@theglitchking/semantic-pages 0.6.6 → 0.8.0

package/.claude-plugin/marketplace.json

@@ -6,13 +6,13 @@
   },
   "metadata": {
     "description": "Official marketplace for semantic-pages - Semantic search + knowledge graph MCP server with auto-wiring for .claude/.vault and hit-em-with-the-docs companion",
-    "version": "0.6.3"
+    "version": "0.8.0"
   },
   "plugins": [
     {
       "name": "semantic-pages",
       "description": "Semantic search + knowledge graph MCP server for markdown vaults. Auto-wires a read/write vault at .claude/.vault, and a read-only docs index at .documentation when hit-em-with-the-docs is also installed.",
-      "version": "0.6.3",
+      "version": "0.8.0",
       "author": {
         "name": "TheGlitchKing"
       },

package/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "semantic-pages",
   "description": "Semantic search + knowledge graph MCP server for markdown vaults. Auto-wires a read/write vault at .claude/.vault, and a read-only docs index at .documentation when hit-em-with-the-docs is also installed.",
-  "version": "0.6.3",
+  "version": "0.8.0",
   "author": {
     "name": "TheGlitchKing",
     "email": "theglitchking@users.noreply.github.com"

package/README.md

@@ -479,6 +479,113 @@ Each flow probes its MCP server independently and degrades gracefully when one i
 
 When you install `semantic-pages` via the Claude Code plugin marketplace or via npm, Claude Code picks up this skill automatically — no extra wiring required.
 
+### How auto-linking works *(0.7.0+)*
+
+When installed as an npm dependency, a `postinstall` script symlinks every directory under the package's `skills/` into your project's `.claude/skills/` (creating that directory if missing). Claude Code only scans `<project>/.claude/skills/` and `~/.claude/skills/` — it does not look inside `node_modules/` — so this link is what makes bundled skills discoverable.
+
+- The link is relative, pointing into `node_modules/@theglitchking/semantic-pages/skills/<name>`, and is refreshed on every install/update.
+- If a regular file or directory already exists at the destination (i.e. someone copied a skill manually), the script leaves it alone and prints a warning.
+- The script is a no-op when you're developing the plugin itself (`INIT_CWD` equals the package root), so the plugin never self-links into its own repo.
+- The linker never hard-fails an install — permission errors and odd filesystems downgrade to a warning.
+
+Add the linked skills to `.gitignore` so they don't get committed in consuming projects:
+
+```
+/.claude/skills/semantic-first/
+```
+
+**Opt-out**: set `SEMANTIC_PAGES_SKIP_LINK=1` to skip linking during install — useful if you want to manage `.claude/skills/` manually.
+
+```bash
+SEMANTIC_PAGES_SKIP_LINK=1 npm install @theglitchking/semantic-pages
+```
+
+---
+
+## Update Policy & Session-Start Hook *(0.8.0+)*
+
+When you install `semantic-pages` as an npm dependency, the postinstall step also:
+
+1. Writes `<project>/.claude/semantic-pages.json` with `{ "updatePolicy": "nudge" }` if one doesn't exist.
+2. Registers a `SessionStart` hook in `<project>/.claude/settings.json` — but **only** if `settings.json` exists and neither the Claude Code plugin nor an existing semantic-pages hook is already handling it.
+
+### What the hook does
+
+At the start of every Claude Code session, the hook:
+
+- Reconciles `.mcp.json` (the same `semantic-vault` + conditional `.documentation` wiring you'd get from the plugin).
+- Checks npm for a newer version of `@theglitchking/semantic-pages` (~3s budget, results cached for 6h, skipped in CI).
+- Acts on the result according to your policy.
+
+### Policies
+
+| Policy | Behavior |
+|--------|----------|
+| `nudge` *(default)* | Print a one-liner when a newer version is available. No changes. |
+| `auto`  | Run `npm update @theglitchking/semantic-pages`, re-link skills, print `⬆️ vX → vY`. |
+| `off`   | Silent — no update check. |
+
+### Setting the policy
+
+Preferred:
+
+```
+/semantic-pages:policy auto
+/semantic-pages:policy nudge
+/semantic-pages:policy off
+```
+
+Or from the terminal:
+
+```bash
+npx --no @theglitchking/semantic-pages policy auto
+```
+
+Resolution order:
+
+1. `SEMANTIC_PAGES_UPDATE_POLICY` env var (one-shot override).
+2. `<project>/.claude/semantic-pages.json` → `updatePolicy`.
+3. Default: `nudge`.
+
+### Plugin-command menu
+
+With `semantic-pages` installed (plugin or npm), you get these slash commands:
+
+| Command | Does |
+|---------|------|
+| `/semantic-pages:update`   | Runs `npm update`, re-links skills, reports before/after. |
+| `/semantic-pages:policy [auto\|nudge\|off]` | Get or set the update policy. |
+| `/semantic-pages:status`   | Installed version, latest on npm, policy, hook state. |
+| `/semantic-pages:relink`   | Re-symlink bundled skills into `.claude/skills/`. |
+
+Each has a CLI equivalent: `npx --no @theglitchking/semantic-pages <subcommand>`.
+
+### Dedup between plugin and npm installs
+
+If you install via **both** the Claude Code plugin and the npm dep, the postinstall detects the plugin in `~/.claude/settings.json` → `enabledPlugins` and skips the settings.json hook registration. One hook fires per session, not two. If you later uninstall the plugin, the next `npm install` re-registers the project-level hook.
+
+### Opt-out
+
+```bash
+# Skip settings.json hook registration:
+SEMANTIC_PAGES_SKIP_HOOK_REGISTER=1 npm install @theglitchking/semantic-pages
+
+# Skip skill symlinking:
+SEMANTIC_PAGES_SKIP_LINK=1 npm install @theglitchking/semantic-pages
+```
+
+### Uninstalling cleanly
+
+```bash
+# 1. Remove the hook entry from .claude/settings.json (look for any SessionStart
+#    entry whose command references "semantic-pages").
+# 2. Remove the policy file:
+rm .claude/semantic-pages.json
+
+# 3. Remove the package:
+npm uninstall @theglitchking/semantic-pages
+```
+
 ---
 
 ## Common Workflows

package/commands/policy.md

@@ -0,0 +1,16 @@
+---
+description: Get or set the semantic-pages 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-pages policy` and report the current policy and config path.
+- If `$ARGUMENTS` is one of `auto`, `nudge`, `off`, run `npx --no @theglitchking/semantic-pages 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-pages` 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

@@ -0,0 +1,6 @@
+---
+description: Re-run the skill linker — refresh symlinks from node_modules into .claude/skills/
+allowed-tools: Bash(npx:*)
+---
+
+Run `npx --no @theglitchking/semantic-pages relink` and report the result.

package/commands/status.md

@@ -0,0 +1,6 @@
+---
+description: Show installed version, latest available version, current update policy, and hook registration state
+allowed-tools: Bash(npx:*)
+---
+
+Run `npx --no @theglitchking/semantic-pages status` and relay the output to the user verbatim.

package/commands/update.md

@@ -0,0 +1,6 @@
+---
+description: Update semantic-pages to the latest version (runs npm update + re-links skills)
+allowed-tools: Bash(npx:*)
+---
+
+Run `npx --no @theglitchking/semantic-pages 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-pages update` and note that in your summary.

package/dist/cli/index.js

@@ -2,10 +2,86 @@
 
 // src/cli/index.ts
 import { program } from "commander";
-import { resolve } from "path";
-import { existsSync } from "fs";
+import { resolve, dirname, join } from "path";
+import { existsSync, readFileSync, writeFileSync, mkdirSync } from "fs";
 import { createRequire } from "module";
-var { version } = createRequire(import.meta.url)("../../package.json");
+import { spawnSync } from "child_process";
+import { fileURLToPath } from "url";
+var require_ = createRequire(import.meta.url);
+var { version } = require_("../../package.json");
+var PKG_NAME = "@theglitchking/semantic-pages";
+var VALID_POLICIES = ["auto", "nudge", "off"];
+function readJsonSafe(p, fallback = null) {
+  try {
+    const raw = readFileSync(p, "utf8");
+    return raw.trim() ? JSON.parse(raw) : fallback;
+  } catch {
+    return fallback;
+  }
+}
+function writeJsonFile(p, value) {
+  mkdirSync(dirname(p), { recursive: true });
+  writeFileSync(p, JSON.stringify(value, null, 2) + "\n");
+}
+function configPath(cwd = process.cwd()) {
+  return join(cwd, ".claude", "semantic-pages.json");
+}
+function currentPolicy(cwd = process.cwd()) {
+  const env = process.env.SEMANTIC_PAGES_UPDATE_POLICY;
+  if (env && VALID_POLICIES.includes(env)) return env;
+  const cfg = readJsonSafe(configPath(cwd));
+  const p = cfg?.updatePolicy;
+  if (p && VALID_POLICIES.includes(p)) return p;
+  return "nudge";
+}
+function installedVersion(cwd = process.cwd()) {
+  const localPkg = join(cwd, "node_modules", "@theglitchking", "semantic-pages", "package.json");
+  const pkg = readJsonSafe(localPkg);
+  if (pkg?.version) return pkg.version;
+  return version;
+}
+async function fetchLatestVersion(timeoutMs = 5e3) {
+  const ctrl = new AbortController();
+  const timer = setTimeout(() => ctrl.abort(), timeoutMs);
+  try {
+    const res = await fetch(`https://registry.npmjs.org/${PKG_NAME}/latest`, {
+      signal: ctrl.signal,
+      headers: { accept: "application/json" }
+    });
+    if (!res.ok) return null;
+    const json = await res.json();
+    return json.version ?? null;
+  } catch {
+    return null;
+  } finally {
+    clearTimeout(timer);
+  }
+}
+function runNpmUpdate(cwd) {
+  return spawnSync("npm", ["update", PKG_NAME], { cwd, stdio: "inherit" });
+}
+function runRelink(cwd) {
+  const linker = join(cwd, "node_modules", "@theglitchking", "semantic-pages", "scripts", "link-skills.js");
+  if (!existsSync(linker)) {
+    const localLinker = resolve(fileURLToPath(import.meta.url), "..", "..", "..", "scripts", "link-skills.js");
+    if (!existsSync(localLinker)) {
+      console.error("link-skills.js not found \u2014 is the package installed?");
+      return 1;
+    }
+    const r2 = spawnSync(process.execPath, [localLinker], {
+      cwd,
+      env: { ...process.env, INIT_CWD: cwd },
+      stdio: "inherit"
+    });
+    return r2.status ?? 1;
+  }
+  const r = spawnSync(process.execPath, [linker], {
+    cwd,
+    env: { ...process.env, INIT_CWD: cwd },
+    stdio: "inherit"
+  });
+  return r.status ?? 1;
+}
 var TOOL_HELP = {
   // Search
   search_semantic: {
@@ -254,5 +330,57 @@ program.command("serve", { isDefault: true }).description("Start the MCP server
     readOnly: opts.readOnly
   });
 });
+program.command("update").description("Update semantic-pages to the latest version (project-local install)").action(async () => {
+  const cwd = process.cwd();
+  const before = installedVersion(cwd);
+  console.log(`Current: ${before ?? "(not installed)"}`);
+  const r = runNpmUpdate(cwd);
+  if (r.status !== 0) {
+    console.error("npm update failed.");
+    process.exit(r.status ?? 1);
+  }
+  const after = installedVersion(cwd);
+  console.log(`Now:     ${after ?? "(not installed)"}`);
+  if (after && before && after !== before) runRelink(cwd);
+  process.exit(0);
+});
+program.command("policy [mode]").description(`Show or set the update policy (${VALID_POLICIES.join(" | ")})`).action((mode) => {
+  const cwd = process.cwd();
+  if (!mode) {
+    console.log(`updatePolicy = ${currentPolicy(cwd)} (${configPath(cwd)})`);
+    process.exit(0);
+  }
+  if (!VALID_POLICIES.includes(mode)) {
+    console.error(`Invalid policy: ${mode}. Valid: ${VALID_POLICIES.join(", ")}`);
+    process.exit(1);
+  }
+  const p = configPath(cwd);
+  const cfg = readJsonSafe(p) ?? {};
+  cfg.updatePolicy = mode;
+  writeJsonFile(p, cfg);
+  console.log(`updatePolicy = ${mode} (${p})`);
+  process.exit(0);
+});
+program.command("status").description("Show installed version, latest available, current policy, and hook registration state").action(async () => {
+  const cwd = process.cwd();
+  const current = installedVersion(cwd);
+  const latest = await fetchLatestVersion();
+  const policy = currentPolicy(cwd);
+  const settings = readJsonSafe(
+    join(cwd, ".claude", "settings.json")
+  );
+  const hookRegistered = !!settings?.hooks?.SessionStart?.some(
+    (g) => (g?.hooks || []).some((h) => typeof h?.command === "string" && h.command.includes("semantic-pages"))
+  );
+  console.log(`semantic-pages status`);
+  console.log(`  installed: ${current ?? "(not installed)"}`);
+  console.log(`  latest:    ${latest ?? "(unknown)"}`);
+  console.log(`  policy:    ${policy}`);
+  console.log(`  hook:      ${hookRegistered ? "registered in .claude/settings.json" : "not in .claude/settings.json"}`);
+  process.exit(0);
+});
+program.command("relink").description("Re-run the skill linker (symlinks bundled skills into .claude/skills/)").action(() => {
+  process.exit(runRelink(process.cwd()));
+});
 program.parse();
 //# sourceMappingURL=index.js.map

package/dist/cli/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/cli/index.ts"],"sourcesContent":["#!/usr/bin/env node\n\nimport { program } from \"commander\";\nimport { resolve } from \"node:path\";\nimport { existsSync } from \"node:fs\";\nimport { createRequire } from \"node:module\";\n\nconst { version } = createRequire(import.meta.url)(\"../../package.json\") as { version: string };\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-pages 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-pages 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-pages 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-pages\")\n  .description(\n    \"Semantic search + knowledge graph MCP server for markdown files\\n\\n\" +\n    \"  Start MCP server:  semantic-pages --notes ./vault\\n\" +\n    \"  Show vault stats:  semantic-pages --notes ./vault --stats\\n\" +\n    \"  Force reindex:     semantic-pages --notes ./vault --reindex\\n\" +\n    \"  List MCP tools:    semantic-pages tools\\n\" +\n    \"  Tool details:      semantic-pages tools search_semantic\"\n  )\n  .version(version);\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 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+{"version":3,"sources":["../../src/cli/index.ts"],"sourcesContent":["#!/usr/bin/env node\n\nimport { program } from \"commander\";\nimport { resolve, dirname, join } from \"node:path\";\nimport { existsSync, readFileSync, writeFileSync, mkdirSync } from \"node:fs\";\nimport { createRequire } from \"node:module\";\nimport { spawnSync } from \"node:child_process\";\nimport { fileURLToPath } from \"node:url\";\n\nconst require_ = createRequire(import.meta.url);\nconst { version } = require_(\"../../package.json\") as { version: string };\n\nconst PKG_NAME = \"@theglitchking/semantic-pages\";\nconst VALID_POLICIES = [\"auto\", \"nudge\", \"off\"] as const;\ntype Policy = (typeof VALID_POLICIES)[number];\n\nfunction readJsonSafe<T = unknown>(p: string, fallback: T | null = null): T | null {\n  try {\n    const raw = readFileSync(p, \"utf8\");\n    return raw.trim() ? (JSON.parse(raw) as T) : fallback;\n  } catch {\n    return fallback;\n  }\n}\n\nfunction writeJsonFile(p: string, value: unknown) {\n  mkdirSync(dirname(p), { recursive: true });\n  writeFileSync(p, JSON.stringify(value, null, 2) + \"\\n\");\n}\n\nfunction configPath(cwd = process.cwd()) {\n  return join(cwd, \".claude\", \"semantic-pages.json\");\n}\n\nfunction currentPolicy(cwd = process.cwd()): Policy {\n  const env = process.env.SEMANTIC_PAGES_UPDATE_POLICY as Policy | undefined;\n  if (env && (VALID_POLICIES as readonly string[]).includes(env)) return env;\n  const cfg = readJsonSafe<{ updatePolicy?: Policy }>(configPath(cwd));\n  const p = cfg?.updatePolicy;\n  if (p && (VALID_POLICIES as readonly string[]).includes(p)) return p;\n  return \"nudge\";\n}\n\nfunction installedVersion(cwd = process.cwd()): string | null {\n  const localPkg = join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-pages\", \"package.json\");\n  const pkg = readJsonSafe<{ version?: string }>(localPkg);\n  if (pkg?.version) return pkg.version;\n  // fallback: our own package.json (when running via plugin dir)\n  return version;\n}\n\nasync function fetchLatestVersion(timeoutMs = 5000): Promise<string | null> {\n  const ctrl = new AbortController();\n  const timer = setTimeout(() => ctrl.abort(), timeoutMs);\n  try {\n    const res = await fetch(`https://registry.npmjs.org/${PKG_NAME}/latest`, {\n      signal: ctrl.signal,\n      headers: { accept: \"application/json\" },\n    });\n    if (!res.ok) return null;\n    const json = (await res.json()) as { version?: string };\n    return json.version ?? null;\n  } catch {\n    return null;\n  } finally {\n    clearTimeout(timer);\n  }\n}\n\nfunction runNpmUpdate(cwd: string) {\n  return spawnSync(\"npm\", [\"update\", PKG_NAME], { cwd, stdio: \"inherit\" });\n}\n\nfunction runRelink(cwd: string) {\n  const linker = join(cwd, \"node_modules\", \"@theglitchking\", \"semantic-pages\", \"scripts\", \"link-skills.js\");\n  if (!existsSync(linker)) {\n    // Running against our own repo — point at the source linker.\n    const localLinker = resolve(fileURLToPath(import.meta.url), \"..\", \"..\", \"..\", \"scripts\", \"link-skills.js\");\n    if (!existsSync(localLinker)) {\n      console.error(\"link-skills.js not found — is the package installed?\");\n      return 1;\n    }\n    const r = spawnSync(process.execPath, [localLinker], {\n      cwd,\n      env: { ...process.env, INIT_CWD: cwd },\n      stdio: \"inherit\",\n    });\n    return r.status ?? 1;\n  }\n  const r = spawnSync(process.execPath, [linker], {\n    cwd,\n    env: { ...process.env, INIT_CWD: cwd },\n    stdio: \"inherit\",\n  });\n  return r.status ?? 1;\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 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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-pages 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-pages 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-pages 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-pages\")\n  .description(\n    \"Semantic search + knowledge graph MCP server for markdown files\\n\\n\" +\n    \"  Start MCP server:  semantic-pages --notes ./vault\\n\" +\n    \"  Show vault stats:  semantic-pages --notes ./vault --stats\\n\" +\n    \"  Force reindex:     semantic-pages --notes ./vault --reindex\\n\" +\n    \"  List MCP tools:    semantic-pages tools\\n\" +\n    \"  Tool details:      semantic-pages tools search_semantic\"\n  )\n  .version(version);\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\nprogram\n  .command(\"update\")\n  .description(\"Update semantic-pages to the latest version (project-local install)\")\n  .action(async () => {\n    const cwd = process.cwd();\n    const before = installedVersion(cwd);\n    console.log(`Current: ${before ?? \"(not installed)\"}`);\n    const r = runNpmUpdate(cwd);\n    if (r.status !== 0) {\n      console.error(\"npm update failed.\");\n      process.exit(r.status ?? 1);\n    }\n    const after = installedVersion(cwd);\n    console.log(`Now:     ${after ?? \"(not installed)\"}`);\n    if (after && before && after !== before) runRelink(cwd);\n    process.exit(0);\n  });\n\nprogram\n  .command(\"policy [mode]\")\n  .description(`Show or set the update policy (${VALID_POLICIES.join(\" | \")})`)\n  .action((mode?: string) => {\n    const cwd = process.cwd();\n    if (!mode) {\n      console.log(`updatePolicy = ${currentPolicy(cwd)} (${configPath(cwd)})`);\n      process.exit(0);\n    }\n    if (!(VALID_POLICIES as readonly string[]).includes(mode)) {\n      console.error(`Invalid policy: ${mode}. 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 );\n    console.log(`semantic-pages status`);\n    console.log(`  installed: ${current ?? \"(not installed)\"}`);\n    console.log(`  latest:    ${latest ?? \"(unknown)\"}`);\n    console.log(`  policy:    ${policy}`);\n    console.log(`  hook:      ${hookRegistered ? \"registered in .claude/settings.json\" : \"not in .claude/settings.json\"}`);\n    process.exit(0);\n  });\n\nprogram\n  .command(\"relink\")\n  .description(\"Re-run the skill linker (symlinks bundled skills into .claude/skills/)\")\n  .action(() => {\n    process.exit(runRelink(process.cwd()));\n  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package/hooks/hooks.json

@@ -1,12 +1,12 @@
 {
-  "description": "semantic-pages SessionStart hook — auto-wires .claude/.vault and, when hit-em-with-the-docs is installed, adds a read-only .documentation index",
+  "description": "semantic-pages SessionStart hook — reconciles .mcp.json wiring and nudges/auto-updates per policy.",
   "hooks": {
     "SessionStart": [
       {
         "hooks": [
           {
             "type": "command",
-            "command": "bash \"${CLAUDE_PLUGIN_ROOT}/hooks/session-start.sh\""
+            "command": "node \"${CLAUDE_PLUGIN_ROOT}/hooks/session-start.js\""
           }
         ]
       }

package/hooks/session-start.js

@@ -0,0 +1,283 @@
+#!/usr/bin/env node
+// semantic-pages SessionStart hook (Node, cross-platform).
+// Does two jobs:
+//   1. Reconcile <project>/.mcp.json (port of the original session-start.sh):
+//        - ensure "semantic-vault" -> ./.claude/.vault (read/write)
+//        - if hit-em-with-the-docs is enabled AND ./.documentation exists:
+//            add "semantic-pages" -> ./.documentation (read-only)
+//          else: remove our own docs entry if present (never touch user entries)
+//   2. Check for package updates and act per policy:
+//        off   -> silent
+//        nudge -> print a one-liner (default)
+//        auto  -> run `npm update` and re-link skills
+//
+// Never hard-fails. Emits a valid SessionStart hookSpecificOutput on stdout and
+// exits 0. Has a ~3s budget when up-to-date (network fetch timeout). Caches the
+// latest version for 6h. Skipped entirely in CI. Self-skips its update section
+// when it detects a project-registered counterpart to avoid double-firing when
+// the user has BOTH the Claude Code plugin AND the npm dep installed.
+
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import { homedir } from "node:os";
+import { dirname, join } from "node:path";
+import { spawnSync } from "node:child_process";
+
+const PKG = "@theglitchking/semantic-pages";
+const CACHE_TTL_MS = 6 * 60 * 60 * 1000;
+const NETWORK_TIMEOUT_MS = 3000;
+const AUTO_UPDATE_TIMEOUT_MS = 60_000;
+
+const VALID_POLICIES = new Set(["auto", "nudge", "off"]);
+
+function emit(additionalContext) {
+  const out = { hookSpecificOutput: { hookEventName: "SessionStart" } };
+  if (additionalContext) out.hookSpecificOutput.additionalContext = additionalContext;
+  process.stdout.write(JSON.stringify(out) + "\n");
+}
+
+function logWarn(msg) {
+  process.stderr.write(`semantic-pages hook: ${msg}\n`);
+}
+
+function readJson(path, fallback = null) {
+  try {
+    const raw = readFileSync(path, "utf8");
+    return raw.trim() ? JSON.parse(raw) : fallback;
+  } catch {
+    return fallback;
+  }
+}
+
+function isCi() {
+  return ["CI", "GITHUB_ACTIONS", "GITLAB_CI", "BUILDKITE", "CIRCLECI"].some(
+    (k) => !!process.env[k],
+  );
+}
+
+function hewtdEnabled() {
+  const settings = readJson(join(homedir(), ".claude", "settings.json"));
+  const enabled = settings?.enabledPlugins || {};
+  return Object.keys(enabled).some(
+    (k) => k.startsWith("hit-em-with-the-docs@") && enabled[k] === true,
+  );
+}
+
+function hasProjectRegisteredHook(projectRoot) {
+  const settings = readJson(join(projectRoot, ".claude", "settings.json"));
+  const groups = settings?.hooks?.SessionStart;
+  if (!Array.isArray(groups)) return false;
+  for (const group of groups) {
+    for (const h of group?.hooks || []) {
+      const cmd = h?.command;
+      if (typeof cmd === "string" && cmd.includes("semantic-pages")) return true;
+    }
+  }
+  return false;
+}
+
+function reconcileMcp(projectRoot) {
+  const vaultDir = join(projectRoot, ".claude", ".vault");
+  const docsDir = join(projectRoot, ".documentation");
+  const mcpPath = join(projectRoot, ".mcp.json");
+
+  try { mkdirSync(vaultDir, { recursive: true }); } catch {}
+
+  const docsWired = hewtdEnabled() && existsSync(docsDir);
+
+  let data = { mcpServers: {} };
+  if (existsSync(mcpPath)) {
+    const parsed = readJson(mcpPath, null);
+    if (parsed === null) {
+      // File exists but didn't parse — leave it alone, don't clobber user data.
+      let raw = "";
+      try { raw = readFileSync(mcpPath, "utf8"); } catch {}
+      if (raw.trim()) {
+        logWarn(`could not parse ${mcpPath}; leaving untouched`);
+        return;
+      }
+    } else if (parsed && typeof parsed === "object") {
+      data = parsed;
+      if (!data.mcpServers || typeof data.mcpServers !== "object") {
+        data.mcpServers = {};
+      }
+    }
+  }
+
+  const before = JSON.stringify(data);
+
+  data.mcpServers["semantic-vault"] = {
+    type: "stdio",
+    command: "npx",
+    args: ["-y", `${PKG}@latest`, "--notes", "./.claude/.vault"],
+  };
+
+  if (docsWired) {
+    data.mcpServers["semantic-pages"] = {
+      type: "stdio",
+      command: "npx",
+      args: ["-y", `${PKG}@latest`, "--notes", "./.documentation", "--read-only"],
+    };
+  } else if (data.mcpServers["semantic-pages"]) {
+    // Only remove if it looks like ours (points at .documentation). Preserves
+    // any user-defined semantic-pages entry pointing elsewhere.
+    const existing = data.mcpServers["semantic-pages"];
+    const args = Array.isArray(existing.args) ? existing.args : [];
+    const looksLikeOurs = args.some(
+      (a) => typeof a === "string" && a.includes(".documentation"),
+    );
+    if (looksLikeOurs) delete data.mcpServers["semantic-pages"];
+  }
+
+  const after = JSON.stringify(data);
+  if (after === before) return;
+
+  mkdirSync(dirname(mcpPath), { recursive: true });
+  writeFileSync(mcpPath, JSON.stringify(data, null, 2) + "\n");
+}
+
+function loadPolicy(projectRoot) {
+  const env = process.env.SEMANTIC_PAGES_UPDATE_POLICY;
+  if (env && VALID_POLICIES.has(env)) return env;
+  const cfg = readJson(join(projectRoot, ".claude", "semantic-pages.json"));
+  if (cfg?.updatePolicy && VALID_POLICIES.has(cfg.updatePolicy)) return cfg.updatePolicy;
+  return "nudge";
+}
+
+function getInstalledVersion(projectRoot) {
+  const candidates = [
+    join(projectRoot, "node_modules", "@theglitchking", "semantic-pages", "package.json"),
+  ];
+  if (process.env.CLAUDE_PLUGIN_ROOT) {
+    candidates.push(join(process.env.CLAUDE_PLUGIN_ROOT, "package.json"));
+  }
+  for (const p of candidates) {
+    const pkg = readJson(p);
+    if (pkg?.version) return pkg.version;
+  }
+  return null;
+}
+
+function compareVersions(a, b) {
+  const pa = String(a).split(/[.-]/).map((p) => (/^\d+$/.test(p) ? +p : p));
+  const pb = String(b).split(/[.-]/).map((p) => (/^\d+$/.test(p) ? +p : p));
+  for (let i = 0; i < Math.max(pa.length, pb.length); i++) {
+    const x = pa[i] ?? 0;
+    const y = pb[i] ?? 0;
+    if (x < y) return -1;
+    if (x > y) return 1;
+  }
+  return 0;
+}
+
+async function fetchLatestVersion(cacheFile) {
+  const cached = readJson(cacheFile);
+  if (
+    cached?.latest &&
+    typeof cached.checkedAt === "number" &&
+    Date.now() - cached.checkedAt < CACHE_TTL_MS
+  ) {
+    return cached.latest;
+  }
+
+  const ctrl = new AbortController();
+  const timer = setTimeout(() => ctrl.abort(), NETWORK_TIMEOUT_MS);
+  try {
+    const res = await fetch(`https://registry.npmjs.org/${PKG}/latest`, {
+      signal: ctrl.signal,
+      headers: { accept: "application/json" },
+    });
+    if (!res.ok) return null;
+    const json = await res.json();
+    const latest = json?.version;
+    if (latest) {
+      try {
+        mkdirSync(dirname(cacheFile), { recursive: true });
+        writeFileSync(cacheFile, JSON.stringify({ latest, checkedAt: Date.now() }));
+      } catch {}
+    }
+    return latest || null;
+  } catch {
+    return null;
+  } finally {
+    clearTimeout(timer);
+  }
+}
+
+function runAutoUpdate(projectRoot) {
+  const r = spawnSync("npm", ["update", PKG], {
+    cwd: projectRoot,
+    timeout: AUTO_UPDATE_TIMEOUT_MS,
+    stdio: "ignore",
+  });
+  if (r.status !== 0) return false;
+  // Re-link skills so any new skills ship to .claude/skills/.
+  const linker = join(
+    projectRoot,
+    "node_modules",
+    "@theglitchking",
+    "semantic-pages",
+    "scripts",
+    "link-skills.js",
+  );
+  if (existsSync(linker)) {
+    spawnSync(process.execPath, [linker], {
+      cwd: projectRoot,
+      env: { ...process.env, INIT_CWD: projectRoot },
+      stdio: "ignore",
+      timeout: 10_000,
+    });
+  }
+  return true;
+}
+
+async function runUpdateCheck(projectRoot) {
+  const policy = loadPolicy(projectRoot);
+  if (policy === "off") return "";
+  const current = getInstalledVersion(projectRoot);
+  if (!current) return "";
+  const cacheFile = join(projectRoot, ".claude", ".semantic-pages-update-cache.json");
+  const latest = await fetchLatestVersion(cacheFile);
+  if (!latest || compareVersions(current, latest) >= 0) return "";
+
+  if (policy === "nudge") {
+    return `💡 semantic-pages v${current} → v${latest} available.\n   Run /plugin semantic-pages → 'Update now' to upgrade.`;
+  }
+
+  // auto
+  const ok = runAutoUpdate(projectRoot);
+  if (ok) return `⬆️  semantic-pages v${current} → v${latest}`;
+  return `💡 semantic-pages v${current} → v${latest} available (auto-update failed — run /plugin semantic-pages → 'Update now').`;
+}
+
+async function main() {
+  const projectRoot = process.env.CLAUDE_PROJECT_DIR || process.cwd();
+  try {
+    process.chdir(projectRoot);
+  } catch {
+    return emit();
+  }
+
+  try { reconcileMcp(projectRoot); } catch (err) { logWarn(`reconcile failed: ${err.message}`); }
+
+  // Dedup: if we're the plugin-registered instance (CLAUDE_PLUGIN_ROOT set) and
+  // the project has its own semantic-pages hook in .claude/settings.json, the
+  // project-registered hook will handle the update check. Defer to it.
+  if (process.env.CLAUDE_PLUGIN_ROOT && hasProjectRegisteredHook(projectRoot)) {
+    return emit();
+  }
+
+  if (isCi()) return emit();
+
+  let msg = "";
+  try {
+    msg = await runUpdateCheck(projectRoot);
+  } catch (err) {
+    logWarn(`update check failed: ${err.message}`);
+  }
+  emit(msg || undefined);
+}
+
+main().catch((err) => {
+  logWarn(`fatal: ${err?.message || err}`);
+  emit();
+});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@theglitchking/semantic-pages",
-  "version": "0.6.6",
+  "version": "0.8.0",
   "description": "Semantic search + knowledge graph MCP server for markdown vaults. Claude Code plugin with auto-wiring for .claude/.vault and read-only .documentation companion when hit-em-with-the-docs is installed.",
   "type": "module",
   "main": "./dist/core/index.js",
@@ -17,6 +17,8 @@
     "dist",
     ".claude-plugin",
     "hooks",
+    "commands",
+    "scripts/link-skills.js",
     "skills/semantic-first",
     "README.md",
     "LICENSE"
@@ -27,7 +29,8 @@
     "test": "vitest run",
     "test:watch": "vitest",
     "lint": "tsc --noEmit",
-    "prepublishOnly": "npm run build"
+    "prepublishOnly": "npm run build",
+    "postinstall": "node scripts/link-skills.js"
   },
   "keywords": [
     "mcp",

package/scripts/link-skills.js

@@ -0,0 +1,205 @@
+#!/usr/bin/env node
+// Postinstall hook. Three jobs (all idempotent, all fail-open):
+//   1. Symlink bundled skills into <consumer>/.claude/skills/ so Claude Code
+//      can discover them (it doesn't scan node_modules/).
+//   2. Write a default update-policy config at <consumer>/.claude/semantic-pages.json
+//      ({ "updatePolicy": "nudge" }) if one doesn't already exist.
+//   3. Register the SessionStart hook in <consumer>/.claude/settings.json —
+//      but only if settings.json already exists, the Claude Code plugin
+//      version isn't already handling it, and no semantic-pages hook is
+//      already registered.
+//
+// Env overrides:
+//   SEMANTIC_PAGES_SKIP_LINK=1            — skip skill linking
+//   SEMANTIC_PAGES_SKIP_HOOK_REGISTER=1   — skip settings.json hook registration
+//
+// Never hard-fails — any error downgrades to a warning and exit 0 so the
+// package still installs.
+
+import {
+  existsSync,
+  lstatSync,
+  mkdirSync,
+  readFileSync,
+  readdirSync,
+  readlinkSync,
+  rmSync,
+  symlinkSync,
+  writeFileSync,
+} from "node:fs";
+import { homedir } from "node:os";
+import { dirname, join, relative, resolve } from "node:path";
+import { fileURLToPath } from "node:url";
+
+const warn = (msg) => console.warn(`[semantic-pages] ${msg}`);
+const info = (msg) => console.log(`[semantic-pages] ${msg}`);
+
+const PACKAGE_ROOT = resolve(dirname(fileURLToPath(import.meta.url)), "..");
+const CONSUMER_ROOT = process.env.INIT_CWD || process.cwd();
+const HOOK_COMMAND = `node ./node_modules/@theglitchking/semantic-pages/hooks/session-start.js`;
+const HOOK_MARKER = "semantic-pages"; // substring we scan for to detect our hooks
+
+function readJson(path, fallback = null) {
+  try {
+    const raw = readFileSync(path, "utf8");
+    return raw.trim() ? JSON.parse(raw) : fallback;
+  } catch {
+    return fallback;
+  }
+}
+
+function writeJson(path, value) {
+  mkdirSync(dirname(path), { recursive: true });
+  writeFileSync(path, JSON.stringify(value, null, 2) + "\n");
+}
+
+function lstatSafe(p) {
+  try { return lstatSync(p); } catch { return null; }
+}
+
+function isDeveloperInPlace() {
+  return resolve(CONSUMER_ROOT) === resolve(PACKAGE_ROOT);
+}
+
+function linkSkills() {
+  if (process.env.SEMANTIC_PAGES_SKIP_LINK === "1") {
+    info("SEMANTIC_PAGES_SKIP_LINK=1 — skipping skill linking.");
+    return 0;
+  }
+
+  const skillsSrcDir = join(PACKAGE_ROOT, "skills");
+  if (!existsSync(skillsSrcDir)) return 0;
+
+  const skillDirs = readdirSync(skillsSrcDir, { withFileTypes: true })
+    .filter((d) => d.isDirectory() && !d.name.endsWith("-workspace"))
+    .map((d) => d.name);
+  if (skillDirs.length === 0) return 0;
+
+  const destDir = join(CONSUMER_ROOT, ".claude", "skills");
+  try { mkdirSync(destDir, { recursive: true }); } catch (err) {
+    warn(`could not create ${destDir}: ${err.message}`);
+    return 0;
+  }
+
+  let linked = 0;
+  for (const name of skillDirs) {
+    const src = join(skillsSrcDir, name);
+    const dest = join(destDir, name);
+    const rel = relative(dirname(dest), src);
+    try {
+      const st = lstatSafe(dest);
+      if (st) {
+        if (st.isSymbolicLink()) {
+          if (readlinkSync(dest) === rel) { linked++; continue; }
+          rmSync(dest, { force: true });
+        } else {
+          warn(`skipping ${dest} — a non-symlink already exists there.`);
+          continue;
+        }
+      }
+      symlinkSync(rel, dest, "dir");
+      linked++;
+    } catch (err) {
+      warn(`could not link skill "${name}": ${err.message}`);
+    }
+  }
+  return linked;
+}
+
+function writeDefaultConfig() {
+  const cfgPath = join(CONSUMER_ROOT, ".claude", "semantic-pages.json");
+  if (existsSync(cfgPath)) {
+    const cur = readJson(cfgPath);
+    return cur?.updatePolicy || "nudge";
+  }
+  try {
+    writeJson(cfgPath, { updatePolicy: "nudge" });
+  } catch (err) {
+    warn(`could not write ${cfgPath}: ${err.message}`);
+  }
+  return "nudge";
+}
+
+function pluginAlreadyHandling() {
+  // If the Claude Code plugin is enabled globally, its own hooks.json handles
+  // SessionStart — no need to also register in project settings.json.
+  const settings = readJson(join(homedir(), ".claude", "settings.json"));
+  const enabled = settings?.enabledPlugins || {};
+  return Object.keys(enabled).some(
+    (k) => k.startsWith("semantic-pages@") && enabled[k] === true,
+  );
+}
+
+function settingsHasOurHook(settings) {
+  const groups = settings?.hooks?.SessionStart;
+  if (!Array.isArray(groups)) return false;
+  return groups.some((g) =>
+    (g?.hooks || []).some(
+      (h) => typeof h?.command === "string" && h.command.includes(HOOK_MARKER),
+    ),
+  );
+}
+
+function registerHookIfApplicable() {
+  if (process.env.SEMANTIC_PAGES_SKIP_HOOK_REGISTER === "1") {
+    return { status: "skipped", reason: "env" };
+  }
+  if (pluginAlreadyHandling()) {
+    return { status: "skipped", reason: "plugin" };
+  }
+
+  const settingsPath = join(CONSUMER_ROOT, ".claude", "settings.json");
+  if (!existsSync(settingsPath)) {
+    // Only register when the user has already opted into project settings.
+    return { status: "skipped", reason: "no-settings" };
+  }
+
+  const settings = readJson(settingsPath);
+  if (!settings || typeof settings !== "object") {
+    warn(`could not parse ${settingsPath}; not registering hook.`);
+    return { status: "skipped", reason: "unparseable" };
+  }
+
+  if (settingsHasOurHook(settings)) {
+    return { status: "already" };
+  }
+
+  settings.hooks ||= {};
+  settings.hooks.SessionStart ||= [];
+  settings.hooks.SessionStart.push({
+    hooks: [{ type: "command", command: HOOK_COMMAND }],
+  });
+
+  try {
+    writeJson(settingsPath, settings);
+    return { status: "registered" };
+  } catch (err) {
+    warn(`could not write ${settingsPath}: ${err.message}`);
+    return { status: "skipped", reason: "write-failed" };
+  }
+}
+
+function main() {
+  if (isDeveloperInPlace()) return;
+
+  const linkedCount = linkSkills();
+  const policy = writeDefaultConfig();
+  const hookResult = registerHookIfApplicable();
+
+  const parts = [];
+  if (linkedCount > 0) parts.push(`${linkedCount} skill(s) linked`);
+  parts.push(`update mode = ${policy}`);
+  if (hookResult.status === "registered") parts.push("hook registered");
+  else if (hookResult.status === "already") parts.push("hook already registered");
+  else if (hookResult.status === "skipped" && hookResult.reason === "plugin") {
+    parts.push("hook deferred to plugin");
+  }
+
+  info(`${parts.join(", ")} (change via /plugin semantic-pages)`);
+}
+
+try {
+  main();
+} catch (err) {
+  warn(`postinstall failed: ${err?.message || err}`);
+}

package/hooks/session-start.sh

@@ -1,147 +0,0 @@
-#!/usr/bin/env bash
-#
-# semantic-pages SessionStart hook
-#
-# Reconciles the project's .mcp.json so that:
-#   1. A "semantic-vault" entry always points at ./.claude/.vault (read/write).
-#   2. A "semantic-pages" entry points at ./.documentation (read-only) ONLY IF
-#      both conditions hold:
-#        - hit-em-with-the-docs is installed+enabled as a Claude Code plugin
-#        - ./.documentation/ exists in this project
-#      Otherwise any stale "semantic-pages" entry is removed.
-#
-# Idempotent: only writes .mcp.json when the computed JSON differs from disk.
-# Fails open: any error logs to stderr and exits 0 so Claude Code isn't blocked.
-#
-# Runs on every SessionStart event. Keeps wiring in sync with plugin state.
-
-set -u
-
-# Fail-open: if anything goes sideways, swallow and return the empty SessionStart
-# response so the session keeps going.
-trap 'emit_empty_response; exit 0' ERR
-
-emit_empty_response() {
-  # SessionStart hooks need to return JSON; empty additionalContext is fine.
-  printf '{"hookSpecificOutput":{"hookEventName":"SessionStart"}}\n'
-}
-
-log() {
-  printf 'semantic-pages hook: %s\n' "$*" >&2
-}
-
-# Project root is cwd when Claude Code invokes the hook.
-PROJECT_ROOT="${CLAUDE_PROJECT_DIR:-$PWD}"
-cd "$PROJECT_ROOT" || { emit_empty_response; exit 0; }
-
-VAULT_DIR="$PROJECT_ROOT/.claude/.vault"
-DOCS_DIR="$PROJECT_ROOT/.documentation"
-MCP_JSON="$PROJECT_ROOT/.mcp.json"
-CLAUDE_SETTINGS="$HOME/.claude/settings.json"
-
-# 1. Ensure .claude/.vault exists (idempotent).
-mkdir -p "$VAULT_DIR" 2>/dev/null || true
-
-# 2. Detect hit-em-with-the-docs: must be listed in enabledPlugins in
-#    ~/.claude/settings.json (covers any marketplace source).
-HEWTD_ENABLED=0
-if [ -f "$CLAUDE_SETTINGS" ]; then
-  if node -e '
-    const fs = require("fs");
-    try {
-      const s = JSON.parse(fs.readFileSync(process.argv[1], "utf8"));
-      const enabled = s.enabledPlugins || {};
-      const hit = Object.keys(enabled).some(
-        (k) => k.startsWith("hit-em-with-the-docs@") && enabled[k] === true
-      );
-      process.exit(hit ? 0 : 1);
-    } catch { process.exit(1); }
-  ' "$CLAUDE_SETTINGS" 2>/dev/null; then
-    HEWTD_ENABLED=1
-  fi
-fi
-
-# 3. Docs MCP entry is conditional on BOTH hewtd enabled AND .documentation present.
-DOCS_WIRED=0
-if [ "$HEWTD_ENABLED" = "1" ] && [ -d "$DOCS_DIR" ]; then
-  DOCS_WIRED=1
-fi
-
-# 4. Reconcile .mcp.json using node (cross-platform JSON edit, idempotent write).
-node - "$MCP_JSON" "$DOCS_WIRED" <<'NODE' || { log "reconcile failed"; emit_empty_response; exit 0; }
-const fs = require("fs");
-const path = require("path");
-const [, , mcpPath, docsWiredArg] = process.argv;
-const docsWired = docsWiredArg === "1";
-
-let data = { mcpServers: {} };
-if (fs.existsSync(mcpPath)) {
-  try {
-    const raw = fs.readFileSync(mcpPath, "utf8");
-    const parsed = raw.trim() ? JSON.parse(raw) : {};
-    if (parsed && typeof parsed === "object") data = parsed;
-    if (!data.mcpServers || typeof data.mcpServers !== "object") data.mcpServers = {};
-  } catch (err) {
-    // Corrupt .mcp.json — leave it alone and emit a note to stderr
-    process.stderr.write(
-      `semantic-pages hook: could not parse ${mcpPath} (${err.message}); leaving untouched\n`
-    );
-    process.exit(0);
-  }
-}
-
-// Canonical entries
-const vaultEntry = {
-  type: "stdio",
-  command: "npx",
-  args: [
-    "-y",
-    "@theglitchking/semantic-pages@latest",
-    "--notes",
-    "./.claude/.vault",
-  ],
-};
-
-const docsEntry = {
-  type: "stdio",
-  command: "npx",
-  args: [
-    "-y",
-    "@theglitchking/semantic-pages@latest",
-    "--notes",
-    "./.documentation",
-    "--read-only",
-  ],
-};
-
-const before = JSON.stringify(data);
-
-// Always ensure semantic-vault
-data.mcpServers["semantic-vault"] = vaultEntry;
-
-// semantic-pages (docs) is conditional
-if (docsWired) {
-  data.mcpServers["semantic-pages"] = docsEntry;
-} else if (data.mcpServers["semantic-pages"]) {
-  // Only remove if it looks like ours (points at .documentation). Don't clobber
-  // a user-custom entry under the same name.
-  const existing = data.mcpServers["semantic-pages"];
-  const args = Array.isArray(existing.args) ? existing.args : [];
-  const looksLikeOurs =
-    args.some((a) => typeof a === "string" && a.includes(".documentation"));
-  if (looksLikeOurs) delete data.mcpServers["semantic-pages"];
-}
-
-const after = JSON.stringify(data, null, 2) + "\n";
-
-// Only write if content actually changed — prevents needless git churn.
-if (JSON.stringify(JSON.parse(after)) === before) {
-  process.exit(0);
-}
-
-fs.mkdirSync(path.dirname(mcpPath), { recursive: true });
-fs.writeFileSync(mcpPath, after);
-NODE
-
-emit_empty_response
-exit 0