npm - @theglitchking/semantic-memory - Versions diffs - 1.1.0 → 1.1.1 - Mend

@theglitchking/semantic-memory 1.1.0 → 1.1.1

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Files changed (16) hide show

package/.claude-plugin/marketplace.json +2 -2
package/CHANGELOG.md +28 -0
package/commands/healthcheck.md +1 -1
package/commands/mode.md +3 -3
package/commands/normalize-config.md +1 -1
package/commands/policy.md +4 -4
package/commands/relink.md +1 -1
package/commands/status.md +1 -1
package/commands/update.md +2 -2
package/dist/cli/index.js +30 -17
package/dist/cli/index.js.map +1 -1
package/hooks/reconcile.js +39 -10
package/hooks/session-start.js +7 -7
package/hooks/vault-context.js +11 -5
package/package.json +1 -1
package/scripts/link-skills.js +5 -5

package/.claude-plugin/marketplace.json CHANGED Viewed

@@ -6,13 +6,13 @@
   },
   "metadata": {
     "description": "Single-plugin marketplace for semantic-memory — the unified memory-layer plugin. v1.1.0 absorbs brain's strengths: AGENTS.md contract artifact, hard-gated verification sessions, multi-agent skill bundler (codex/copilot/pi), and SessionStart drift detection — all backwards-compatible with v1.0.x via deprecation shims.",
-    "version": "1.1.0"
+    "version": "1.1.1"
   },
   "plugins": [
     {
       "name": "semantic-memory",
       "description": "Unified memory-layer plugin for Claude Code. One MCP server, 40 tools across multi-corpus search/read/write/graph/lint/sessions/contract. v1.1.0 adds: AGENTS.md contract artifact, hard-gated verification sessions (session_start/run/finish/status), proposal-mode synthesize_note + synthesize_promote, multi-agent skill bundler (codex/copilot/pi via the new `skills` CLI), and SessionStart drift detection. Backwards-compatible with v1.0.x — every previous tool name remains callable through deprecation shims (removed in v2.0.0).",
-      "version": "1.1.0",
+      "version": "1.1.1",
       "author": {
         "name": "TheGlitchKing"
       },

package/CHANGELOG.md CHANGED Viewed

@@ -2,6 +2,34 @@
 All notable changes to semantic-memory (formerly semantic-sidekick) will be documented here.
+## [1.1.1] - 2026-05-08 — Hotfix: complete the rebrand wiring
+v1.1.0 published with the rebrand-to-`semantic-memory` half-finished: the npm package, marketplace entry, and tool surface all moved to the new name, but the postinstall, SessionStart reconcile, slash commands, and CLI helpers were still hardcoded to the legacy `@theglitchking/semantic-sidekick` package path. Fresh `npm install @theglitchking/semantic-memory@1.1.0` installs failed to register hooks correctly and slash commands hit ancient code from the legacy npm package (still on the registry at 0.2.x).
+### Fixed
+- **Postinstall (`scripts/link-skills.js`)** — `runPostinstall` now passes `packageName: "@theglitchking/semantic-memory"`, `pluginName: "semantic-memory"`, and `hookCommand` pointing at the new node_modules path. Hooks now register correctly on fresh installs.
+- **SessionStart reconcile (`hooks/reconcile.js`)** — `findLocalBin` checks the rebranded package path first, falls back to the legacy path for machines mid-migration. `isOurEntry` recognizes both old and new shapes when removing stale `.mcp.json` entries.
+- **SessionStart hook (`hooks/session-start.js`)** — `runSessionStart` delegate now passes the new package name + plugin name + config file.
+- **vault-context hook (`hooks/vault-context.js`)** — vault path discovery now matches `semantic-memory` server entries in `.mcp.json` (was only matching `semantic-vault` and `semantic-sidekick`). CLI bin discovery prefers the new path with legacy fallback.
+- **Slash commands** — all 7 (`/healthcheck`, `/status`, `/normalize-config`, `/policy`, `/mode`, `/update`, `/relink`) now invoke `@theglitchking/semantic-memory` instead of the legacy package.
+- **CLI helpers (`src/cli/index.ts`)** — `PKG_NAME`, `findLocalBin`, `runRelink`, `isLocalForm` updated. Error messages reference the new path. `registerUpdateCommands` passes the new plugin name + config file.
+### Storage paths preserved (unchanged)
+- `<vault>/.semantic-sidekick-index/` — vector index location, kept for backwards-compat with existing v1.0.x indices
+- `~/.semantic-sidekick/models/` — model cache location, kept for backwards-compat
+These intentionally retain the legacy `semantic-sidekick` name in the path — renaming would invalidate every existing user's index and force a re-download of the embedding model. The path-name mismatch with the package name is a one-time cost; we eat it.
+### Backwards compatibility
+All legacy fallbacks preserved. Users with `@theglitchking/semantic-sidekick` still installed (from v0.x or v1.0 pre-rebrand) continue to work — `findLocalBin`, `runRelink`, hook discovery, and `isOurEntry` all check both paths. The DOCS_KEY entry name in `.mcp.json` stays as `"semantic-sidekick"` for existing-user compatibility.
+### How v1.1.0 slipped through
+Phase 9's automated validation ran tests against `createServer()` directly with in-memory MCP clients — it never simulated a fresh `npm install` from the published tarball. The bug only fires at install time and slash-command invocation time, both of which were on the manual-smoke-deferred list. The hotfix re-emphasizes that "manual smoke against an existing v1.0.x install" needs to happen BEFORE publish, not after.
 ## [1.1.0] - 2026-05-08 — brain-absorption
 Adapts four targeted strengths from `JimmyMcBride/brain` into semantic-memory: AGENTS.md contract artifact, hard-gated verification sessions, multi-agent skill bundler, distill/synthesize unification — plus a server.ts refactor that makes future additions cheap, a deprecation-shimmed tool consolidation, and an opt-in SessionStart drift-detection layer.

package/commands/healthcheck.md CHANGED Viewed

@@ -10,7 +10,7 @@ When the user runs `/healthcheck`:
 The fast-tier auto-check also runs on every `SessionStart` via `vault-context.js` — healthy installs see nothing at session start, drifted installs see a one-block warning with a pointer to this command.
-Implementation: shell out to `node ./node_modules/@theglitchking/semantic-sidekick/bin/semantic-sidekick healthcheck [--fast]` (or `npx --no @theglitchking/semantic-sidekick healthcheck [--fast]` if no local install).
+Implementation: shell out to `node ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory healthcheck [--fast]` (or `npx --no @theglitchking/semantic-memory healthcheck [--fast]` if no local install). Falls back to the legacy `@theglitchking/semantic-sidekick` package on machines mid-migration.
 Drift findings are categorized by check:
 - `mcp_json_entry` — `.mcp.json` missing the semantic-memory server entry. Fix: `/normalize-config`.

package/commands/mode.md CHANGED Viewed

@@ -1,12 +1,12 @@
 ---
-description: Set or query the active semantic-sidekick mode (vault-first | research | outage-silence)
+description: Set or query the active semantic-memory mode (vault-first | research | outage-silence)
 argument-hint: "[research|vault-first|outage-silence|status]"
 allowed-tools: Bash(cat:*), Bash(cp:*), Bash(test:*), Bash(node:*), Read, Write
 ---
-# /mode — semantic-sidekick mode control
+# /mode — semantic-memory mode control
-The user invoked `/mode $ARGUMENTS`. This is the explicit ground-truth override for the semantic-sidekick routing layer.
+The user invoked `/mode $ARGUMENTS`. This is the explicit ground-truth override for the semantic-memory routing layer.
 ## Your job

package/commands/normalize-config.md CHANGED Viewed

@@ -3,4 +3,4 @@ description: Rewrite fragile npx-@latest entries in .mcp.json to the stable node
 allowed-tools: Bash(npx:*)
 ---
-Run `npx --no @theglitchking/semantic-sidekick normalize-config` and report the result to the user. Mention that `.mcp.json.bak` was created as a safety backup, and that the MCPs need to be toggled in `/mcp` to pick up the change.
+Run `npx --no @theglitchking/semantic-memory normalize-config` and report the result to the user. Mention that `.mcp.json.bak` was created as a safety backup, and that the MCPs need to be toggled in `/mcp` to pick up the change.

package/commands/policy.md CHANGED Viewed

@@ -1,16 +1,16 @@
 ---
-description: Get or set the semantic-sidekick update policy (auto | nudge | off)
+description: Get or set the semantic-memory update policy (auto | nudge | off)
 allowed-tools: Bash(npx:*)
 argument-hint: "[auto|nudge|off]"
 ---
 Arguments: $ARGUMENTS
-- If `$ARGUMENTS` is empty, run `npx --no @theglitchking/semantic-sidekick policy` and report the current policy and config path.
-- If `$ARGUMENTS` is one of `auto`, `nudge`, `off`, run `npx --no @theglitchking/semantic-sidekick policy $ARGUMENTS` and confirm the new setting to the user.
+- If `$ARGUMENTS` is empty, run `npx --no @theglitchking/semantic-memory policy` and report the current policy and config path.
+- If `$ARGUMENTS` is one of `auto`, `nudge`, `off`, run `npx --no @theglitchking/semantic-memory policy $ARGUMENTS` and confirm the new setting to the user.
 - If `$ARGUMENTS` is anything else, tell the user the valid values are `auto`, `nudge`, `off`.
 Policies:
-- `auto`  — auto-run `npm update @theglitchking/semantic-sidekick` at session start when a newer version is available.
+- `auto`  — auto-run `npm update @theglitchking/semantic-memory` at session start when a newer version is available.
 - `nudge` — print a one-liner when a newer version is available (default).
 - `off`   — do not check for updates.

package/commands/relink.md CHANGED Viewed

@@ -3,4 +3,4 @@ description: Re-run the skill linker — refresh symlinks from node_modules into
 allowed-tools: Bash(npx:*)
 ---
-Run `npx --no @theglitchking/semantic-sidekick relink` and report the result.
+Run `npx --no @theglitchking/semantic-memory relink` and report the result.

package/commands/status.md CHANGED Viewed

@@ -3,4 +3,4 @@ description: Show installed version, latest available version, current update po
 allowed-tools: Bash(npx:*)
 ---
-Run `npx --no @theglitchking/semantic-sidekick status` and relay the output to the user verbatim.
+Run `npx --no @theglitchking/semantic-memory status` and relay the output to the user verbatim.

package/commands/update.md CHANGED Viewed

@@ -1,6 +1,6 @@
 ---
-description: Update semantic-sidekick to the latest version (runs npm update + re-links skills)
+description: Update semantic-memory to the latest version (runs npm update + re-links skills)
 allowed-tools: Bash(npx:*)
 ---
-Run `npx --no @theglitchking/semantic-sidekick update` and report the before/after versions to the user. If the project doesn't have a local install, fall back to `npx -y @theglitchking/semantic-sidekick update` and note that in your summary.
+Run `npx --no @theglitchking/semantic-memory update` and report the before/after versions to the user. If the project doesn't have a local install, fall back to `npx -y @theglitchking/semantic-memory update` and note that in your summary.

package/dist/cli/index.js CHANGED Viewed

@@ -181,11 +181,16 @@ var SKILL_BUNDLER_AGENTS = ["claude", "codex", "copilot", "pi"];
 // src/cli/index.ts
 var require_ = createRequire(import.meta.url);
 var { version } = require_("../../package.json");
-var PKG_NAME = "@theglitchking/semantic-sidekick";
+var PKG_NAME = "@theglitchking/semantic-memory";
+var LEGACY_PKG_NAME = "@theglitchking/semantic-sidekick";
 function runRelink(cwd) {
-  const linker = join2(cwd, "node_modules", "@theglitchking", "semantic-sidekick", "scripts", "link-skills.js");
-  const script = existsSync2(linker) ? linker : resolve2(process.cwd(), "scripts", "link-skills.js");
-  if (!existsSync2(script)) {
+  const candidates = [
+    join2(cwd, "node_modules", "@theglitchking", "semantic-memory", "scripts", "link-skills.js"),
+    join2(cwd, "node_modules", "@theglitchking", "semantic-sidekick", "scripts", "link-skills.js"),
+    resolve2(process.cwd(), "scripts", "link-skills.js")
+  ];
+  const script = candidates.find((p) => existsSync2(p));
+  if (!script) {
     console.error("link-skills.js not found \u2014 is the package installed?");
     return;
   }
@@ -196,8 +201,14 @@ function runRelink(cwd) {
   });
 }
 function findLocalBin(cwd) {
-  const p = join2(cwd, "node_modules", "@theglitchking", "semantic-sidekick", "bin", "semantic-sidekick");
-  return existsSync2(p) ? p : null;
+  const candidates = [
+    join2(cwd, "node_modules", "@theglitchking", "semantic-memory", "bin", "semantic-memory"),
+    join2(cwd, "node_modules", "@theglitchking", "semantic-sidekick", "bin", "semantic-sidekick")
+  ];
+  for (const p of candidates) {
+    if (existsSync2(p)) return p;
+  }
+  return null;
 }
 function localBinArg(cwd) {
   const abs = findLocalBin(cwd);
@@ -217,7 +228,9 @@ function isNpxForm(entry) {
   if (!entry || typeof entry !== "object") return false;
   const cmd = entry.command;
   const args = Array.isArray(entry.args) ? entry.args : [];
-  return cmd === "npx" && args.some((a) => typeof a === "string" && a.includes(PKG_NAME));
+  return cmd === "npx" && args.some(
+    (a) => typeof a === "string" && (a.includes(PKG_NAME) || a.includes(LEGACY_PKG_NAME))
+  );
 }
 function extractNotesPath(entry) {
   const args = Array.isArray(entry?.args) ? entry.args : [];
@@ -390,7 +403,7 @@ var TOOL_CATEGORIES = {
 function printToolList() {
   console.log("\nSemantic Pages \u2014 21 MCP Tools\n");
   console.log("Usage: These tools are available via MCP when the server is running.");
-  console.log("       Run `semantic-sidekick tools <name>` for details on a specific tool.\n");
+  console.log("       Run `semantic-memory tools <name>` for details on a specific tool.\n");
   for (const [category, tools] of Object.entries(TOOL_CATEGORIES)) {
     console.log(`  ${category}:`);
     for (const name of tools) {
@@ -399,13 +412,13 @@ function printToolList() {
     }
     console.log();
   }
-  console.log("Run `semantic-sidekick tools <tool-name>` for arguments and examples.");
+  console.log("Run `semantic-memory tools <tool-name>` for arguments and examples.");
 }
 function printToolDetail(name) {
   const tool = TOOL_HELP[name];
   if (!tool) {
     console.error(`Unknown tool: ${name}`);
-    console.error(`Run \`semantic-sidekick tools\` to see all available tools.`);
+    console.error(`Run \`semantic-memory tools\` to see all available tools.`);
     process.exit(1);
   }
   console.log(`
@@ -552,8 +565,8 @@ program.command("serve", { isDefault: true }).description("Start the MCP server
 });
 registerUpdateCommands(program, {
   packageName: PKG_NAME,
-  pluginName: "semantic-sidekick",
-  configFile: "semantic-sidekick.json",
+  pluginName: "semantic-memory",
+  configFile: "semantic-memory.json",
   onAfterUpdate: (cwd) => runRelink(cwd)
 });
 program.command("normalize-config").description(
@@ -573,8 +586,8 @@ program.command("normalize-config").description(
   const bin = localBinArg(cwd);
   if (!bin) {
     console.error(
-      `no local install found at ./node_modules/@theglitchking/semantic-sidekick/bin/semantic-sidekick.
-run 'npm install --save @theglitchking/semantic-sidekick' first, then re-run this command.`
+      `no local install found at ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory (or the legacy semantic-sidekick path).
+run 'npm install --save @theglitchking/semantic-memory' first, then re-run this command.`
     );
     process.exit(1);
   }
@@ -627,8 +640,8 @@ program.command("healthcheck").description(
   const cwd = process.cwd();
   const bin = findLocalBin(cwd);
   if (!bin) {
-    console.error(`no local install at ./node_modules/@theglitchking/semantic-sidekick/bin/semantic-sidekick`);
-    console.error(`run 'npm install --save @theglitchking/semantic-sidekick' to install.`);
+    console.error(`no local install at ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory (or legacy semantic-sidekick path)`);
+    console.error(`run 'npm install --save @theglitchking/semantic-memory' to install.`);
     process.exit(1);
   }
   const mcpPath = join2(cwd, ".mcp.json");
@@ -641,7 +654,7 @@ program.command("healthcheck").description(
         `\u26A0\uFE0F  .mcp.json uses the fragile npx-@latest form for: ${fragile.join(", ")}`
       );
       console.warn(`   Rewrite to the stable form:`);
-      console.warn(`     npx --no @theglitchking/semantic-sidekick normalize-config`);
+      console.warn(`     npx --no @theglitchking/semantic-memory normalize-config`);
     }
   }
   const r = spawnSync("node", [bin, "--version"], { cwd, stdio: "pipe", timeout: 15e3 });

package/dist/cli/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"sources":["../../src/cli/index.ts","../../src/cli/skills.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\";\n\nconst require_ = createRequire(import.meta.url);\nconst { version } = require_(\"../../package.json\") as { version: string };\n\nconst PKG_NAME = \"@theglitchking/semantic-sidekick\";\n\nfunction runRelink(cwd: string) {\n const linker = join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-sidekick\", \"scripts\", \"link-skills.js\");\n const script = existsSync(linker) ? linker : resolve(process.cwd(), \"scripts\", \"link-skills.js\");\n if (!existsSync(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 p = join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-sidekick\", \"bin\", \"semantic-sidekick\");\n return existsSync(p) ? p : 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 cmd === \"npx\" && args.some((a: unknown) => typeof a === \"string\" && a.includes(PKG_NAME));\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((a: unknown) => typeof a === \"string\" && a.includes(\"node_modules/@theglitchking/semantic-sidekick\"))\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-sidekick 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-sidekick 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-sidekick 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-sidekick\",\n configFile: \"semantic-sidekick.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-sidekick/bin/semantic-sidekick.\\n` +\n `run 'npm install --save @theglitchking/semantic-sidekick' 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-sidekick/bin/semantic-sidekick`);\n console.error(`run 'npm install --save @theglitchking/semantic-sidekick' 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: ${fragile.join(\", \")}`,\n );\n console.warn(` Rewrite to the stable form:`);\n console.warn(` npx --no @theglitchking/semantic-sidekick normalize-config`);\n }\n }\n\n // 2. Smoke-test the local bin.\n const r = spawnSync(\"node\", [bin, \"--version\"], { cwd, stdio: \"pipe\", timeout: 15_000 });\n if (r.status === 0) {\n console.log(`✓ local install starts cleanly (v${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\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\", 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1	+ {"version":3,"sources":["../../src/cli/index.ts","../../src/cli/skills.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\";\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\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\", 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package/hooks/reconcile.js CHANGED Viewed

@@ -1,11 +1,11 @@
-// Plugin-specific SessionStart reconciliation for semantic-sidekick.
+// Plugin-specific SessionStart reconciliation for semantic-memory.
 //
 // Responsibilities (all conservative — the user's config always wins):
 //   1. Ensure <project>/.claude/.vault exists.
 //   2. If .mcp.json is missing a "semantic-vault" entry AND the package is
 //      installed locally, add one in the node-against-node_modules form.
 //      Existing entries (any shape) are preserved — if you want to rewrite
-//      a stale entry, run `npx --no @theglitchking/semantic-sidekick
+//      a stale entry, run `npx --no @theglitchking/semantic-memory
 //      normalize-config`.
 //   3. If hit-em-with-the-docs is enabled AND ./.documentation exists,
 //      conditionally add a read-only "semantic-sidekick" entry pointed at
@@ -15,14 +15,23 @@
 // Any write is preceded by a backup to .mcp.json.bak. Never writes the
 // `npx @latest` form — that shape is fragile (npx cache corruption causes
 // ERR_MODULE_NOT_FOUND) and was the root cause of the 0.10.0 bugfix.
+//
+// Package-name resolution (post-1.1.1):
+//   Prefer the rebranded `@theglitchking/semantic-memory`. Fall back to the
+//   legacy `@theglitchking/semantic-sidekick` if the new package isn't
+//   installed — supports machines mid-migration. The DOCS_KEY entry name
+//   stays "semantic-sidekick" for backwards-compat with existing .mcp.json
+//   entries; renaming it would orphan user state without offering a
+//   meaningful behavioral upgrade.
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { dirname, join, relative } from "node:path";
-const PKG = "@theglitchking/semantic-sidekick";
+const PKG = "@theglitchking/semantic-memory";
+const LEGACY_PKG = "@theglitchking/semantic-sidekick";
 const VAULT_KEY = "semantic-vault";
-const DOCS_KEY = "semantic-sidekick";
+const DOCS_KEY = "semantic-sidekick"; // preserved for backwards-compat with existing .mcp.json entries
 function readJson(path, fallback = null) {
   try {
@@ -55,10 +64,24 @@ function hewtdEnabled(projectRoot) {
   return false;
 }
-/** Absolute path to the locally-installed bin script, or null. */
+/**
+ * Absolute path to the locally-installed bin script, or null.
+ *
+ * Prefers the rebranded @theglitchking/semantic-memory package. Falls back to
+ * the legacy @theglitchking/semantic-sidekick install for machines that
+ * haven't migrated yet.
+ */
 export function findLocalBin(projectRoot) {
-  const p = join(projectRoot, "node_modules", "@theglitchking", "semantic-sidekick", "bin", "semantic-sidekick");
-  return existsSync(p) ? p : null;
+  const candidates = [
+    // Rebranded package (preferred)
+    join(projectRoot, "node_modules", "@theglitchking", "semantic-memory", "bin", "semantic-memory"),
+    // Legacy package (fallback for in-progress migrations)
+    join(projectRoot, "node_modules", "@theglitchking", "semantic-sidekick", "bin", "semantic-sidekick"),
+  ];
+  for (const p of candidates) {
+    if (existsSync(p)) return p;
+  }
+  return null;
 }
 /** Returns the arg form that goes into .mcp.json for this project. */
@@ -82,6 +105,7 @@ function buildEntry(binArgStr, notesPath, extraArgs = []) {
  * Detect an entry as "one of ours" so we can safely remove it when the
  * condition that created it no longer holds. Matches both shapes we've ever
  * written: the legacy npx-form and the new node-against-node_modules form.
+ * Both rebranded and legacy package paths are recognized.
  */
 function isOurEntry(entry, notesPath) {
   if (!entry || typeof entry !== "object") return false;
@@ -90,11 +114,16 @@ function isOurEntry(entry, notesPath) {
   const argStr = args.map((a) => String(a)).join(" ");
   // Legacy npx form we shipped in 0.8.0 and prior SessionStart hooks.
-  if (cmd === "npx" && argStr.includes(PKG) && argStr.includes(notesPath)) return true;
+  if (cmd === "npx" && (argStr.includes(PKG) || argStr.includes(LEGACY_PKG)) && argStr.includes(notesPath)) return true;
   // Current node-against-node_modules form (0.10.0+).
   if (
     cmd === "node" &&
-    args.some((a) => typeof a === "string" && a.includes("node_modules/@theglitchking/semantic-sidekick")) &&
+    args.some(
+      (a) =>
+        typeof a === "string" &&
+        (a.includes("node_modules/@theglitchking/semantic-memory") ||
+          a.includes("node_modules/@theglitchking/semantic-sidekick"))
+    ) &&
     argStr.includes(notesPath)
   ) {
     return true;
@@ -126,7 +155,7 @@ export function reconcile(projectRoot) {
       let raw = "";
       try { raw = readFileSync(mcpPath, "utf8"); } catch {}
       if (raw.trim()) {
-        process.stderr.write(`semantic-sidekick hook: could not parse ${mcpPath}; leaving untouched\n`);
+        process.stderr.write(`semantic-memory hook: could not parse ${mcpPath}; leaving untouched\n`);
         return;
       }
     } else if (parsed && typeof parsed === "object") {

package/hooks/session-start.js CHANGED Viewed

@@ -1,5 +1,5 @@
 #!/usr/bin/env node
-// semantic-sidekick SessionStart hook.
+// semantic-memory SessionStart hook.
 //
 // Critical path (zero external deps): run reconcile.js to wire .mcp.json +
 // create .claude/.vault. This ALWAYS runs, even if the plugin is installed
@@ -32,7 +32,7 @@ async function main() {
   try {
     await reconcile(projectRoot);
   } catch (err) {
-    process.stderr.write(`[semantic-sidekick] reconcile failed: ${err?.message || err}\n`);
+    process.stderr.write(`[semantic-memory] reconcile failed: ${err?.message || err}\n`);
   }
   // 2. Optional runtime-backed update check. Skip silently if the runtime
@@ -45,9 +45,9 @@ async function main() {
       // that's idempotent (reconcile writes only what's missing), so the
       // double-invocation is harmless. We return early to avoid double-emit.
       await mod.runSessionStart({
-        packageName: "@theglitchking/semantic-sidekick",
-        pluginName: "semantic-sidekick",
-        configFile: "semantic-sidekick.json",
+        packageName: "@theglitchking/semantic-memory",
+        pluginName: "semantic-memory",
+        configFile: "semantic-memory.json",
         reconcile,
       });
       return;
@@ -57,7 +57,7 @@ async function main() {
     // resolvable. Any other error gets logged but doesn't block the session.
     const msg = String(err?.message || err);
     if (!msg.includes("Cannot find package") && !msg.includes("ERR_MODULE_NOT_FOUND")) {
-      process.stderr.write(`[semantic-sidekick] runtime import failed: ${msg}\n`);
+      process.stderr.write(`[semantic-memory] runtime import failed: ${msg}\n`);
     }
   }
@@ -75,7 +75,7 @@ function emit(additionalContext) {
 }
 main().catch((err) => {
-  process.stderr.write(`[semantic-sidekick] session-start.js fatal: ${err?.message || err}\n`);
+  process.stderr.write(`[semantic-memory] session-start.js fatal: ${err?.message || err}\n`);
   // Still emit — never block the session.
   emit();
 });

package/hooks/vault-context.js CHANGED Viewed

@@ -53,7 +53,7 @@ function findVaultPath(projectRoot) {
       const entries = data?.mcpServers || {};
       for (const [name, entry] of Object.entries(entries)) {
         if (!entry || typeof entry !== "object") continue;
-        if (name !== "semantic-vault" && name !== "semantic-sidekick") continue;
+        if (name !== "semantic-vault" && name !== "semantic-sidekick" && name !== "semantic-memory") continue;
         const args = Array.isArray(entry.args) ? entry.args : [];
         const i = args.indexOf("--notes");
         if (i >= 0 && i + 1 < args.length) {
@@ -71,9 +71,15 @@ function findVaultPath(projectRoot) {
 }
 function findCliBin(projectRoot) {
-  // Prefer local installed bin (when sidekick is a dependency)
-  const installed = join(projectRoot, "node_modules", "@theglitchking", "semantic-sidekick", "bin", "semantic-sidekick");
-  if (existsSync(installed)) return installed;
+  // Prefer local installed bin. Try the rebranded package first; fall back to the
+  // legacy semantic-sidekick path for machines mid-migration.
+  const candidates = [
+    join(projectRoot, "node_modules", "@theglitchking", "semantic-memory", "bin", "semantic-memory"),
+    join(projectRoot, "node_modules", "@theglitchking", "semantic-sidekick", "bin", "semantic-sidekick"),
+  ];
+  for (const p of candidates) {
+    if (existsSync(p)) return p;
+  }
   // Dev fallback: this hook lives in <repo>/hooks/, the built CLI is at <repo>/dist/cli/index.js
   const dev = resolve(new URL("../dist/cli/index.js", import.meta.url).pathname);
   if (existsSync(dev)) return dev;
@@ -130,7 +136,7 @@ export function formatContextBlock(source, query, hits) {
   if (!hits || hits.length === 0) return "";
   const lines = [];
   lines.push(`<vault-context source="${source}" query="${escapeAttr(query)}">`);
-  lines.push(`The vault (semantic-sidekick) was proactively searched. Top hits:`);
+  lines.push(`The vault (semantic-memory) was proactively searched. Top hits:`);
   lines.push("");
   for (const h of hits.slice(0, 6)) {
     const score = typeof h.score === "number" ? h.score.toFixed(2) : "";

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@theglitchking/semantic-memory",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "description": "Unified memory-layer plugin for Claude Code. One MCP server, multiple typed corpora (vault, code, plans, docs, research, project-map), unified cross-corpus knowledge graph, conditional tool registration, in-process drift detection, and human↔code translation. Rebrand of @theglitchking/semantic-sidekick at v1.0 — see CHANGELOG for migration.",
   "type": "module",
   "main": "./dist/core/index.js",

package/scripts/link-skills.js CHANGED Viewed

@@ -12,14 +12,14 @@ const packageRoot = resolve(dirname(fileURLToPath(import.meta.url)), "..");
 try {
   runPostinstall({
-    packageName: "@theglitchking/semantic-sidekick",
-    pluginName: "semantic-sidekick",
-    configFile: "semantic-sidekick.json",
+    packageName: "@theglitchking/semantic-memory",
+    pluginName: "semantic-memory",
+    configFile: "semantic-memory.json",
     skillsDir: "skills",
     packageRoot,
     hookCommand:
-      "node ./node_modules/@theglitchking/semantic-sidekick/hooks/session-start.js",
+      "node ./node_modules/@theglitchking/semantic-memory/hooks/session-start.js",
   });
 } catch (err) {
-  console.warn(`[semantic-sidekick] postinstall failed: ${err?.message || err}`);
+  console.warn(`[semantic-memory] postinstall failed: ${err?.message || err}`);
 }