmatter\",\n    args: '{ \"path\": \"string\", \"content\": \"string\", \"frontmatter?\": {} }',\n    examples: [\n      '{ \"path\": \"new-guide.md\", \"content\": \"# Guide\\\\n\\\\nContent here.\" }',\n      '{ \"path\": \"tagged.md\", \"content\": \"Content.\", \"frontmatter\": { \"title\": \"Tagged Note\", \"tags\": [\"test\"] } }',\n    ],\n  },\n  update_note: {\n    description: \"Edit note content — overwrite, append, prepend, or patch by heading\",\n    args: '{ \"path\": \"string\", \"content\": \"string\", \"mode\": \"overwrite|append|prepend|patch-by-heading\", \"heading?\": \"string\" }',\n    examples: [\n      '{ \"path\": \"guide.md\", \"content\": \"New content.\", \"mode\": \"overwrite\" }',\n      '{ \"path\": \"guide.md\", \"content\": \"\\\\n## Appendix\\\\nExtra info.\", \"mode\": \"append\" }',\n      '{ \"path\": \"guide.md\", \"content\": \"Updated architecture section.\", \"mode\": \"patch-by-heading\", \"heading\": \"Architecture\" }',\n    ],\n  },\n  delete_note: {\n    description: \"Delete a note permanently (requires confirm=true)\",\n    args: '{ \"path\": \"string\", \"confirm\": true }',\n    examples: [\n      '{ \"path\": \"old-note.md\", \"confirm\": true }',\n      '{ \"path\": \"old-note.md\", \"confirm\": false }  // returns warning, does not delete',\n    ],\n  },\n  move_note: {\n    description: \"Move or rename a note — automatically updates wikilinks across the vault\",\n    args: '{ \"from\": \"string\", \"to\": \"string\" }',\n    examples: [\n      '{ \"from\": \"user-service.md\", \"to\": \"auth-service.md\" }',\n      '{ \"from\": \"old/note.md\", \"to\": \"new/location/note.md\" }',\n    ],\n  },\n\n  // Metadata\n  get_frontmatter: {\n    description: \"Read parsed YAML frontmatter from a note as JSON\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"project-overview.md\" }'],\n  },\n  update_frontmatter: {\n    description: \"Set or delete YAML frontmatter keys — pass null to delete a key\",\n    args: '{ \"path\": \"string\", \"fields\": {} }',\n    examples: [\n      '{ \"path\": \"note.md\", \"fields\": { \"status\": \"active\", \"priority\": 1 } }',\n      '{ \"path\": \"note.md\", \"fields\": { \"deprecated_field\": null } }  // deletes the key',\n    ],\n  },\n  manage_tags: {\n    description: \"Add, remove, or list tags on a note (frontmatter and inline)\",\n    args: '{ \"path\": \"string\", \"action\": \"add|remove|list\", \"tags?\": [\"string\"] }',\n    examples: [\n      '{ \"path\": \"note.md\", \"action\": \"list\" }',\n      '{ \"path\": \"note.md\", \"action\": \"add\", \"tags\": [\"important\", \"reviewed\"] }',\n      '{ \"path\": \"note.md\", \"action\": \"remove\", \"tags\": [\"draft\"] }',\n    ],\n  },\n  rename_tag: {\n    description: \"Rename a tag across all notes in the vault (frontmatter + inline)\",\n    args: '{ \"oldTag\": \"string\", \"newTag\": \"string\" }',\n    examples: ['{ \"oldTag\": \"architecture\", \"newTag\": \"arch\" }'],\n  },\n\n  // Graph\n  backlinks: {\n    description: \"Find all notes that link TO a given note via [[wikilinks]]\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"microservices.md\" }'],\n  },\n  forwardlinks: {\n    description: \"Find all notes linked FROM a given note\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"project-overview.md\" }'],\n  },\n  graph_path: {\n    description: \"Find the shortest path between two notes in the knowledge graph\",\n    args: '{ \"from\": \"string\", \"to\": \"string\" }',\n    examples: ['{ \"from\": \"project-overview.md\", \"to\": \"user-service.md\" }'],\n  },\n  graph_statistics: {\n    description: \"Knowledge graph stats — most connected nodes, orphans, density\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n\n  // System\n  get_stats: {\n    description: \"Vault and index statistics — note count, chunks, embeddings, graph density\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n  reindex: {\n    description: \"Force a full reindex of the vault\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n};\n\nconst TOOL_CATEGORIES: Record<string, string[]> = {\n  Search: [\"search_semantic\", \"search_text\", \"search_graph\", \"search_hybrid\"],\n  Read: [\"read_note\", \"read_multiple_notes\", \"list_notes\"],\n  Write: [\"create_note\", \"update_note\", \"delete_note\", \"move_note\"],\n  Metadata: [\"get_frontmatter\", \"update_frontmatter\", \"manage_tags\", \"rename_tag\"],\n  Graph: [\"backlinks\", \"forwardlinks\", \"graph_path\", \"graph_statistics\"],\n  System: [\"get_stats\", \"reindex\"],\n};\n\nfunction printToolList() {\n  console.log(\"\\nSemantic Pages — 21 MCP Tools\\n\");\n  console.log(\"Usage: These tools are available via MCP when the server is running.\");\n  console.log(\"       Run `semantic-memory tools <name>` for details on a specific tool.\\n\");\n\n  for (const [category, tools] of Object.entries(TOOL_CATEGORIES)) {\n    console.log(`  ${category}:`);\n    for (const name of tools) {\n      const tool = TOOL_HELP[name];\n      console.log(`    ${name.padEnd(24)} ${tool.description}`);\n    }\n    console.log();\n  }\n\n  console.log(\"Run `semantic-memory tools <tool-name>` for arguments and examples.\");\n}\n\nfunction printToolDetail(name: string) {\n  const tool = TOOL_HELP[name];\n  if (!tool) {\n    console.error(`Unknown tool: ${name}`);\n    console.error(`Run \\`semantic-memory tools\\` to see all available tools.`);\n    process.exit(1);\n  }\n\n  console.log(`\\n  ${name}`);\n  console.log(`  ${\"─\".repeat(name.length)}`);\n  console.log(`  ${tool.description}\\n`);\n  console.log(`  Arguments:`);\n  console.log(`    ${tool.args}\\n`);\n  console.log(`  Examples:`);\n  for (const ex of tool.examples) {\n    console.log(`    ${ex}`);\n  }\n  console.log();\n}\n\nprogram\n  .name(\"semantic-memory\")\n  .description(\n    \"Unified memory-layer MCP server for Claude Code (rebrand of semantic-sidekick at v1.0.0).\\n\" +\n    \"The `semantic-sidekick` command is preserved as an alias.\\n\\n\" +\n    \"  Start MCP server:  semantic-memory --notes ./vault\\n\" +\n    \"  Show vault stats:  semantic-memory --notes ./vault --stats\\n\" +\n    \"  Force reindex:     semantic-memory --notes ./vault --reindex\\n\" +\n    \"  List MCP tools:    semantic-memory tools\\n\" +\n    \"  Tool details:      semantic-memory tools search_semantic\"\n  )\n  .version(version);\n\nprogram\n  .command(\"search <query>\")\n  .description(\"Run a vault search and print top hits as JSON (used by activation hooks)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--limit <n>\", \"Max results\", (v) => parseInt(v, 10), 8)\n  .option(\"--text-only\", \"Skip embedder — keyword-only search (fast path, no model init)\")\n  .option(\"--json\", \"Emit raw JSON (default)\", true)\n  .action(async (query: string, opts) => {\n    const { runSearch } = await import(\"./search.js\");\n    try {\n      const hits = await runSearch({\n        notes: opts.notes,\n        query,\n        limit: opts.limit,\n        textOnly: opts.textOnly,\n      });\n      process.stdout.write(JSON.stringify(hits, null, 2) + \"\\n\");\n      process.exit(0);\n    } catch (err: any) {\n      console.error(`search failed: ${err.message}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"lint\")\n  .description(\"Lint the vault against vault.schema.yml (schema violations + missing provenance + stale)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--rule <name>\", \"Limit output to one rule: schema_violations | missing_provenance | stale\")\n  .option(\"--json\", \"Emit JSON instead of the human-readable report\")\n  .option(\"--strict\", \"Exit non-zero on warnings too (default: exit non-zero only on errors)\")\n  .action(async (opts) => {\n    const { lintVault, formatLintReport } = await import(\"../core/lint.js\");\n    const report = await lintVault(resolve(opts.notes));\n    // Use console.log + process.exitCode (not process.exit) so Node flushes\n    // stdout fully before the process ends. Early process.exit with a large\n    // buffered JSON payload can truncate output.\n    if (opts.json) {\n      const out = opts.rule ? report.byRule[opts.rule as keyof typeof report.byRule] : report;\n      console.log(JSON.stringify(out, null, 2));\n    } else {\n      console.log(formatLintReport(report, { rule: opts.rule }));\n    }\n    const bad = opts.strict ? report.counts.errors + report.counts.warnings : report.counts.errors;\n    process.exitCode = bad > 0 ? 1 : 0;\n  });\n\nprogram\n  .command(\"log-event\")\n  .description(\"Append a structured event to the vault's log.md (used by hooks and CI scripts — same shape as mcp__semantic-vault__log_event)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .requiredOption(\"--kind <name>\", \"Event category: ingest, synthesis, error, mode_change, etc.\")\n  .requiredOption(\"--summary <text>\", \"One-line human summary\")\n  .option(\"--payload <json>\", \"Structured payload as JSON string\")\n  .action(async (opts) => {\n    const { logEvent } = await import(\"../core/log.js\");\n    let payload: Record<string, unknown> | undefined;\n    if (opts.payload) {\n      try {\n        payload = JSON.parse(opts.payload);\n      } catch (e: any) {\n        console.error(`invalid --payload JSON: ${e.message}`);\n        process.exitCode = 1;\n        return;\n      }\n    }\n    try {\n      const entry = await logEvent(resolve(opts.notes), {\n        kind: opts.kind,\n        summary: opts.summary,\n        payload,\n      });\n      console.log(JSON.stringify(entry));\n    } catch (e: any) {\n      console.error(`log-event failed: ${e.message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command(\"log-query\")\n  .description(\"Read structured log entries from log.md — filters by kind, date range, limit\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--kind <name>\", \"Filter by kind (ingest, synthesis, error, mode_change, etc.)\")\n  .option(\"--after <iso>\", \"ISO timestamp — only entries on or after\")\n  .option(\"--before <iso>\", \"ISO timestamp — only entries on or before\")\n  .option(\"--limit <n>\", \"Max entries (most recent)\", (v) => parseInt(v, 10))\n  .action(async (opts) => {\n    const { logQuery } = await import(\"../core/log.js\");\n    try {\n      const entries = await logQuery(resolve(opts.notes), {\n        kind: opts.kind,\n        after: opts.after,\n        before: opts.before,\n        limit: opts.limit,\n      });\n      console.log(JSON.stringify(entries));\n    } catch (e: any) {\n      console.error(`log-query failed: ${e.message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command(\"install-schema\")\n  .description(\"Bootstrap vault.schema.yml in the vault root with the default schema\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--force\", \"Overwrite existing schema file\")\n  .action(async (opts) => {\n    const { installDefaultSchema } = await import(\"../core/schema.js\");\n    const r = await installDefaultSchema(resolve(opts.notes), opts.force);\n    console.log(r.written ? `Installed default schema: ${r.path}` : `Schema already exists: ${r.path} (use --force to overwrite)`);\n    process.exit(0);\n  });\n\nprogram\n  .command(\"tools [name]\")\n  .description(\"List all MCP tools, or show details for a specific tool\")\n  .action((name?: string) => {\n    if (name) {\n      printToolDetail(name);\n    } else {\n      printToolList();\n    }\n    process.exit(0);\n  });\n\nprogram\n  .command(\"serve\", { isDefault: true })\n  .description(\"Start the MCP server (default command)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--reindex\", \"Force full reindex and exit\")\n  .option(\"--stats\", \"Show vault statistics and exit\")\n  .option(\"--wait-for-ready\", \"Block startup until index is fully built before serving (default: index in background; tools return 'Indexing in progress' until ready)\")\n  .option(\"--read-only\", \"Suppress write tools (create_note, update_note, delete_note, move_note, update_frontmatter, manage_tags, rename_tag) — use for shared docs vaults owned by another tool\")\n  .option(\"--model <name>\", \"Embedding model to use (default: all-MiniLM-L6-v2, fast; use nomic-ai/nomic-embed-text-v1.5 for higher quality)\")\n  .option(\"--workers <n>\", \"Number of worker threads for parallel embedding\", parseInt)\n  .option(\"--batch-size <n>\", \"Texts per ONNX forward pass (default: 8)\", parseInt)\n  .option(\"--no-quantized\", \"Use full-precision model instead of quantized (slower, slightly higher quality)\")\n  .option(\"--no-watch\", \"Disable file watcher\")\n  .action(async (opts) => {\n    const notesPath = resolve(opts.notes);\n\n    if (!existsSync(notesPath)) {\n      console.error(`Error: notes directory not found: ${notesPath}`);\n      process.exit(1);\n    }\n\n    if (opts.stats) {\n      const { Indexer } = await import(\"../core/indexer.js\");\n      const indexer = new Indexer(notesPath);\n      const docs = await indexer.indexAll();\n      console.log(`Notes: ${docs.length}`);\n      console.log(`Chunks: ${docs.reduce((n: number, d: any) => n + d.chunks.length, 0)}`);\n      console.log(`Wikilinks: ${docs.reduce((n: number, d: any) => n + d.wikilinks.length, 0)}`);\n      console.log(`Tags: ${new Set(docs.flatMap((d: any) => d.tags)).size} unique`);\n      process.exit(0);\n    }\n\n    if (opts.reindex) {\n      const { createServer } = await import(\"../mcp/server.js\");\n      await createServer(notesPath, {\n        watch: false,\n        waitForReady: true,\n        model: opts.model,\n        workers: opts.workers,\n        batchSize: opts.batchSize,\n        quantized: opts.quantized,\n        onProgress: (embedded, total) => {\n          process.stderr.write(`\\rEmbedding ${embedded}/${total} chunks...`);\n        },\n      });\n      process.stderr.write(\"\\n\");\n      console.log(\"Reindex complete.\");\n      process.exit(0);\n    }\n\n    // Default: start MCP server on stdio\n    const { startServer } = await import(\"../mcp/server.js\");\n    await startServer(notesPath, {\n      watch: opts.watch,\n      waitForReady: opts.waitForReady,\n      model: opts.model,\n      workers: opts.workers,\n      batchSize: opts.batchSize,\n      quantized: opts.quantized,\n      readOnly: opts.readOnly,\n    });\n  });\n\nregisterUpdateCommands(program, {\n  packageName: PKG_NAME,\n  pluginName: \"semantic-memory\",\n  configFile: \"semantic-memory.json\",\n  onAfterUpdate: (cwd) => runRelink(cwd),\n});\n\nprogram\n  .command(\"normalize-config\")\n  .description(\n    \"Rewrite fragile `npx @latest` entries in .mcp.json to the stable node-against-node_modules form (with backup and validation)\",\n  )\n  .option(\"--dry-run\", \"print the proposed changes but don't write\")\n  .action((opts: { dryRun?: boolean }) => {\n    const cwd = process.cwd();\n    const mcpPath = join(cwd, \".mcp.json\");\n    if (!existsSync(mcpPath)) {\n      console.log(\"no .mcp.json in current directory — nothing to do\");\n      process.exit(0);\n    }\n    const data = readJsonSafe(mcpPath);\n    if (!data || typeof data !== \"object\" || !data.mcpServers || typeof data.mcpServers !== \"object\") {\n      console.error(`could not parse ${mcpPath}`);\n      process.exit(1);\n    }\n    const bin = localBinArg(cwd);\n    if (!bin) {\n      console.error(\n        `no local install found at ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory ` +\n          `(or the legacy semantic-sidekick path).\\n` +\n          `run 'npm install --save @theglitchking/semantic-memory' first, then re-run this command.`,\n      );\n      process.exit(1);\n    }\n    const rewritten: string[] = [];\n    for (const [key, entry] of Object.entries<any>(data.mcpServers)) {\n      if (!isNpxForm(entry)) continue;\n      const notes = extractNotesPath(entry) ?? \"./.claude/.vault\";\n      const extra = extractExtraFlags(entry);\n      data.mcpServers[key] = {\n        type: \"stdio\",\n        command: \"node\",\n        args: [bin, \"--notes\", notes, ...extra],\n      };\n      rewritten.push(key);\n    }\n    if (rewritten.length === 0) {\n      console.log(\"no npx-form entries found — .mcp.json is already in the stable form.\");\n      process.exit(0);\n    }\n    console.log(`Rewriting ${rewritten.length} entr${rewritten.length === 1 ? \"y\" : \"ies\"}: ${rewritten.join(\", \")}`);\n    if (opts.dryRun) {\n      console.log(\"--- proposed .mcp.json:\");\n      console.log(JSON.stringify(data, null, 2));\n      console.log(\"--- (dry-run; no changes written)\");\n      process.exit(0);\n    }\n    // Back up\n    const bakPath = join(dirname(mcpPath), \".mcp.json.bak\");\n    try {\n      writeFileSync(bakPath, readFileSync(mcpPath, \"utf8\"));\n      console.log(`backup written: ${bakPath}`);\n    } catch (err: any) {\n      console.error(`could not write backup: ${err.message}`);\n      process.exit(1);\n    }\n    writeFileSync(mcpPath, JSON.stringify(data, null, 2) + \"\\n\");\n\n    // Verify the local bin starts cleanly. We just run --version — fast and\n    // enough to catch ERR_MODULE_NOT_FOUND type failures.\n    const verify = spawnSync(\"node\", [bin, \"--version\"], { cwd, stdio: \"pipe\", timeout: 15_000 });\n    if (verify.status !== 0) {\n      console.error(`verification failed (exit ${verify.status}):\\n${verify.stderr?.toString() || \"\"}`);\n      console.error(`rolling back from ${bakPath}`);\n      writeFileSync(mcpPath, readFileSync(bakPath, \"utf8\"));\n      process.exit(1);\n    }\n    console.log(`✓ .mcp.json normalized and verified. Toggle the MCPs in /mcp to reconnect.`);\n    process.exit(0);\n  });\n\nprogram\n  .command(\"healthcheck\")\n  .description(\n    \"Verify the local install starts cleanly + run drift detection. Self-heals common npx-cache corruption (ERR_MODULE_NOT_FOUND). With --fast, skips the slow tier (full vault lint).\",\n  )\n  .option(\"--fast\", \"Run only the fast-tier drift checks (file-system probes). Skips the slow tier (full vault lint).\", false)\n  .option(\"--json\", \"Emit structured JSON output instead of human-readable text.\", false)\n  .action(async (opts) => {\n    const cwd = process.cwd();\n    const bin = findLocalBin(cwd);\n    if (!bin) {\n      console.error(`no local install at ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory (or legacy semantic-sidekick path)`);\n      console.error(`run 'npm install --save @theglitchking/semantic-memory' to install.`);\n      process.exit(1);\n    }\n\n    // 1. Warn if .mcp.json uses the fragile form.\n    const mcpPath = join(cwd, \".mcp.json\");\n    if (existsSync(mcpPath)) {\n      const data = readJsonSafe(mcpPath);\n      const entries = data?.mcpServers && typeof data.mcpServers === \"object\" ? Object.entries<any>(data.mcpServers) : [];\n      const fragile = entries.filter(([, e]) => isNpxForm(e)).map(([k]) => k);\n      if (fragile.length > 0) {\n        console.warn(\n          `⚠️  .mcp.json uses the fragile npx-@latest form for: ${fragile.join(\", \")}`,\n        );\n        console.warn(`   Rewrite to the stable form:`);\n        console.warn(`     npx --no @theglitchking/semantic-memory normalize-config`);\n      }\n    }\n\n    // 2. Smoke-test the local bin.\n    const r = spawnSync(\"node\", [bin, \"--version\"], { cwd, stdio: \"pipe\", timeout: 15_000 });\n    if (r.status === 0) {\n      console.log(`✓ local install starts cleanly (v${r.stdout?.toString().trim()})`);\n      process.exit(0);\n    }\n\n    const stderr = r.stderr?.toString() ?? \"\";\n\n    // 3. Self-heal ERR_MODULE_NOT_FOUND in npx cache (rare but the classic\n    //    failure mode that triggered 0.10.0). Extract the offending npx cache\n    //    dir from the error message, rm -rf it, retry once.\n    if (stderr.includes(\"ERR_MODULE_NOT_FOUND\")) {\n      const match = stderr.match(/([\\/~][^'\"\\s]*\\/_npx\\/[^\\/'\"\\s]+)/);\n      if (match) {\n        const bad = match[1];\n        console.warn(`detected broken npx cache at ${bad} — clearing and retrying...`);\n        try { rmSync(bad, { recursive: true, force: true }); } catch {}\n        const r2 = spawnSync(\"node\", [bin, \"--version\"], { cwd, stdio: \"pipe\", timeout: 15_000 });\n        if (r2.status === 0) {\n          console.log(`✓ cleared npx cache and verified (v${r2.stdout?.toString().trim()})`);\n          process.exit(0);\n        }\n        console.error(`retry still failed:\\n${r2.stderr?.toString() || \"\"}`);\n      } else {\n        console.error(`ERR_MODULE_NOT_FOUND but could not locate offending cache path in the error.`);\n      }\n    }\n\n    if (stderr) console.error(stderr);\n    if (r.status !== 0) {\n      console.error(`local install failed (exit ${r.status})`);\n      process.exit(1);\n    }\n  });\n\n// Append drift detection to the healthcheck handler (Phase 8). Wraps the original\n// handler — the function above runs first (npx-cache self-heal), then drift detection\n// runs and prints additional findings. --fast skips the slow tier (full vault lint).\nconst driftHealthcheckActionPostprocess = async (opts: { fast?: boolean; json?: boolean }) => {\n  try {\n    const { runHealthcheck, formatDriftBanner } = await import(\"../core/healthcheck.js\");\n    const projectRoot = process.cwd();\n    // For the auto-derived vault path, prefer .claude/.vault if present\n    const vaultCandidate = join(projectRoot, \".claude\", \".vault\");\n    const vaultPath = existsSync(vaultCandidate) ? vaultCandidate : undefined;\n    const result = await runHealthcheck({\n      projectRoot,\n      vaultPath,\n      tier: opts.fast ? \"fast\" : \"all\",\n      force: true,\n    });\n    if (opts.json) {\n      console.log(JSON.stringify(result, null, 2));\n      return;\n    }\n    const banner = formatDriftBanner(result);\n    if (banner) {\n      console.log(\"\");\n      console.log(banner);\n    } else {\n      console.log(\"\");\n      console.log(`✓ no drift detected (${result.findings.length} checks ran in ${result.duration_ms}ms)`);\n    }\n  } catch (err: any) {\n    console.error(`drift check threw: ${err?.message ?? err}`);\n  }\n};\n\n// Wire the drift-detection postprocess. We do this by attaching to the existing\n// healthcheck command's postAction hook so the original handler still runs first.\nconst healthcheckCmd = program.commands.find((c) => c.name() === \"healthcheck\");\nif (healthcheckCmd) {\n  healthcheckCmd.hook(\"postAction\", async (thisCmd) => {\n    const opts = thisCmd.opts();\n    await driftHealthcheckActionPostprocess({ fast: !!opts.fast, json: !!opts.json });\n  });\n}\n\n// --- Skill bundler (Phase 6) ---\n\nfunction parseAgent(input: string): AgentName {\n  const a = input.toLowerCase();\n  if (!SKILL_BUNDLER_AGENTS.includes(a as AgentName)) {\n    console.error(`Unknown agent: ${input}. Supported: ${SKILL_BUNDLER_AGENTS.join(\", \")}.`);\n    process.exit(2);\n  }\n  return a as AgentName;\n}\n\nfunction parseScope(input: string): Scope {\n  if (input !== \"global\" && input !== \"local\") {\n    console.error(`Unknown scope: ${input}. Use 'global' or 'local'.`);\n    process.exit(2);\n  }\n  return input;\n}\n\nfunction findSourceRoot(): string {\n  // 1. Installed: <cwd>/node_modules/@theglitchking/semantic-sidekick or semantic-memory\n  for (const pkg of [\"semantic-memory\", \"semantic-sidekick\"]) {\n    const installed = join(process.cwd(), \"node_modules\", \"@theglitchking\", pkg);\n    if (existsSync(installed)) return installed;\n  }\n  // 2. Dev: derive from the bin location (this file lives at <root>/dist/cli/index.js)\n  const dev = resolve(new URL(\"../../\", import.meta.url).pathname);\n  return dev;\n}\n\nconst skillsCmd = program.command(\"skills\").description(\"Install, target, or uninstall skill bundles for non-Claude agents (codex, copilot, pi). Claude installs continue to use the npm postinstall flow.\");\n\nskillsCmd\n  .command(\"targets\")\n  .description(\"Preview where skill bundles would be installed for one or more agents.\")\n  .option(\"--agent <name...>\", \"One or more agents (default: all). Repeatable.\", undefined as any)\n  .option(\"--scope <scope>\", \"global or local (default: local)\", \"local\")\n  .option(\"--project <path>\", \"Project root for local-scope paths (default: cwd)\", process.cwd())\n  .action((opts) => {\n    const scope = parseScope(opts.scope);\n    const agents: AgentName[] = (opts.agent && opts.agent.length > 0 ? opts.agent : SKILL_BUNDLER_AGENTS).map(parseAgent);\n    const out = agents.map((a) => resolveTarget(a, scope, opts.project));\n    console.log(JSON.stringify(out, null, 2));\n  });\n\nskillsCmd\n  .command(\"install\")\n  .description(\"Install skill bundles into an agent's skill directory. Non-destructive by default; --force to overwrite.\")\n  .requiredOption(\"--agent <name>\", \"Agent runtime (claude, codex, copilot, pi)\")\n  .option(\"--scope <scope>\", \"global or local (default: local)\", \"local\")\n  .option(\"--project <path>\", \"Project root for local-scope paths (default: cwd)\", process.cwd())\n  .option(\"--only <names...>\", \"Restrict to specific skill names (default: all shipped)\")\n  .option(\"--force\", \"Overwrite even if drift is detected against an existing manifest\", false)\n  .action(async (opts) => {\n    const agent = parseAgent(opts.agent);\n    const scope = parseScope(opts.scope);\n    if (agent === \"claude\") {\n      console.error(\n        \"Claude skill installs are handled by the npm postinstall (claude-plugin-runtime). \" +\n          \"Run `npm install @theglitchking/semantic-memory` instead — that flow symlinks \" +\n          \"skills into ~/.claude/skills/ or .claude/skills/ automatically. The skills CLI \" +\n          \"is intended for non-Claude agents (codex, copilot, pi) which do not have that \" +\n          \"postinstall integration.\"\n      );\n      process.exit(2);\n    }\n    const sourceRoot = findSourceRoot();\n    const result = await installSkills({\n      agent,\n      scope,\n      sourceRoot,\n      projectRoot: opts.project,\n      version,\n      only: opts.only,\n      force: opts.force === true,\n    });\n    console.log(JSON.stringify(result, null, 2));\n    if (result.installed.length === 0 && result.reason) process.exit(1);\n  });\n\nskillsCmd\n  .command(\"uninstall\")\n  .description(\"Remove skill bundles tracked by the semantic-memory manifest. User-written skills outside the manifest are left untouched.\")\n  .requiredOption(\"--agent <name>\", \"Agent runtime (claude, codex, copilot, pi)\")\n  .option(\"--scope <scope>\", \"global or local (default: local)\", \"local\")\n  .option(\"--project <path>\", \"Project root for local-scope paths (default: cwd)\", process.cwd())\n  .action(async (opts) => {\n    const agent = parseAgent(opts.agent);\n    const scope = parseScope(opts.scope);\n    if (agent === \"claude\") {\n      console.error(\"Claude skill uninstalls go through the npm uninstall flow. The skills CLI is for non-Claude agents.\");\n      process.exit(2);\n    }\n    const result = await uninstallSkills({ agent, scope, projectRoot: opts.project });\n    console.log(JSON.stringify(result, null, 2));\n  });\n\nskillsCmd\n  .command(\"list\")\n  .description(\"List the skill bundles shipped with this plugin version.\")\n  .action(async () => {\n    const sourceRoot = findSourceRoot();\n    const shipped = await listShippedSkills(sourceRoot);\n    console.log(JSON.stringify(shipped.map((s) => s.name), null, 2));\n  });\n\n// --- State migration (Phase 3, v1.2) ---\n\nprogram\n  .command(\"migrate-state\")\n  .description(\n    \"Move legacy .claude/.sidekick-* state files to .claude/.semantic-memory/. Idempotent. \" +\n      \"Conflicts (both paths exist) require --force. Pass --dry-run to preview without changes.\",\n  )\n  .option(\"--dry-run\", \"Print the planned migration without renaming any files.\", false)\n  .option(\n    \"--force\",\n    \"When both old and new paths exist, prefer the new path and delete the old one.\",\n    false,\n  )\n  .option(\"--project <path>\", \"Project root (default: cwd)\", process.cwd())\n  .action((opts) => {\n    const result = migrateState({\n      projectRoot: opts.project,\n      dryRun: opts.dryRun === true,\n      force: opts.force === true,\n    });\n    console.log(JSON.stringify(result, null, 2));\n    if (result.conflicts.length > 0 && !opts.force && !opts.dryRun) {\n      console.error(\n        `\\n${result.conflicts.length} conflict${result.conflicts.length === 1 ? \"\" : \"s\"} detected. Re-run with --force to resolve (keeps new path, deletes old).`,\n      );\n      process.exit(1);\n    }\n  });\n\nprogram.parse();\n","import { mkdir, readFile, writeFile, copyFile, readdir, rm } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { join, basename, resolve } from \"node:path\";\nimport { homedir } from \"node:os\";\nimport { createHash } from \"node:crypto\";\n\nexport type AgentName = \"claude\" | \"codex\" | \"copilot\" | \"pi\";\nexport type Scope = \"global\" | \"local\";\n\nexport interface AgentTargetSpec {\n  agent: AgentName;\n  scope: Scope;\n  /** Absolute resolved path where the skill bundles will land. */\n  path: string;\n}\n\nexport interface SkillManifest {\n  package: string;\n  version: string;\n  agent: AgentName;\n  scope: Scope;\n  installed_at: string;\n  skills: { name: string; sha256: string }[];\n}\n\nexport interface InstallResult {\n  agent: AgentName;\n  scope: Scope;\n  target_path: string;\n  installed: string[];\n  skipped: string[];\n  reason?: string;\n  manifest_path?: string;\n}\n\nconst MANIFEST_FILE = \".semantic-memory-skill-manifest.json\";\n\n/**\n * Resolve where a given (agent, scope) tuple should land. Project root is required for local\n * scope (to anchor relative paths); for global scope it's not used.\n */\nexport function resolveTarget(agent: AgentName, scope: Scope, projectRoot: string): AgentTargetSpec {\n  const root = resolve(projectRoot);\n  const home = homedir();\n  const map: Record<AgentName, { global: string; local: string }> = {\n    claude: { global: join(home, \".claude\", \"skills\"), local: join(root, \".claude\", \"skills\") },\n    codex: { global: join(home, \".codex\", \"skills\"), local: join(root, \".codex\", \"skills\") },\n    copilot: { global: join(home, \".copilot\", \"skills\"), local: join(root, \".github\", \"skills\") },\n    pi: { global: join(home, \".pi\", \"agent\", \"skills\"), local: join(root, \".pi\", \"skills\") },\n  };\n  return { agent, scope, path: map[agent][scope] };\n}\n\n/**\n * Enumerate the canonical skill bundles shipped by this plugin. Each bundle is a directory\n * under `<sourceRoot>/skills/` containing at least a SKILL.md file. Entries without\n * SKILL.md are silently skipped (allows future non-skill files like `/skills/.gitkeep`).\n */\nexport async function listShippedSkills(sourceRoot: string): Promise<{ name: string; dir: string }[]> {\n  const skillsDir = join(sourceRoot, \"skills\");\n  if (!existsSync(skillsDir)) return [];\n  const entries = await readdir(skillsDir, { withFileTypes: true });\n  const out: { name: string; dir: string }[] = [];\n  for (const e of entries) {\n    if (!e.isDirectory()) continue;\n    const dir = join(skillsDir, e.name);\n    const skillFile = join(dir, \"SKILL.md\");\n    if (!existsSync(skillFile)) continue;\n    out.push({ name: e.name, dir });\n  }\n  return out;\n}\n\nasync function sha256OfFile(path: string): Promise<string> {\n  const buf = await readFile(path);\n  return createHash(\"sha256\").update(buf).digest(\"hex\");\n}\n\n/**\n * Copy a single skill bundle (SKILL.md plus any sibling files in the same directory) into\n * the target directory, overlaying it with the agent name. Returns the list of files written.\n *\n * The target layout is `<targetPath>/<skillName>/SKILL.md` plus mirrored siblings, so each\n * bundle is namespaced and easy to remove later.\n */\nasync function copyBundle(srcDir: string, destDir: string): Promise<string[]> {\n  await mkdir(destDir, { recursive: true });\n  const entries = await readdir(srcDir, { withFileTypes: true });\n  const written: string[] = [];\n  for (const e of entries) {\n    const src = join(srcDir, e.name);\n    const dest = join(destDir, e.name);\n    if (e.isDirectory()) {\n      const childWritten = await copyBundle(src, dest);\n      written.push(...childWritten);\n      continue;\n    }\n    if (!e.isFile()) continue;\n    await copyFile(src, dest);\n    written.push(dest);\n  }\n  return written;\n}\n\nexport interface InstallOptions {\n  agent: AgentName;\n  scope: Scope;\n  /** Path to the package's source root (usually the repo root, where `skills/` lives). */\n  sourceRoot: string;\n  /** Used to anchor local-scope target paths. */\n  projectRoot: string;\n  /** Plugin version, recorded in the manifest. */\n  version: string;\n  /** Specific skills to install. When omitted, all shipped skills are installed. */\n  only?: string[];\n  /**\n   * When false, refuse to overwrite an existing install (manifest present + sha mismatch\n   * indicates upstream drift). When true, overwrite. Default false.\n   */\n  force?: boolean;\n}\n\n/**\n * Install all (or selected) skill bundles into an agent's skill directory.\n *\n * Behavior:\n *  - Resolves the destination via resolveTarget.\n *  - Reads any existing manifest. If a manifest exists, version differs from `version`,\n *    AND any skill sha256 differs from the source: this is a drift event. Without\n *    `force: true`, returns a refusal with reason \"drift detected\". With force, proceeds\n *    and overwrites.\n *  - For each shipped skill (or each in `only`), copies the bundle into\n *    <target>/<skillName>/, overwriting any existing files in that subdirectory.\n *  - Writes a fresh manifest at <target>/<MANIFEST_FILE> recording sha256 of each\n *    SKILL.md installed, the plugin version, agent, and scope.\n */\nexport async function installSkills(opts: InstallOptions): Promise<InstallResult> {\n  const target = resolveTarget(opts.agent, opts.scope, opts.projectRoot);\n  const shipped = await listShippedSkills(opts.sourceRoot);\n  const filter = opts.only && opts.only.length > 0 ? new Set(opts.only) : null;\n  const toInstall = filter ? shipped.filter((s) => filter.has(s.name)) : shipped;\n\n  if (toInstall.length === 0) {\n    return {\n      agent: opts.agent,\n      scope: opts.scope,\n      target_path: target.path,\n      installed: [],\n      skipped: [],\n      reason: filter ? `No matching skills found (only=${[...filter].join(\",\")}).` : \"No shipped skills found at sourceRoot/skills/.\",\n    };\n  }\n\n  const manifestPath = join(target.path, MANIFEST_FILE);\n  const existing = await readManifest(manifestPath);\n\n  if (existing && !opts.force) {\n    const drift = await detectDrift(existing, toInstall);\n    if (drift.length > 0) {\n      return {\n        agent: opts.agent,\n        scope: opts.scope,\n        target_path: target.path,\n        installed: [],\n        skipped: toInstall.map((s) => s.name),\n        reason: `Drift detected on ${drift.length} skill(s): ${drift.join(\", \")}. Pass --force to overwrite.`,\n        manifest_path: manifestPath,\n      };\n    }\n  }\n\n  await mkdir(target.path, { recursive: true });\n  const installed: string[] = [];\n  const skillEntries: { name: string; sha256: string }[] = [];\n  for (const skill of toInstall) {\n    const destDir = join(target.path, skill.name);\n    await copyBundle(skill.dir, destDir);\n    const skillFile = join(skill.dir, \"SKILL.md\");\n    skillEntries.push({ name: skill.name, sha256: await sha256OfFile(skillFile) });\n    installed.push(skill.name);\n  }\n\n  const manifest: SkillManifest = {\n    package: \"@theglitchking/semantic-memory\",\n    version: opts.version,\n    agent: opts.agent,\n    scope: opts.scope,\n    installed_at: new Date().toISOString(),\n    skills: skillEntries,\n  };\n  await writeFile(manifestPath, JSON.stringify(manifest, null, 2), \"utf-8\");\n\n  return {\n    agent: opts.agent,\n    scope: opts.scope,\n    target_path: target.path,\n    installed,\n    skipped: [],\n    manifest_path: manifestPath,\n  };\n}\n\nexport interface UninstallOptions {\n  agent: AgentName;\n  scope: Scope;\n  projectRoot: string;\n}\n\nexport interface UninstallResult {\n  agent: AgentName;\n  scope: Scope;\n  target_path: string;\n  removed: string[];\n  manifest_present: boolean;\n  reason?: string;\n}\n\n/**\n * Remove only the skill bundles tracked in the manifest. User-written skills outside\n * the manifest are left untouched.\n */\nexport async function uninstallSkills(opts: UninstallOptions): Promise<UninstallResult> {\n  const target = resolveTarget(opts.agent, opts.scope, opts.projectRoot);\n  const manifestPath = join(target.path, MANIFEST_FILE);\n  const manifest = await readManifest(manifestPath);\n  if (!manifest) {\n    return {\n      agent: opts.agent,\n      scope: opts.scope,\n      target_path: target.path,\n      removed: [],\n      manifest_present: false,\n      reason: \"No semantic-memory manifest found — nothing to uninstall.\",\n    };\n  }\n  const removed: string[] = [];\n  for (const skill of manifest.skills) {\n    const dir = join(target.path, skill.name);\n    if (existsSync(dir)) {\n      await rm(dir, { recursive: true, force: true });\n      removed.push(skill.name);\n    }\n  }\n  await rm(manifestPath, { force: true });\n  return {\n    agent: opts.agent,\n    scope: opts.scope,\n    target_path: target.path,\n    removed,\n    manifest_present: true,\n  };\n}\n\nasync function readManifest(path: string): Promise<SkillManifest | null> {\n  if (!existsSync(path)) return null;\n  try {\n    const raw = await readFile(path, \"utf-8\");\n    const parsed = JSON.parse(raw);\n    if (typeof parsed?.package !== \"string\") return null;\n    return parsed as SkillManifest;\n  } catch {\n    return null;\n  }\n}\n\nasync function detectDrift(\n  existing: SkillManifest,\n  toInstall: { name: string; dir: string }[]\n): Promise<string[]> {\n  const driftNames: string[] = [];\n  const existingByName = new Map(existing.skills.map((s) => [s.name, s.sha256]));\n  for (const skill of toInstall) {\n    const sourceSha = await sha256OfFile(join(skill.dir, \"SKILL.md\"));\n    const existingSha = existingByName.get(skill.name);\n    if (existingSha !== undefined && existingSha !== sourceSha) {\n      driftNames.push(skill.name);\n    }\n  }\n  return driftNames;\n}\n\nexport const SKILL_BUNDLER_AGENTS: AgentName[] = [\"claude\", \"codex\", \"copilot\", \"pi\"];\n","import { existsSync, mkdirSync, statSync, renameSync, unlinkSync } from \"node:fs\";\nimport { join } from \"node:path\";\n\n/**\n * State files that moved/renamed in v1.2.\n *\n * Each entry: legacy path (relative to <projectRoot>/.claude) → new path (relative to\n * <projectRoot>/.claude). Reads in v1.x check new first, fall back to old; writes always\n * go to new. This command does the explicit move so the legacy files stop existing.\n *\n * Order matters only for human-readable output; the migrations themselves are independent.\n */\nconst STATE_MIGRATIONS: { name: string; old: string; new: string }[] = [\n  { name: \"mode\", old: \".sidekick-mode\", new: \".semantic-memory/mode\" },\n  { name: \"fingerprints\", old: \".sidekick-fingerprints.json\", new: \".semantic-memory/fingerprints.json\" },\n  { name: \"capture-pending\", old: \".sidekick-capture-pending.json\", new: \".semantic-memory/capture-pending.json\" },\n];\n\nexport type MigrationStatus = \"migrated\" | \"skipped-no-source\" | \"skipped-already-migrated\" | \"conflict\" | \"resolved-by-force\";\n\nexport interface MigrationFinding {\n  name: string;\n  status: MigrationStatus;\n  oldPath: string;\n  newPath: string;\n  detail?: string;\n}\n\nexport interface MigrateStateOptions {\n  projectRoot: string;\n  dryRun?: boolean;\n  force?: boolean;\n}\n\nexport interface MigrateStateResult {\n  migrated: MigrationFinding[];\n  skipped: MigrationFinding[];\n  conflicts: MigrationFinding[];\n}\n\n/**\n * Move legacy `.claude/.sidekick-*` state files to the canonical\n * `.claude/.semantic-memory/<name>` paths.\n *\n * Behavior per file:\n *  - old exists, new does not       → MIGRATE: rename old to new\n *  - old does not exist             → SKIP (skipped-no-source)\n *  - old does not exist, new exists → SKIP (skipped-already-migrated)\n *  - both old and new exist         → CONFLICT (refused without --force)\n *                                     With --force: prefer new, delete old\n *\n * Idempotent: a second run after a successful migration is all-no-ops.\n */\nexport function migrateState(opts: MigrateStateOptions): MigrateStateResult {\n  const result: MigrateStateResult = {\n    migrated: [],\n    skipped: [],\n    conflicts: [],\n  };\n\n  const stateDir = join(opts.projectRoot, \".claude\", \".semantic-memory\");\n  if (!opts.dryRun && !existsSync(stateDir)) {\n    mkdirSync(stateDir, { recursive: true });\n  }\n\n  for (const m of STATE_MIGRATIONS) {\n    const oldPath = join(opts.projectRoot, \".claude\", m.old);\n    const newPath = join(opts.projectRoot, \".claude\", m.new);\n    const oldExists = existsSync(oldPath);\n    const newExists = existsSync(newPath);\n\n    if (!oldExists && !newExists) {\n      result.skipped.push({ name: m.name, status: \"skipped-no-source\", oldPath, newPath, detail: \"neither path exists\" });\n      continue;\n    }\n    if (!oldExists && newExists) {\n      result.skipped.push({ name: m.name, status: \"skipped-already-migrated\", oldPath, newPath, detail: \"already at new path\" });\n      continue;\n    }\n    if (oldExists && newExists) {\n      if (!opts.force) {\n        const oldMtime = safeMtime(oldPath);\n        const newMtime = safeMtime(newPath);\n        result.conflicts.push({\n          name: m.name,\n          status: \"conflict\",\n          oldPath,\n          newPath,\n          detail: `both paths exist (old: ${oldMtime}, new: ${newMtime}); pass --force to keep new and delete old`,\n        });\n        continue;\n      }\n      // --force: prefer new, delete old\n      if (!opts.dryRun) {\n        try { unlinkSync(oldPath); } catch (e: any) {\n          result.conflicts.push({ name: m.name, status: \"conflict\", oldPath, newPath, detail: `force-delete of old failed: ${e?.message ?? e}` });\n          continue;\n        }\n      }\n      result.migrated.push({\n        name: m.name,\n        status: \"resolved-by-force\",\n        oldPath,\n        newPath,\n        detail: opts.dryRun ? \"dry-run: would delete old\" : \"old deleted; new preserved\",\n      });\n      continue;\n    }\n    // oldExists && !newExists → migrate\n    if (!opts.dryRun) {\n      try { renameSync(oldPath, newPath); } catch (e: any) {\n        // Cross-device rename failure is theoretically possible; for state files all\n        // under .claude/, both paths are 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Actions are de-duplicated (running skill-link once\n * covers every skill-link finding) and each is best-effort: a failure is captured\n * as an outcome, never thrown. Returns one outcome per distinct action attempted.\n */\nasync function executeFixes(cwd: string, fixes: PlannedFix[]): Promise<FixOutcome[]> {\n  const outcomes: FixOutcome[] = [];\n  const actions = [...new Set(fixes.map((f) => f.action))];\n  for (const action of actions) {\n    const checks = fixes.filter((f) => f.action === action).map((f) => f.check).join(\", \");\n    try {\n      switch (action) {\n        case \"skill-link\": {\n          runRelink(cwd);\n          outcomes.push({ check: checks, action, status: \"fixed\", detail: \"re-linked skills\" });\n          break;\n        }\n        case \"state-migrate\": {\n          const r = migrateState({ projectRoot: cwd, force: true });\n          outcomes.push({\n            check: checks,\n            action,\n            status: \"fixed\",\n            detail: `migrated ${r.migrated.length} file(s), resolved ${r.conflicts.length} conflict(s)`,\n          });\n          break;\n        }\n        case \"mcp-reconcile\": {\n          const reconcilePath = join(findSourceRoot(), \"hooks\", \"reconcile.js\");\n          if (!existsSync(reconcilePath)) {\n            outcomes.push({ check: checks, action, status: \"failed\", detail: \"reconcile.js not found\" });\n            break;\n          }\n          const mod = await import(pathToFileURL(reconcilePath).href);\n          mod.reconcile(cwd);\n          outcomes.push({ check: checks, action, status: \"fixed\", detail: \"reconciled .mcp.json\" });\n          break;\n        }\n        case \"reindex\": {\n          const bin = findLocalBin(cwd);\n          if (!bin) {\n            outcomes.push({ check: checks, action, status: \"failed\", detail: \"no local bin to run reindex\" });\n            break;\n          }\n          const vault = join(cwd, \".claude\", \".vault\");\n          const r = spawnSync(\"node\", [bin, \"--notes\", vault, \"--reindex\"], { cwd, stdio: \"pipe\", timeout: 120_000 });\n          if (r.status === 0) {\n            outcomes.push({ check: checks, action, status: \"fixed\", detail: \"reindexed vault\" });\n          } else {\n            outcomes.push({ check: checks, action, status: \"failed\", detail: (r.stderr?.toString() || \"reindex failed\").slice(0, 200) });\n          }\n          break;\n        }\n      }\n    } catch (err: any) {\n      outcomes.push({ check: checks, action, status: \"failed\", detail: err?.message ?? String(err) });\n    }\n  }\n  return outcomes;\n}\n\nfunction findLocalBin(cwd: string): string | null {\n  const candidates = [\n    join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-memory\", \"bin\", \"semantic-memory\"),\n    join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-sidekick\", \"bin\", \"semantic-sidekick\"),\n  ];\n  for (const p of candidates) {\n    if (existsSync(p)) return p;\n  }\n  return null;\n}\n\nfunction localBinArg(cwd: string): string | null {\n  const abs = findLocalBin(cwd);\n  if (!abs) return null;\n  const rel = relative(cwd, abs);\n  return rel.startsWith(\"..\") ? abs : `./${rel}`;\n}\n\nfunction readJsonSafe(path: string): any {\n  try {\n    const raw = readFileSync(path, \"utf8\");\n    return raw.trim() ? JSON.parse(raw) : null;\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Returns the fragile npx-form pattern we used to write in pre-0.10.0\n * SessionStart hooks, so normalize-config can detect and rewrite it.\n */\nfunction isNpxForm(entry: any): boolean {\n  if (!entry || typeof entry !== \"object\") return false;\n  const cmd = entry.command;\n  const args = Array.isArray(entry.args) ? entry.args : [];\n  return (\n    cmd === \"npx\" &&\n    args.some(\n      (a: unknown) => typeof a === \"string\" && (a.includes(PKG_NAME) || a.includes(LEGACY_PKG_NAME))\n    )\n  );\n}\n\nfunction isLocalForm(entry: any): boolean {\n  if (!entry || typeof entry !== \"object\") return false;\n  const cmd = entry.command;\n  const args = Array.isArray(entry.args) ? entry.args : [];\n  return (\n    cmd === \"node\" &&\n    args.some(\n      (a: unknown) =>\n        typeof a === \"string\" &&\n        (a.includes(\"node_modules/@theglitchking/semantic-memory\") ||\n          a.includes(\"node_modules/@theglitchking/semantic-sidekick\"))\n    )\n  );\n}\n\nfunction extractNotesPath(entry: any): string | null {\n  const args = Array.isArray(entry?.args) ? entry.args : [];\n  const i = args.indexOf(\"--notes\");\n  if (i === -1 || i + 1 >= args.length) return null;\n  return String(args[i + 1]);\n}\n\nfunction extractExtraFlags(entry: any): string[] {\n  const args = Array.isArray(entry?.args) ? entry.args : [];\n  return args.filter((a: unknown): a is string => typeof a === \"string\" && a.startsWith(\"--\") && a !== \"--notes\");\n}\n\nconst TOOL_HELP: Record<string, { description: string; args: string; examples: string[] }> = {\n  // Search\n  search_semantic: {\n    description: \"Vector similarity search — find notes by meaning, not just keywords\",\n    args: '{ \"query\": \"string\", \"limit?\": 10 }',\n    examples: [\n      '{ \"query\": \"microservices architecture\", \"limit\": 5 }',\n      '{ \"query\": \"how to deploy to production\" }',\n    ],\n  },\n  search_text: {\n    description: \"Full-text keyword or regex search with optional filters\",\n    args: '{ \"pattern\": \"string\", \"regex?\": false, \"caseSensitive?\": false, \"pathGlob?\": \"string\", \"tagFilter?\": [\"string\"], \"limit?\": 20 }',\n    examples: [\n      '{ \"pattern\": \"RabbitMQ\" }',\n      '{ \"pattern\": \"OAuth\\\\\\\\d\", \"regex\": true }',\n      '{ \"pattern\": \"deploy\", \"pathGlob\": \"devops/**\", \"tagFilter\": [\"kubernetes\"] }',\n    ],\n  },\n  search_graph: {\n    description: \"Graph traversal — find notes connected to a concept via wikilinks and tags\",\n    args: '{ \"concept\": \"string\", \"maxDepth?\": 2 }',\n    examples: [\n      '{ \"concept\": \"microservices\" }',\n      '{ \"concept\": \"auth\", \"maxDepth\": 3 }',\n    ],\n  },\n  search_hybrid: {\n    description: \"Combined semantic + graph search — vector results re-ranked by graph proximity\",\n    args: '{ \"query\": \"string\", \"limit?\": 10 }',\n    examples: [\n      '{ \"query\": \"event driven architecture\", \"limit\": 5 }',\n    ],\n  },\n\n  // Read\n  read_note: {\n    description: \"Read the full content of a specific note by path\",\n    args: '{ \"path\": \"string\" }',\n    examples: [\n      '{ \"path\": \"project-overview.md\" }',\n      '{ \"path\": \"notes/meeting-2024-01-15.md\" }',\n    ],\n  },\n  read_multiple_notes: {\n    description: \"Batch read multiple notes in one call\",\n    args: '{ \"paths\": [\"string\"] }',\n    examples: [\n      '{ \"paths\": [\"overview.md\", \"architecture.md\", \"deployment.md\"] }',\n    ],\n  },\n  list_notes: {\n    description: \"List all indexed notes with metadata (title, tags, link count)\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n\n  // Write\n  create_note: {\n    description: \"Create a new markdown note with optional YAML frontmatter\",\n    args: '{ \"path\": \"string\", \"content\": \"string\", \"frontmatter?\": {} }',\n    examples: [\n      '{ \"path\": \"new-guide.md\", \"content\": \"# Guide\\\\n\\\\nContent here.\" }',\n      '{ \"path\": \"tagged.md\", \"content\": \"Content.\", \"frontmatter\": { \"title\": \"Tagged Note\", \"tags\": [\"test\"] } }',\n    ],\n  },\n  update_note: {\n    description: \"Edit note content — overwrite, append, prepend, or patch by heading\",\n    args: '{ \"path\": \"string\", \"content\": \"string\", \"mode\": \"overwrite|append|prepend|patch-by-heading\", \"heading?\": \"string\" }',\n    examples: [\n      '{ \"path\": \"guide.md\", \"content\": \"New content.\", \"mode\": \"overwrite\" }',\n      '{ \"path\": \"guide.md\", \"content\": \"\\\\n## Appendix\\\\nExtra info.\", \"mode\": \"append\" }',\n      '{ \"path\": \"guide.md\", \"content\": \"Updated architecture section.\", \"mode\": \"patch-by-heading\", \"heading\": \"Architecture\" }',\n    ],\n  },\n  delete_note: {\n    description: \"Delete a note permanently (requires confirm=true)\",\n    args: '{ \"path\": \"string\", \"confirm\": true }',\n    examples: [\n      '{ \"path\": \"old-note.md\", \"confirm\": true }',\n      '{ \"path\": \"old-note.md\", \"confirm\": false }  // returns warning, does not delete',\n    ],\n  },\n  move_note: {\n    description: \"Move or rename a note — automatically updates wikilinks across the vault\",\n    args: '{ \"from\": \"string\", \"to\": \"string\" }',\n    examples: [\n      '{ \"from\": \"user-service.md\", \"to\": \"auth-service.md\" }',\n      '{ \"from\": \"old/note.md\", \"to\": \"new/location/note.md\" }',\n    ],\n  },\n\n  // Metadata\n  get_frontmatter: {\n    description: \"Read parsed YAML frontmatter from a note as JSON\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"project-overview.md\" }'],\n  },\n  update_frontmatter: {\n    description: \"Set or delete YAML frontmatter keys — pass null to delete a key\",\n    args: '{ \"path\": \"string\", \"fields\": {} }',\n    examples: [\n      '{ \"path\": \"note.md\", \"fields\": { \"status\": \"active\", \"priority\": 1 } }',\n      '{ \"path\": \"note.md\", \"fields\": { \"deprecated_field\": null } }  // deletes the key',\n    ],\n  },\n  manage_tags: {\n    description: \"Add, remove, or list tags on a note (frontmatter and inline)\",\n    args: '{ \"path\": \"string\", \"action\": \"add|remove|list\", \"tags?\": [\"string\"] }',\n    examples: [\n      '{ \"path\": \"note.md\", \"action\": \"list\" }',\n      '{ \"path\": \"note.md\", \"action\": \"add\", \"tags\": [\"important\", \"reviewed\"] }',\n      '{ \"path\": \"note.md\", \"action\": \"remove\", \"tags\": [\"draft\"] }',\n    ],\n  },\n  rename_tag: {\n    description: \"Rename a tag across all notes in the vault (frontmatter + inline)\",\n    args: '{ \"oldTag\": \"string\", \"newTag\": \"string\" }',\n    examples: ['{ \"oldTag\": \"architecture\", \"newTag\": \"arch\" }'],\n  },\n\n  // Graph\n  backlinks: {\n    description: \"Find all notes that link TO a given note via [[wikilinks]]\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"microservices.md\" }'],\n  },\n  forwardlinks: {\n    description: \"Find all notes linked FROM a given note\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"project-overview.md\" }'],\n  },\n  graph_path: {\n    description: \"Find the shortest path between two notes in the knowledge graph\",\n    args: '{ \"from\": \"string\", \"to\": \"string\" }',\n    examples: ['{ \"from\": \"project-overview.md\", \"to\": \"user-service.md\" }'],\n  },\n  graph_statistics: {\n    description: \"Knowledge graph stats — most connected nodes, orphans, density\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n\n  // System\n  get_stats: {\n    description: \"Vault and index statistics — note count, chunks, embeddings, graph density\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n  reindex: {\n    description: \"Force a full reindex of the vault\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n};\n\nconst TOOL_CATEGORIES: Record<string, string[]> = {\n  Search: [\"search_semantic\", \"search_text\", \"search_graph\", \"search_hybrid\"],\n  Read: [\"read_note\", \"read_multiple_notes\", \"list_notes\"],\n  Write: [\"create_note\", \"update_note\", \"delete_note\", \"move_note\"],\n  Metadata: [\"get_frontmatter\", \"update_frontmatter\", \"manage_tags\", \"rename_tag\"],\n  Graph: [\"backlinks\", \"forwardlinks\", \"graph_path\", \"graph_statistics\"],\n  System: [\"get_stats\", \"reindex\"],\n};\n\nfunction printToolList() {\n  console.log(\"\\nSemantic Pages — 21 MCP Tools\\n\");\n  console.log(\"Usage: These tools are available via MCP when the server is running.\");\n  console.log(\"       Run `semantic-memory tools <name>` for details on a specific tool.\\n\");\n\n  for (const [category, tools] of Object.entries(TOOL_CATEGORIES)) {\n    console.log(`  ${category}:`);\n    for (const name of tools) {\n      const tool = TOOL_HELP[name];\n      console.log(`    ${name.padEnd(24)} ${tool.description}`);\n    }\n    console.log();\n  }\n\n  console.log(\"Run `semantic-memory tools <tool-name>` for arguments and examples.\");\n}\n\nfunction printToolDetail(name: string) {\n  const tool = TOOL_HELP[name];\n  if (!tool) {\n    console.error(`Unknown tool: ${name}`);\n    console.error(`Run \\`semantic-memory tools\\` to see all available tools.`);\n    process.exit(1);\n  }\n\n  console.log(`\\n  ${name}`);\n  console.log(`  ${\"─\".repeat(name.length)}`);\n  console.log(`  ${tool.description}\\n`);\n  console.log(`  Arguments:`);\n  console.log(`    ${tool.args}\\n`);\n  console.log(`  Examples:`);\n  for (const ex of tool.examples) {\n    console.log(`    ${ex}`);\n  }\n  console.log();\n}\n\nprogram\n  .name(\"semantic-memory\")\n  .description(\n    \"Unified memory-layer MCP server for Claude Code (rebrand of semantic-sidekick at v1.0.0).\\n\" +\n    \"The `semantic-sidekick` command is preserved as an alias.\\n\\n\" +\n    \"  Start MCP server:  semantic-memory --notes ./vault\\n\" +\n    \"  Show vault stats:  semantic-memory --notes ./vault --stats\\n\" +\n    \"  Force reindex:     semantic-memory --notes ./vault --reindex\\n\" +\n    \"  List MCP tools:    semantic-memory tools\\n\" +\n    \"  Tool details:      semantic-memory tools search_semantic\"\n  )\n  .version(version);\n\nprogram\n  .command(\"search <query>\")\n  .description(\"Run a vault search and print top hits as JSON (used by activation hooks)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--limit <n>\", \"Max results\", (v) => parseInt(v, 10), 8)\n  .option(\"--text-only\", \"Skip embedder — keyword-only search (fast path, no model init)\")\n  .option(\"--json\", \"Emit raw JSON (default)\", true)\n  .action(async (query: string, opts) => {\n    const { runSearch } = await import(\"./search.js\");\n    try {\n      const hits = await runSearch({\n        notes: opts.notes,\n        query,\n        limit: opts.limit,\n        textOnly: opts.textOnly,\n      });\n      process.stdout.write(JSON.stringify(hits, null, 2) + \"\\n\");\n      process.exit(0);\n    } catch (err: any) {\n      console.error(`search failed: ${err.message}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"lint\")\n  .description(\"Lint the vault against vault.schema.yml (schema violations + missing provenance + stale)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--rule <name>\", \"Limit output to one rule: schema_violations | missing_provenance | stale\")\n  .option(\"--json\", \"Emit JSON instead of the human-readable report\")\n  .option(\"--strict\", \"Exit non-zero on warnings too (default: exit non-zero only on errors)\")\n  .action(async (opts) => {\n    const { lintVault, formatLintReport } = await import(\"../core/lint.js\");\n    const report = await lintVault(resolve(opts.notes));\n    // Use console.log + process.exitCode (not process.exit) so Node flushes\n    // stdout fully before the process ends. Early process.exit with a large\n    // buffered JSON payload can truncate output.\n    if (opts.json) {\n      const out = opts.rule ? report.byRule[opts.rule as keyof typeof report.byRule] : report;\n      console.log(JSON.stringify(out, null, 2));\n    } else {\n      console.log(formatLintReport(report, { rule: opts.rule }));\n    }\n    const bad = opts.strict ? report.counts.errors + report.counts.warnings : report.counts.errors;\n    process.exitCode = bad > 0 ? 1 : 0;\n  });\n\nprogram\n  .command(\"log-event\")\n  .description(\"Append a structured event to the vault's log.md (used by hooks and CI scripts — same shape as mcp__semantic-vault__log_event)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .requiredOption(\"--kind <name>\", \"Event category: ingest, synthesis, error, mode_change, etc.\")\n  .requiredOption(\"--summary <text>\", \"One-line human summary\")\n  .option(\"--payload <json>\", \"Structured payload as JSON string\")\n  .action(async (opts) => {\n    const { logEvent } = await import(\"../core/log.js\");\n    let payload: Record<string, unknown> | undefined;\n    if (opts.payload) {\n      try {\n        payload = JSON.parse(opts.payload);\n      } catch (e: any) {\n        console.error(`invalid --payload JSON: ${e.message}`);\n        process.exitCode = 1;\n        return;\n      }\n    }\n    try {\n      const entry = await logEvent(resolve(opts.notes), {\n        kind: opts.kind,\n        summary: opts.summary,\n        payload,\n      });\n      console.log(JSON.stringify(entry));\n    } catch (e: any) {\n      console.error(`log-event failed: ${e.message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command(\"log-query\")\n  .description(\"Read structured log entries from log.md — filters by kind, date range, limit\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--kind <name>\", \"Filter by kind (ingest, synthesis, error, mode_change, etc.)\")\n  .option(\"--after <iso>\", \"ISO timestamp — only entries on or after\")\n  .option(\"--before <iso>\", \"ISO timestamp — only entries on or before\")\n  .option(\"--limit <n>\", \"Max entries (most recent)\", (v) => parseInt(v, 10))\n  .action(async (opts) => {\n    const { logQuery } = await import(\"../core/log.js\");\n    try {\n      const entries = await logQuery(resolve(opts.notes), {\n        kind: opts.kind,\n        after: opts.after,\n        before: opts.before,\n        limit: opts.limit,\n      });\n      console.log(JSON.stringify(entries));\n    } catch (e: any) {\n      console.error(`log-query failed: ${e.message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command(\"install-schema\")\n  .description(\"Bootstrap vault.schema.yml in the vault root with the default schema\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--force\", \"Overwrite existing schema file\")\n  .action(async (opts) => {\n    const { installDefaultSchema } = await import(\"../core/schema.js\");\n    const r = await installDefaultSchema(resolve(opts.notes), opts.force);\n    console.log(r.written ? `Installed default schema: ${r.path}` : `Schema already exists: ${r.path} (use --force to overwrite)`);\n    process.exit(0);\n  });\n\nprogram\n  .command(\"tools [name]\")\n  .description(\"List all MCP tools, or show details for a specific tool\")\n  .action((name?: string) => {\n    if (name) {\n      printToolDetail(name);\n    } else {\n      printToolList();\n    }\n    process.exit(0);\n  });\n\nprogram\n  .command(\"serve\", { isDefault: true })\n  .description(\"Start the MCP server (default command)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--reindex\", \"Force full reindex and exit\")\n  .option(\"--stats\", \"Show vault statistics and exit\")\n  .option(\"--wait-for-ready\", \"Block startup until index is fully built before serving (default: index in background; tools return 'Indexing in progress' until ready)\")\n  .option(\"--read-only\", \"Suppress write tools (create_note, update_note, delete_note, move_note, update_frontmatter, manage_tags, rename_tag) — use for shared docs vaults owned by another tool\")\n  .option(\"--model <name>\", \"Embedding model to use (default: all-MiniLM-L6-v2, fast; use nomic-ai/nomic-embed-text-v1.5 for higher quality)\")\n  .option(\"--workers <n>\", \"Number of worker threads for parallel embedding\", parseInt)\n  .option(\"--batch-size <n>\", \"Texts per ONNX forward pass (default: 8)\", parseInt)\n  .option(\"--no-quantized\", \"Use full-precision model instead of quantized (slower, slightly higher quality)\")\n  .option(\"--no-watch\", \"Disable file watcher\")\n  .action(async (opts) => {\n    const notesPath = resolve(opts.notes);\n\n    if (!existsSync(notesPath)) {\n      console.error(`Error: notes directory not found: ${notesPath}`);\n      process.exit(1);\n    }\n\n    if (opts.stats) {\n      const { Indexer } = await import(\"../core/indexer.js\");\n      const indexer = new Indexer(notesPath);\n      const docs = await indexer.indexAll();\n      console.log(`Notes: ${docs.length}`);\n      console.log(`Chunks: ${docs.reduce((n: number, d: any) => n + d.chunks.length, 0)}`);\n      console.log(`Wikilinks: ${docs.reduce((n: number, d: any) => n + d.wikilinks.length, 0)}`);\n      console.log(`Tags: ${new Set(docs.flatMap((d: any) => d.tags)).size} unique`);\n      process.exit(0);\n    }\n\n    if (opts.reindex) {\n      const { createServer } = await import(\"../mcp/server.js\");\n      await createServer(notesPath, {\n        watch: false,\n        waitForReady: true,\n        model: opts.model,\n        workers: opts.workers,\n        batchSize: opts.batchSize,\n        quantized: opts.quantized,\n        onProgress: (embedded, total) => {\n          process.stderr.write(`\\rEmbedding ${embedded}/${total} chunks...`);\n        },\n      });\n      process.stderr.write(\"\\n\");\n      console.log(\"Reindex complete.\");\n      process.exit(0);\n    }\n\n    // Default: start MCP server on stdio\n    const { startServer } = await import(\"../mcp/server.js\");\n    await startServer(notesPath, {\n      watch: opts.watch,\n      waitForReady: opts.waitForReady,\n      model: opts.model,\n      workers: opts.workers,\n      batchSize: opts.batchSize,\n      quantized: opts.quantized,\n      readOnly: opts.readOnly,\n    });\n  });\n\nregisterUpdateCommands(program, {\n  packageName: PKG_NAME,\n  pluginName: \"semantic-memory\",\n  configFile: \"semantic-memory.json\",\n  onAfterUpdate: (cwd) => runRelink(cwd),\n});\n\nprogram\n  .command(\"normalize-config\")\n  .description(\n    \"Rewrite fragile `npx @latest` entries in .mcp.json to the stable node-against-node_modules form (with backup and validation)\",\n  )\n  .option(\"--dry-run\", \"print the proposed changes but don't write\")\n  .action((opts: { dryRun?: boolean }) => {\n    const cwd = process.cwd();\n    const mcpPath = join(cwd, \".mcp.json\");\n    if (!existsSync(mcpPath)) {\n      console.log(\"no .mcp.json in current directory — nothing to do\");\n      process.exit(0);\n    }\n    const data = readJsonSafe(mcpPath);\n    if (!data || typeof data !== \"object\" || !data.mcpServers || typeof data.mcpServers !== \"object\") {\n      console.error(`could not parse ${mcpPath}`);\n      process.exit(1);\n    }\n    const bin = localBinArg(cwd);\n    if (!bin) {\n      console.error(\n        `no local install found at ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory ` +\n          `(or the legacy semantic-sidekick path).\\n` +\n          `run 'npm install --save @theglitchking/semantic-memory' first, then re-run this command.`,\n      );\n      process.exit(1);\n    }\n    const rewritten: string[] = [];\n    for (const [key, entry] of Object.entries<any>(data.mcpServers)) {\n      if (!isNpxForm(entry)) continue;\n      const notes = extractNotesPath(entry) ?? \"./.claude/.vault\";\n      const extra = extractExtraFlags(entry);\n      data.mcpServers[key] = {\n        type: \"stdio\",\n        command: \"node\",\n        args: [bin, \"--notes\", notes, ...extra],\n      };\n      rewritten.push(key);\n    }\n    if (rewritten.length === 0) {\n      console.log(\"no npx-form entries found — .mcp.json is already in the stable form.\");\n      process.exit(0);\n    }\n    console.log(`Rewriting ${rewritten.length} entr${rewritten.length === 1 ? \"y\" : \"ies\"}: ${rewritten.join(\", \")}`);\n    if (opts.dryRun) {\n      console.log(\"--- proposed .mcp.json:\");\n      console.log(JSON.stringify(data, null, 2));\n      console.log(\"--- (dry-run; no changes written)\");\n      process.exit(0);\n    }\n    // Back up\n    const bakPath = join(dirname(mcpPath), \".mcp.json.bak\");\n    try {\n      writeFileSync(bakPath, readFileSync(mcpPath, \"utf8\"));\n      console.log(`backup written: ${bakPath}`);\n    } catch (err: any) {\n      console.error(`could not write backup: ${err.message}`);\n      process.exit(1);\n    }\n    writeFileSync(mcpPath, JSON.stringify(data, null, 2) + \"\\n\");\n\n    // Verify the local bin starts cleanly. We just run --version — fast and\n    // enough to catch ERR_MODULE_NOT_FOUND type failures.\n    const verify = spawnSync(\"node\", [bin, \"--version\"], { cwd, stdio: \"pipe\", timeout: 15_000 });\n    if (verify.status !== 0) {\n      console.error(`verification failed (exit ${verify.status}):\\n${verify.stderr?.toString() || \"\"}`);\n      console.error(`rolling back from ${bakPath}`);\n      writeFileSync(mcpPath, readFileSync(bakPath, \"utf8\"));\n      process.exit(1);\n    }\n    console.log(`✓ .mcp.json normalized and verified. Toggle the MCPs in /mcp to reconnect.`);\n    process.exit(0);\n  });\n\nprogram\n  .command(\"healthcheck\")\n  .description(\n    \"Verify the local install starts cleanly + run drift detection. Self-heals common npx-cache corruption (ERR_MODULE_NOT_FOUND). With --fast, skips the slow tier (full vault lint). With --fix, auto-applies safe fixes for fixable findings.\",\n  )\n  .option(\"--fast\", \"Run only the fast-tier drift checks (file-system probes). Skips the slow tier (full vault lint).\", false)\n  .option(\"--json\", \"Emit structured JSON output instead of human-readable text.\", false)\n  .option(\"--fix\", \"Auto-apply safe fixes for fixable drift findings (re-link skills, reconcile .mcp.json, reindex, migrate state). Findings that need human review are reported, not touched.\", false)\n  .action(async (opts) => {\n    const cwd = process.cwd();\n    const bin = findLocalBin(cwd);\n    if (!bin) {\n      console.error(`no local install at ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory (or legacy semantic-sidekick path)`);\n      console.error(`run 'npm install --save @theglitchking/semantic-memory' to install.`);\n      process.exit(1);\n    }\n\n    // 1. Warn if .mcp.json uses the fragile form.\n    const mcpPath = join(cwd, \".mcp.json\");\n    if (existsSync(mcpPath) && !opts.json) {\n      const data = readJsonSafe(mcpPath);\n      const entries = data?.mcpServers && typeof data.mcpServers === \"object\" ? Object.entries<any>(data.mcpServers) : [];\n      const fragile = entries.filter(([, e]) => isNpxForm(e)).map(([k]) => k);\n      if (fragile.length > 0) {\n        console.warn(`⚠️  .mcp.json uses the fragile npx-@latest form for: ${fragile.join(\", \")}`);\n        console.warn(`   Rewrite to the stable form:`);\n        console.warn(`     npx --no @theglitchking/semantic-memory normalize-config`);\n      }\n    }\n\n    // 2. Smoke-test the local bin (with npx-cache self-heal on ERR_MODULE_NOT_FOUND).\n    //    Unlike prior versions, this does NOT exit early — drift detection and\n    //    --fix always run afterwards.\n    let smokeOk = false;\n    let smokeVersion = \"\";\n    {\n      const r = spawnSync(\"node\", [bin, \"--version\"], { cwd, stdio: \"pipe\", timeout: 15_000 });\n      if (r.status === 0) {\n        smokeOk = true;\n        smokeVersion = r.stdout?.toString().trim() ?? \"\";\n      } else {\n        const stderr = r.stderr?.toString() ?? \"\";\n        if (stderr.includes(\"ERR_MODULE_NOT_FOUND\")) {\n          const match = stderr.match(/([\\/~][^'\"\\s]*\\/_npx\\/[^\\/'\"\\s]+)/);\n          if (match) {\n            const bad = match[1];\n            if (!opts.json) console.warn(`detected broken npx cache at ${bad} — clearing and retrying...`);\n            try { rmSync(bad, { recursive: true, force: true }); } catch {}\n            const r2 = spawnSync(\"node\", [bin, \"--version\"], { cwd, stdio: \"pipe\", timeout: 15_000 });\n            if (r2.status === 0) {\n              smokeOk = true;\n              smokeVersion = r2.stdout?.toString().trim() ?? \"\";\n            } else if (!opts.json) {\n              console.error(`retry still failed:\\n${r2.stderr?.toString() || \"\"}`);\n            }\n          }\n        }\n        if (!smokeOk && !opts.json && stderr) console.error(stderr);\n      }\n    }\n    if (smokeOk && !opts.json) console.log(`✓ local install starts cleanly (v${smokeVersion})`);\n\n    // 3. Run drift detection.\n    const { runHealthcheck, formatDriftBanner, filterToDrift } = await import(\"../core/healthcheck.js\");\n    const vaultCandidate = join(cwd, \".claude\", \".vault\");\n    const vaultPath = existsSync(vaultCandidate) ? vaultCandidate : undefined;\n    let result = await runHealthcheck({ projectRoot: cwd, vaultPath, tier: opts.fast ? \"fast\" : \"all\", force: true });\n\n    // 4. Apply fixes if requested.\n    let fixOutcomes: FixOutcome[] = [];\n    let plan = { fixes: [] as PlannedFix[], skipped: [] as { check: string; reason: string }[] };\n    if (opts.fix) {\n      plan = planFixes(filterToDrift(result));\n      if (plan.fixes.length > 0) {\n        fixOutcomes = await executeFixes(cwd, plan.fixes);\n        // Re-run fast-tier drift to reflect the post-fix state.\n        result = await runHealthcheck({ projectRoot: cwd, vaultPath, tier: opts.fast ? \"fast\" : \"all\", force: true });\n      }\n    }\n\n    // 5. Emit.\n    if (opts.json) {\n      console.log(JSON.stringify({ smoke: { ok: smokeOk, version: smokeVersion }, result, fix: opts.fix ? { plan, outcomes: fixOutcomes } : undefined }, null, 2));\n    } else {\n      if (opts.fix) {\n        if (fixOutcomes.length === 0 && plan.skipped.length === 0) {\n          console.log(`\\n✓ nothing to fix`);\n        } else {\n          console.log(`\\n--fix applied ${fixOutcomes.filter((o) => o.status === \"fixed\").length}/${fixOutcomes.length} action(s):`);\n          for (const o of fixOutcomes) console.log(`  ${o.status === \"fixed\" ? \"✓\" : \"✗\"} ${o.action} (${o.check}) — ${o.detail}`);\n          for (const s of plan.skipped) console.log(`  • skipped ${s.check} — ${s.reason}`);\n        }\n      }\n      const banner = formatDriftBanner(result);\n      if (banner) {\n        console.log(\"\");\n        console.log(banner);\n      } else {\n        console.log(`\\n✓ no drift detected (${result.findings.length} checks ran in ${result.duration_ms}ms)`);\n      }\n    }\n\n    process.exit(smokeOk ? 0 : 1);\n  });\n\n// --- Skill bundler (Phase 6) ---\n\nfunction parseAgent(input: string): AgentName {\n  const a = input.toLowerCase();\n  if (!SKILL_BUNDLER_AGENTS.includes(a as AgentName)) {\n    console.error(`Unknown agent: ${input}. Supported: ${SKILL_BUNDLER_AGENTS.join(\", \")}.`);\n    process.exit(2);\n  }\n  return a as AgentName;\n}\n\nfunction parseScope(input: string): Scope {\n  if (input !== \"global\" && input !== \"local\") {\n    console.error(`Unknown scope: ${input}. Use 'global' or 'local'.`);\n    process.exit(2);\n  }\n  return input;\n}\n\nfunction findSourceRoot(): string {\n  // 1. Installed: <cwd>/node_modules/@theglitchking/semantic-sidekick or semantic-memory\n  for (const pkg of [\"semantic-memory\", \"semantic-sidekick\"]) {\n    const installed = join(process.cwd(), \"node_modules\", \"@theglitchking\", pkg);\n    if (existsSync(installed)) return installed;\n  }\n  // 2. Dev: derive from the bin location (this file lives at <root>/dist/cli/index.js)\n  const dev = resolve(new URL(\"../../\", import.meta.url).pathname);\n  return dev;\n}\n\nconst skillsCmd = program.command(\"skills\").description(\"Install, target, or uninstall skill bundles for non-Claude agents (codex, copilot, pi). Claude installs continue to use the npm postinstall flow.\");\n\nskillsCmd\n  .command(\"targets\")\n  .description(\"Preview where skill bundles would be installed for one or more agents.\")\n  .option(\"--agent <name...>\", \"One or more agents (default: all). Repeatable.\", undefined as any)\n  .option(\"--scope <scope>\", \"global or local (default: local)\", \"local\")\n  .option(\"--project <path>\", \"Project root for local-scope paths (default: cwd)\", process.cwd())\n  .action((opts) => {\n    const scope = parseScope(opts.scope);\n    const agents: AgentName[] = (opts.agent && opts.agent.length > 0 ? opts.agent : SKILL_BUNDLER_AGENTS).map(parseAgent);\n    const out = agents.map((a) => resolveTarget(a, scope, opts.project));\n    console.log(JSON.stringify(out, null, 2));\n  });\n\nskillsCmd\n  .command(\"install\")\n  .description(\"Install skill bundles into an agent's skill directory. Non-destructive by default; --force to overwrite.\")\n  .requiredOption(\"--agent <name>\", \"Agent runtime (claude, codex, copilot, pi)\")\n  .option(\"--scope <scope>\", \"global or local (default: local)\", \"local\")\n  .option(\"--project <path>\", \"Project root for local-scope paths (default: cwd)\", process.cwd())\n  .option(\"--only <names...>\", \"Restrict to specific skill names (default: all shipped)\")\n  .option(\"--force\", \"Overwrite even if drift is detected against an existing manifest\", false)\n  .action(async (opts) => {\n    const agent = parseAgent(opts.agent);\n    const scope = parseScope(opts.scope);\n    if (agent === \"claude\") {\n      console.error(\n        \"Claude skill installs are handled by the npm postinstall (claude-plugin-runtime). \" +\n          \"Run `npm install @theglitchking/semantic-memory` instead — that flow symlinks \" +\n          \"skills into ~/.claude/skills/ or .claude/skills/ automatically. The skills CLI \" +\n          \"is intended for non-Claude agents (codex, copilot, pi) which do not have that \" +\n          \"postinstall integration.\"\n      );\n      process.exit(2);\n    }\n    const sourceRoot = findSourceRoot();\n    const result = await installSkills({\n      agent,\n      scope,\n      sourceRoot,\n      projectRoot: opts.project,\n      version,\n      only: opts.only,\n      force: opts.force === true,\n    });\n    console.log(JSON.stringify(result, null, 2));\n    if (result.installed.length === 0 && result.reason) process.exit(1);\n  });\n\nskillsCmd\n  .command(\"uninstall\")\n  .description(\"Remove skill bundles tracked by the semantic-memory manifest. User-written skills outside the manifest are left untouched.\")\n  .requiredOption(\"--agent <name>\", \"Agent runtime (claude, codex, copilot, pi)\")\n  .option(\"--scope <scope>\", \"global or local (default: local)\", \"local\")\n  .option(\"--project <path>\", \"Project root for local-scope paths (default: cwd)\", process.cwd())\n  .action(async (opts) => {\n    const agent = parseAgent(opts.agent);\n    const scope = parseScope(opts.scope);\n    if (agent === \"claude\") {\n      console.error(\"Claude skill uninstalls go through the npm uninstall flow. The skills CLI is for non-Claude agents.\");\n      process.exit(2);\n    }\n    const result = await uninstallSkills({ agent, scope, projectRoot: opts.project });\n    console.log(JSON.stringify(result, null, 2));\n  });\n\nskillsCmd\n  .command(\"list\")\n  .description(\"List the skill bundles shipped with this plugin version.\")\n  .action(async () => {\n    const sourceRoot = findSourceRoot();\n    const shipped = await listShippedSkills(sourceRoot);\n    console.log(JSON.stringify(shipped.map((s) => s.name), null, 2));\n  });\n\n// --- State migration (Phase 3, v1.2) ---\n\nprogram\n  .command(\"migrate-state\")\n  .description(\n    \"Move legacy .claude/.sidekick-* state files to .claude/.semantic-memory/. Idempotent. \" +\n      \"Conflicts (both paths exist) require --force. Pass --dry-run to preview without changes.\",\n  )\n  .option(\"--dry-run\", \"Print the planned migration without renaming any files.\", false)\n  .option(\n    \"--force\",\n    \"When both old and new paths exist, prefer the new path and delete the old one.\",\n    false,\n  )\n  .option(\"--project <path>\", \"Project root (default: cwd)\", process.cwd())\n  .action((opts) => {\n    const result = migrateState({\n      projectRoot: opts.project,\n      dryRun: opts.dryRun === true,\n      force: opts.force === true,\n    });\n    console.log(JSON.stringify(result, null, 2));\n    if (result.conflicts.length > 0 && !opts.force && !opts.dryRun) {\n      console.error(\n        `\\n${result.conflicts.length} conflict${result.conflicts.length === 1 ? \"\" : \"s\"} detected. Re-run with --force to resolve (keeps new path, deletes old).`,\n      );\n      process.exit(1);\n    }\n  });\n\n// --- Confidence decay introspection (v1.3) ---\n\nprogram\n  .command(\"decay-config\")\n  .description(\"Print the active confidence-decay config (shipped defaults + any vault.schema.yml override).\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .action(async (opts) => {\n    const { loadDecayConfig, DEFAULT_DECAY_CONFIG } = await import(\"../core/decay.js\");\n    const cfg = loadDecayConfig(resolve(opts.notes));\n    const source = JSON.stringify(cfg) === JSON.stringify(DEFAULT_DECAY_CONFIG) ? \"defaults\" : \"vault.schema.yml (overridden)\";\n    console.log(JSON.stringify({ source, config: cfg }, null, 2));\n    process.exit(0);\n  });\n\nprogram\n  .command(\"decay-trace <notePath>\")\n  .description(\"Show the decay calculation for one note: type, last_verified, age, half-life, evergreen, multiplier.\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .action(async (notePath: string, opts) => {\n    const { loadDecayConfig, computeDecay, normalizeVerifiedDate } = await import(\"../core/decay.js\");\n    const matter = (await import(\"gray-matter\")).default;\n    const abs = resolve(opts.notes, notePath);\n    if (!existsSync(abs)) {\n      console.error(`note not found: ${abs}`);\n      process.exit(1);\n    }\n    const { data: fm } = matter(readFileSync(abs, \"utf8\"));\n    const lastVerified = normalizeVerifiedDate(fm.last_verified);\n    const d = computeDecay({\n      type: typeof fm.type === \"string\" ? fm.type : undefined,\n      last_verified: lastVerified,\n      evergreen: fm.evergreen === true,\n      config: loadDecayConfig(resolve(opts.notes)),\n    });\n    console.log(\n      JSON.stringify(\n        {\n          path: notePath,\n          type: fm.type ?? null,\n          last_verified: lastVerified ?? null,\n          evergreen: fm.evergreen === true,\n          multiplier: d.multiplier,\n          age_days: Math.round(d.age_days),\n          effective_half_life: d.effective_half_life,\n          reason: d.reason,\n        },\n        null,\n        2\n      )\n    );\n    process.exit(0);\n  });\n\n// --- Lexicon (v1.4) ---\n\nconst lexiconCmd = program.command(\"lexicon\").description(\"Manage the learned human→artifact lexicon (aliases).\");\n\nlexiconCmd\n  .command(\"list\")\n  .description(\"List all aliases in the lexicon.\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .action(async (opts) => {\n    const { loadLexiconCache } = await import(\"../core/lexicon.js\");\n    console.log(JSON.stringify(await loadLexiconCache(resolve(opts.notes)), null, 2));\n    process.exit(0);\n  });\n\nlexiconCmd\n  .command(\"compile\")\n  .description(\"Rebuild the derived lexicon cache from the lexicon/ notes.\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .action(async (opts) => {\n    const { compileLexicon } = await import(\"../core/lexicon.js\");\n    const entries = await compileLexicon(resolve(opts.notes));\n    console.log(`compiled ${entries.length} alias(es)`);\n    process.exit(0);\n  });\n\nlexiconCmd\n  .command(\"add <canonical> <phrases...>\")\n  .description(\"Upsert an alias: a canonical target and the human phrases that refer to it.\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--authored\", \"Mark as human-authored (default: learned)\")\n  .action(async (canonical: string, phrases: string[], opts) => {\n    const { addAlias } = await import(\"../core/lexicon.js\");\n    const r = await addAlias(resolve(opts.notes), { canonical, phrases, source: opts.authored ? \"authored\" : \"learned\" });\n    console.log(JSON.stringify(r, null, 2));\n    process.exit(0);\n  });\n\n// --- Entity dossiers (v1.5 Phase 8) ---\n\nconst dossierCmd = program.command(\"dossier\").description(\"Manage entity dossiers — per-component living notes (purpose / failure modes / knobs / incident log / current state).\");\n\ndossierCmd\n  .command(\"init <entity>\")\n  .description(\"Scaffold a dossier for an entity (no-op if one already exists). Optionally seed aliases and provenance.\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--alias <phrase...>\", \"Human phrase(s) for this entity — fed to the lexicon compiler\")\n  .option(\"--seeded-from <ref>\", \"Provenance of the scaffold (e.g. a babel-fish project-map entry)\")\n  .action(async (entity: string, opts) => {\n    const { initDossier } = await import(\"../core/dossier.js\");\n    const r = await initDossier(resolve(opts.notes), entity, { aliases: opts.alias, seeded_from: opts.seededFrom });\n    console.log(JSON.stringify(r, null, 2));\n    process.exit(0);\n  });\n\ndossierCmd\n  .command(\"list\")\n  .description(\"List all dossiers with their entity, aliases, and current state.\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .action(async (opts) => {\n    const { listDossiers } = await import(\"../core/dossier.js\");\n    console.log(JSON.stringify(await listDossiers(resolve(opts.notes)), null, 2));\n    process.exit(0);\n  });\n\n// --- Speaker profile (v1.5 Phase 11) ---\n\nconst profileCmd = program.command(\"profile\").description(\"Manage the speaker profile — how THIS human communicates (severity calibration, chronic omissions, verbosity, shorthand).\");\n\nprofileCmd\n  .command(\"init\")\n  .description(\"Scaffold profile/speaker.md with the fixed sections (no-op if it exists).\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .action(async (opts) => {\n    const { initSpeakerProfile } = await import(\"../core/profile.js\");\n    const r = await initSpeakerProfile(resolve(opts.notes));\n    console.log(JSON.stringify(r, null, 2));\n    process.exit(0);\n  });\n\nprofileCmd\n  .command(\"show\")\n  .description(\"Print the speaker profile's injection head (the capped, placeholder-stripped view).\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .action(async (opts) => {\n    const { readSpeakerProfile } = await import(\"../core/profile.js\");\n    const p = await readSpeakerProfile(resolve(opts.notes));\n    console.log(p ? p.head || \"(profile is empty — only placeholders)\" : \"(no speaker profile — run `profile init`)\");\n    process.exit(0);\n  });\n\n// --- Selection-logging telemetry introspection (v1.3.1) ---\n\nprogram\n  .command(\"selection-stats\")\n  .description(\"Summarize the local selection log: searches, selections, most-cited notes, and retrieved-but-never-cited notes.\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--json\", \"Emit raw JSON instead of a human summary\")\n  .action(async (opts) => {\n    const { computeSelectionStats, selectionLogPath } = await import(\"../core/telemetry.js\");\n    const stats = await computeSelectionStats(resolve(opts.notes));\n    if (opts.json) {\n      console.log(JSON.stringify(stats, null, 2));\n      process.exit(0);\n    }\n    console.log(`Selection log: ${selectionLogPath(resolve(opts.notes))}`);\n    console.log(`  searches:   ${stats.searches}`);\n    console.log(`  selections: ${stats.selections}`);\n    const topCited = Object.entries(stats.citedPaths).sort((a, b) => b[1] - a[1]).slice(0, 10);\n    if (topCited.length) {\n      console.log(`  most cited:`);\n      for (const [p, n] of topCited) console.log(`    ${n}×  ${p}`);\n    }\n    if (stats.retrievedNeverCited.length) {\n      console.log(`  retrieved but never cited (${stats.retrievedNeverCited.length}): ${stats.retrievedNeverCited.slice(0, 10).join(\", \")}${stats.retrievedNeverCited.length > 10 ? \" …\" : \"\"}`);\n    }\n    process.exit(0);\n  });\n\nprogram.parse();\n","import type { DriftFinding } from \"./healthcheck.js\";\n\n/**\n * The `--fix` planner. Pure, side-effect-free: it maps drift findings onto safe\n * auto-fix actions, or explains why a finding needs a human. The CLI executes the\n * plan; keeping the decision logic here makes it unit-testable without spawning.\n *\n * \"Safe\" means: idempotent, non-destructive, and derivable from the install itself\n * (re-link skills, reconcile .mcp.json, rebuild the derived index, migrate state).\n * Anything that touches user-authored content (stale notes, broken wikilinks,\n * hand-edited AGENTS.md) is deliberately NOT auto-fixed — it drops to `skipped`\n * with a pointer to the manual remedy.\n */\n\nexport type FixAction = \"skill-link\" | \"mcp-reconcile\" | \"reindex\" | \"state-migrate\";\n\nexport interface PlannedFix {\n  check: string;\n  action: FixAction;\n  summary: string;\n}\n\nexport interface SkippedFinding {\n  check: string;\n  reason: string;\n}\n\nexport interface FixPlan {\n  fixes: PlannedFix[];\n  skipped: SkippedFinding[];\n}\n\n/** Human-readable reason a finding is not auto-fixable. */\nconst MANUAL_REASON: Record<string, string> = {\n  \"regenerate-contract\":\n    \"AGENTS.md needs a human decision — run `/contract` (regenerate_contract), or move custom content into a Local Notes section outside the managed block.\",\n  lint_vault:\n    \"Vault lint findings (stale notes, broken wikilinks, schema violations) require human review — run `lint_vault` for the full report.\",\n  session_staleness:\n    \"Resume the session (session_run / session_finish) or remove .claude/.semantic-memory/session.json to abandon it.\",\n};\n\n/**\n * Build the fix plan from a set of drift findings. Only findings with\n * severity !== \"ok\" are considered.\n */\nexport function planFixes(findings: DriftFinding[]): FixPlan {\n  const fixes: PlannedFix[] = [];\n  const skipped: SkippedFinding[] = [];\n\n  for (const f of findings) {\n    if (f.severity === \"ok\") continue;\n\n    switch (f.fixable_via) {\n      case \"skill-link\":\n        fixes.push({ check: f.check, action: \"skill-link\", summary: f.summary });\n        break;\n      case \"mcp-reconcile\":\n        fixes.push({ check: f.check, action: \"mcp-reconcile\", summary: f.summary });\n        break;\n      case \"reindex\":\n        fixes.push({ check: f.check, action: \"reindex\", summary: f.summary });\n        break;\n      case \"state-migrate\":\n        fixes.push({ check: f.check, action: \"state-migrate\", summary: f.summary });\n        break;\n      case \"regenerate-contract\":\n        // The only case this fires is a custom AGENTS.md without managed markers,\n        // where regeneration would refuse anyway. Treat as human-review.\n        skipped.push({ check: f.check, reason: MANUAL_REASON[\"regenerate-contract\"] });\n        break;\n      default:\n        skipped.push({\n          check: f.check,\n          reason: MANUAL_REASON[f.check] ?? \"No automatic fix available — needs human review.\",\n        });\n    }\n  }\n\n  return { fixes, skipped };\n}\n","import { mkdir, readFile, writeFile, copyFile, readdir, rm } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { join, basename, resolve } from \"node:path\";\nimport { homedir } from \"node:os\";\nimport { createHash } from \"node:crypto\";\n\nexport type AgentName = \"claude\" | \"codex\" | \"copilot\" | \"pi\";\nexport type Scope = \"global\" | \"local\";\n\nexport interface AgentTargetSpec {\n  agent: AgentName;\n  scope: Scope;\n  /** Absolute resolved path where the skill bundles will land. */\n  path: string;\n}\n\nexport interface SkillManifest {\n  package: string;\n  version: string;\n  agent: AgentName;\n  scope: Scope;\n  installed_at: string;\n  skills: { name: string; sha256: string }[];\n}\n\nexport interface InstallResult {\n  agent: AgentName;\n  scope: Scope;\n  target_path: string;\n  installed: string[];\n  skipped: string[];\n  reason?: string;\n  manifest_path?: string;\n}\n\nconst MANIFEST_FILE = \".semantic-memory-skill-manifest.json\";\n\n/**\n * Resolve where a given (agent, scope) tuple should land. Project root is required for local\n * scope (to anchor relative paths); for global scope it's not used.\n */\nexport function resolveTarget(agent: AgentName, scope: Scope, projectRoot: string): AgentTargetSpec {\n  const root = resolve(projectRoot);\n  const home = homedir();\n  const map: Record<AgentName, { global: string; local: string }> = {\n    claude: { global: join(home, \".claude\", \"skills\"), local: join(root, \".claude\", \"skills\") },\n    codex: { global: join(home, \".codex\", \"skills\"), local: join(root, \".codex\", \"skills\") },\n    copilot: { global: join(home, \".copilot\", \"skills\"), local: join(root, \".github\", \"skills\") },\n    pi: { global: join(home, \".pi\", \"agent\", \"skills\"), local: join(root, \".pi\", \"skills\") },\n  };\n  return { agent, scope, path: map[agent][scope] };\n}\n\n/**\n * Enumerate the canonical skill bundles shipped by this plugin. Each bundle is a directory\n * under `<sourceRoot>/skills/` containing at least a SKILL.md file. Entries without\n * SKILL.md are silently skipped (allows future non-skill files like `/skills/.gitkeep`).\n */\nexport async function listShippedSkills(sourceRoot: string): Promise<{ name: string; dir: string }[]> {\n  const skillsDir = join(sourceRoot, \"skills\");\n  if (!existsSync(skillsDir)) return [];\n  const entries = await readdir(skillsDir, { withFileTypes: true });\n  const out: { name: string; dir: string }[] = [];\n  for (const e of entries) {\n    if (!e.isDirectory()) continue;\n    const dir = join(skillsDir, e.name);\n    const skillFile = join(dir, \"SKILL.md\");\n    if (!existsSync(skillFile)) continue;\n    out.push({ name: e.name, dir });\n  }\n  return out;\n}\n\nasync function sha256OfFile(path: string): Promise<string> {\n  const buf = await readFile(path);\n  return createHash(\"sha256\").update(buf).digest(\"hex\");\n}\n\n/**\n * Copy a single skill bundle (SKILL.md plus any sibling files in the same directory) into\n * the target directory, overlaying it with the agent name. Returns the list of files written.\n *\n * The target layout is `<targetPath>/<skillName>/SKILL.md` plus mirrored siblings, so each\n * bundle is namespaced and easy to remove later.\n */\nasync function copyBundle(srcDir: string, destDir: string): Promise<string[]> {\n  await mkdir(destDir, { recursive: true });\n  const entries = await readdir(srcDir, { withFileTypes: true });\n  const written: string[] = [];\n  for (const e of entries) {\n    const src = join(srcDir, e.name);\n    const dest = join(destDir, e.name);\n    if (e.isDirectory()) {\n      const childWritten = await copyBundle(src, dest);\n      written.push(...childWritten);\n      continue;\n    }\n    if (!e.isFile()) continue;\n    await copyFile(src, dest);\n    written.push(dest);\n  }\n  return written;\n}\n\nexport interface InstallOptions {\n  agent: AgentName;\n  scope: Scope;\n  /** Path to the package's source root (usually the repo root, where `skills/` lives). */\n  sourceRoot: string;\n  /** Used to anchor local-scope target paths. */\n  projectRoot: string;\n  /** Plugin version, recorded in the manifest. */\n  version: string;\n  /** Specific skills to install. 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Pass --force to overwrite.`,\n        manifest_path: manifestPath,\n      };\n    }\n  }\n\n  await mkdir(target.path, { recursive: true });\n  const installed: string[] = [];\n  const skillEntries: { name: string; sha256: string }[] = [];\n  for (const skill of toInstall) {\n    const destDir = join(target.path, skill.name);\n    await copyBundle(skill.dir, destDir);\n    const skillFile = join(skill.dir, \"SKILL.md\");\n    skillEntries.push({ name: skill.name, sha256: await sha256OfFile(skillFile) });\n    installed.push(skill.name);\n  }\n\n  const manifest: SkillManifest = {\n    package: \"@theglitchking/semantic-memory\",\n    version: opts.version,\n    agent: opts.agent,\n    scope: opts.scope,\n    installed_at: new Date().toISOString(),\n    skills: skillEntries,\n  };\n  await writeFile(manifestPath, JSON.stringify(manifest, null, 2), \"utf-8\");\n\n  return {\n    agent: opts.agent,\n    scope: opts.scope,\n    target_path: target.path,\n    installed,\n    skipped: [],\n    manifest_path: manifestPath,\n  };\n}\n\nexport interface UninstallOptions {\n  agent: AgentName;\n  scope: Scope;\n  projectRoot: string;\n}\n\nexport interface UninstallResult {\n  agent: AgentName;\n  scope: Scope;\n  target_path: string;\n  removed: string[];\n  manifest_present: boolean;\n  reason?: string;\n}\n\n/**\n * Remove only the skill bundles tracked in the manifest. User-written skills outside\n * the manifest are left untouched.\n */\nexport async function uninstallSkills(opts: UninstallOptions): Promise<UninstallResult> {\n  const target = resolveTarget(opts.agent, opts.scope, opts.projectRoot);\n  const manifestPath = join(target.path, MANIFEST_FILE);\n  const manifest = await readManifest(manifestPath);\n  if (!manifest) {\n    return {\n      agent: opts.agent,\n      scope: opts.scope,\n      target_path: target.path,\n      removed: [],\n      manifest_present: false,\n      reason: \"No semantic-memory manifest found — nothing to uninstall.\",\n    };\n  }\n  const removed: string[] = [];\n  for (const skill of manifest.skills) {\n    const dir = join(target.path, skill.name);\n    if (existsSync(dir)) {\n      await rm(dir, { recursive: true, force: true });\n      removed.push(skill.name);\n    }\n  }\n  await rm(manifestPath, { force: true });\n  return {\n    agent: opts.agent,\n    scope: opts.scope,\n    target_path: target.path,\n    removed,\n    manifest_present: true,\n  };\n}\n\nasync function readManifest(path: string): Promise<SkillManifest | null> {\n  if (!existsSync(path)) return null;\n  try {\n    const raw = await readFile(path, \"utf-8\");\n    const parsed = JSON.parse(raw);\n    if (typeof parsed?.package !== \"string\") return null;\n    return parsed as SkillManifest;\n  } catch {\n    return null;\n  }\n}\n\nasync function detectDrift(\n  existing: SkillManifest,\n  toInstall: { name: string; dir: string }[]\n): Promise<string[]> {\n  const driftNames: string[] = [];\n  const existingByName = new Map(existing.skills.map((s) => [s.name, s.sha256]));\n  for (const skill of toInstall) {\n    const sourceSha = await sha256OfFile(join(skill.dir, \"SKILL.md\"));\n    const existingSha = existingByName.get(skill.name);\n    if (existingSha !== undefined && existingSha !== sourceSha) {\n      driftNames.push(skill.name);\n    }\n  }\n  return driftNames;\n}\n\nexport const SKILL_BUNDLER_AGENTS: AgentName[] = [\"claude\", \"codex\", \"copilot\", \"pi\"];\n","import { existsSync, mkdirSync, statSync, renameSync, unlinkSync } from \"node:fs\";\nimport { join } from \"node:path\";\n\n/**\n * State files that moved/renamed in v1.2.\n *\n * Each entry: legacy path (relative to <projectRoot>/.claude) → new path (relative to\n * <projectRoot>/.claude). 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This command does the explicit move so the legacy files stop existing.\n *\n * Order matters only for human-readable output; the migrations themselves are independent.\n */\nconst STATE_MIGRATIONS: { name: string; old: string; new: string }[] = [\n  { name: \"mode\", old: \".sidekick-mode\", new: \".semantic-memory/mode\" },\n  { name: \"fingerprints\", old: \".sidekick-fingerprints.json\", new: \".semantic-memory/fingerprints.json\" },\n  { name: \"capture-pending\", old: \".sidekick-capture-pending.json\", new: \".semantic-memory/capture-pending.json\" },\n];\n\nexport type MigrationStatus = \"migrated\" | \"skipped-no-source\" | \"skipped-already-migrated\" | \"conflict\" | \"resolved-by-force\";\n\nexport interface MigrationFinding {\n  name: string;\n  status: MigrationStatus;\n  oldPath: string;\n  newPath: string;\n  detail?: string;\n}\n\nexport interface MigrateStateOptions {\n  projectRoot: string;\n  dryRun?: boolean;\n  force?: boolean;\n}\n\nexport interface MigrateStateResult {\n  migrated: MigrationFinding[];\n  skipped: MigrationFinding[];\n  conflicts: MigrationFinding[];\n}\n\n/**\n * Move legacy `.claude/.sidekick-*` state files to the canonical\n * `.claude/.semantic-memory/<name>` paths.\n *\n * Behavior per file:\n *  - old exists, new does not       → MIGRATE: rename old to new\n *  - old does not exist             → SKIP (skipped-no-source)\n *  - old does not exist, new exists → SKIP (skipped-already-migrated)\n *  - both old and new exist         → CONFLICT (refused without --force)\n *                                     With --force: prefer new, delete old\n *\n * Idempotent: a second run after a successful migration is all-no-ops.\n */\nexport function migrateState(opts: MigrateStateOptions): MigrateStateResult {\n  const result: MigrateStateResult = {\n    migrated: [],\n    skipped: [],\n    conflicts: [],\n  };\n\n  const stateDir = join(opts.projectRoot, \".claude\", \".semantic-memory\");\n  if (!opts.dryRun && !existsSync(stateDir)) {\n    mkdirSync(stateDir, { recursive: true });\n  }\n\n  for (const m of STATE_MIGRATIONS) {\n    const oldPath = join(opts.projectRoot, \".claude\", m.old);\n    const newPath = join(opts.projectRoot, \".claude\", m.new);\n    const oldExists = existsSync(oldPath);\n    const newExists = existsSync(newPath);\n\n    if (!oldExists && !newExists) {\n      result.skipped.push({ name: m.name, status: \"skipped-no-source\", oldPath, newPath, detail: \"neither path exists\" });\n      continue;\n    }\n    if (!oldExists && newExists) {\n      result.skipped.push({ name: m.name, status: \"skipped-already-migrated\", oldPath, newPath, detail: \"already at new path\" });\n      continue;\n    }\n    if (oldExists && newExists) {\n      if (!opts.force) {\n        const oldMtime = safeMtime(oldPath);\n        const newMtime = safeMtime(newPath);\n        result.conflicts.push({\n          name: m.name,\n          status: \"conflict\",\n          oldPath,\n          newPath,\n          detail: `both paths exist (old: ${oldMtime}, new: ${newMtime}); pass --force to keep new and delete old`,\n        });\n        continue;\n      }\n      // --force: prefer new, delete old\n      if (!opts.dryRun) {\n        try { unlinkSync(oldPath); } catch (e: any) {\n          result.conflicts.push({ name: m.name, status: \"conflict\", oldPath, newPath, detail: `force-delete of old failed: ${e?.message ?? e}` });\n          continue;\n        }\n      }\n      result.migrated.push({\n        name: m.name,\n        status: \"resolved-by-force\",\n        oldPath,\n        newPath,\n        detail: opts.dryRun ? \"dry-run: would delete old\" : \"old deleted; new preserved\",\n      });\n      continue;\n    }\n    // oldExists && !newExists → migrate\n    if (!opts.dryRun) {\n      try { renameSync(oldPath, newPath); } catch (e: any) {\n        // Cross-device rename failure is theoretically possible; for state files all\n        // under .claude/, both paths are 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package/dist/core/index.d.ts

@@ -252,7 +252,7 @@ interface VaultSchema {
 type Severity$1 = "warn" | "error";
 interface LintFinding {
     path: string;
-    rule: "missing_provenance" | "stale" | "schema_violations" | "broken_links";
+    rule: "missing_provenance" | "stale" | "schema_violations" | "broken_links" | "code_symbols" | "decay_candidates" | "alias_conflicts" | "decoys";
     severity: Severity$1;
     message: string;
 }
@@ -443,6 +443,8 @@ interface SynthesizeNoteInput {
     decision_maker?: string;
     decided_on?: string;
     severity?: string;
+    /** Verbatim symptom phrases (the user's own words) — symptom-keyed for retrieval. */
+    symptoms?: string[];
     extra_frontmatter?: Record<string, unknown>;
     /**
      * When true, the resulting note is filed under `proposals/<date>-<slug>.md` with
@@ -524,6 +526,10 @@ interface LintReport {
         missing_provenance: LintFinding[];
         stale: LintFinding[];
         broken_links: LintFinding[];
+        code_symbols: LintFinding[];
+        decay_candidates: LintFinding[];
+        alias_conflicts: LintFinding[];
+        decoys: LintFinding[];
     };
     counts: {
         errors: number;
@@ -535,6 +541,37 @@ declare function lintVault(notesPath: string, opts?: {
     pathGlob?: string;
     schemaOverride?: VaultSchema;
     todayIso?: string;
+    /**
+     * When true, run the code-symbol drift check: flag inline-code file-path
+     * references in notes that no longer exist under the project root. Opt-in
+     * (off by default) so the standard report and the healthcheck slow tier stay
+     * quiet and byte-stable. Fails open when the project root is not a code repo.
+     */
+    checkCodeSymbols?: boolean;
+    /** Override the project root for code-symbol resolution (default: derived from notesPath). */
+    projectRoot?: string;
+    /**
+     * When true, run the decay-candidates check: cross-reference the selection
+     * log (notes that appeared in recent search results) against each note's
+     * current decay multiplier, and flag notes that are frequently retrieved yet
+     * heavily decayed ("relevant but going stale — verify or revise"). Opt-in;
+     * a silent no-op when no selection log exists.
+     */
+    checkDecayCandidates?: boolean;
+    /**
+     * When true, run the alias-conflict check: flag lexicon phrases that map to
+     * more than one canonical target (a wrong binding misroutes queries). Opt-in;
+     * no-op when the vault has no lexicon.
+     */
+    checkAliasConflicts?: boolean;
+    /**
+     * When true, run the decoys check: flag notes that were retrieved often (per
+     * the selection log) but NEVER cited in an answer. Surfaced for a human to
+     * judge — a decoy might be genuine noise OR a note the answers were wrong to
+     * skip; usage-feedback ranking (v1.5) never auto-down-ranks on this ambiguous
+     * signal (decision Q5). Opt-in; a no-op with no selection log.
+     */
+    checkDecoys?: boolean;
 }): Promise<LintReport>;
 declare function formatLintReport(report: LintReport, opts?: {
     rule?: keyof LintReport["byRule"];
@@ -704,7 +741,7 @@ interface DriftFinding {
     severity: Severity;
     summary: string;
     detail?: string;
-    fixable_via?: "skill-link" | "mcp-reconcile" | "regenerate-contract" | "reindex" | "none";
+    fixable_via?: "skill-link" | "mcp-reconcile" | "regenerate-contract" | "reindex" | "state-migrate" | "none";
 }
 interface HealthcheckResult {
     tier_run: Tier;

package/dist/core/index.js

@@ -2,26 +2,35 @@ import {
   filterToDrift,
   formatDriftBanner,
   runHealthcheck
-} from "../chunk-EVAJGOCB.js";
+} from "../chunk-2EELGTLX.js";
 import {
   FrontmatterManager,
   INDEX_FILE,
   INDEX_OVERFLOW_THRESHOLD,
   NoteCrud,
-  SessionManager,
   TagManager,
   Watcher,
   applyPatch,
   buildIngestChangeSet,
   buildPromoteChangeSet,
   buildSynthesizeChangeSet,
-  deriveProjectRoot,
-  deriveSessionDir,
   inspectAgentsContract,
   regenDirectoryIndex,
   regenIndexesForPaths,
   regenerateAgentsContract
-} from "../chunk-CYWPDFNI.js";
+} from "../chunk-CSXZ7QUU.js";
+import {
+  formatLintReport,
+  lintVault
+} from "../chunk-FM26NFTR.js";
+import "../chunk-NTYYS53O.js";
+import "../chunk-A3KYHKB5.js";
+import "../chunk-WSU4QIPB.js";
+import {
+  SessionManager,
+  deriveProjectRoot,
+  deriveSessionDir
+} from "../chunk-S4KW7VH4.js";
 import {
   Embedder,
   GraphBuilder,
@@ -30,20 +39,17 @@ import {
 } from "../chunk-25EIQWXL.js";
 import {
   Indexer
-} from "../chunk-HODDRXJK.js";
+} from "../chunk-V45NJIHI.js";
 import {
   logEvent,
   logQuery
 } from "../chunk-JPQHNG3R.js";
-import {
-  formatLintReport,
-  lintVault
-} from "../chunk-CAN2GWUG.js";
 import {
   installDefaultSchema,
   loadSchema,
   validateNote
-} from "../chunk-E2Z4J4MK.js";
+} from "../chunk-OWZWMB4P.js";
+import "../chunk-5ZKNO6ZD.js";
 import "../chunk-PZ5AY32C.js";
 export {
   Embedder,

package/dist/decay-ELJUKVQG.js

@@ -0,0 +1,14 @@
+import {
+  DEFAULT_DECAY_CONFIG,
+  computeDecay,
+  loadDecayConfig,
+  normalizeVerifiedDate
+} from "./chunk-5ZKNO6ZD.js";
+import "./chunk-PZ5AY32C.js";
+export {
+  DEFAULT_DECAY_CONFIG,
+  computeDecay,
+  loadDecayConfig,
+  normalizeVerifiedDate
+};
+//# sourceMappingURL=decay-ELJUKVQG.js.map

package/dist/dossier-2UG724LB.js

@@ -0,0 +1,39 @@
+import {
+  DOSSIER_DIR,
+  DOSSIER_SECTIONS,
+  appendIncident,
+  appendToSection,
+  compileDossiers,
+  dossierTemplate,
+  findDossier,
+  initDossier,
+  listDossiers,
+  loadDossierCache,
+  normalizeEntity,
+  replaceSectionBody,
+  resolveDossierForQuery,
+  resolveDossierPath,
+  setCurrentState,
+  slugifyEntity
+} from "./chunk-WSU4QIPB.js";
+import "./chunk-S4KW7VH4.js";
+import "./chunk-PZ5AY32C.js";
+export {
+  DOSSIER_DIR,
+  DOSSIER_SECTIONS,
+  appendIncident,
+  appendToSection,
+  compileDossiers,
+  dossierTemplate,
+  findDossier,
+  initDossier,
+  listDossiers,
+  loadDossierCache,
+  normalizeEntity,
+  replaceSectionBody,
+  resolveDossierForQuery,
+  resolveDossierPath,
+  setCurrentState,
+  slugifyEntity
+};
+//# sourceMappingURL=dossier-2UG724LB.js.map