@theglitchking/semantic-memory 1.0.1 → 1.1.1

package/hooks/reconcile.js

@@ -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

@@ -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

@@ -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) : "";
@@ -305,10 +311,98 @@ async function handleSessionStart(projectRoot, vaultPath, cliBin) {
   const searchBlock = hits && hits.length > 0 ? formatContextBlock("sessionstart", query, hits) : "";
   const stateBlock = formatStateDeltaBlock(sinceIso, recentEntries);
 
-  const parts = [stateBlock, searchBlock].filter(Boolean);
+  // Phase 8 (drift detection): inline fast-tier check. Hard requirements: <100ms total,
+  // fail open, silent on healthy installs. Caching via mtime stat is light enough that
+  // we don't need a separate cache file for the JS-side path.
+  const driftBlock = await fastDriftCheck(projectRoot).catch((err) => {
+    debug(`drift check failed: ${err?.message || err}`);
+    return "";
+  });
+
+  const parts = [driftBlock, stateBlock, searchBlock].filter(Boolean);
   emit("SessionStart", parts.join("\n\n"));
 }
 
+/**
+ * Fast-tier drift check for the SessionStart hook. Pure JS for zero spawn cost.
+ * Surfaces a one-block warning ONLY when at least one drift signal fires; healthy
+ * installs return "" and the hook stays silent.
+ *
+ * Checks:
+ *   - .mcp.json server entry presence
+ *   - hook registration in .claude/settings.json (SessionStart, UserPromptSubmit, Stop)
+ *   - skill manifests across global + local agent dirs (presence + version)
+ *   - AGENTS.md managed-block markers (if file exists)
+ *   - session staleness (>24h since last_activity_at on an open session)
+ *
+ * Heavy work (full vault lint, code-symbol drift) is reserved for the manual
+ * `/healthcheck` command; this auto path stays cheap.
+ */
+async function fastDriftCheck(projectRoot) {
+  const findings = [];
+  // .mcp.json
+  try {
+    const mcpPath = join(projectRoot, ".mcp.json");
+    if (existsSync(mcpPath)) {
+      const data = JSON.parse(readFileSync(mcpPath, "utf8"));
+      const servers = (data && data.mcpServers) || {};
+      const hasEntry = Object.keys(servers).some((k) => k === "semantic-vault" || k === "semantic-sidekick" || k === "semantic-memory");
+      if (!hasEntry) findings.push({ check: "mcp_json_entry", summary: ".mcp.json has no semantic-* server entry" });
+    }
+  } catch (e) { debug(`mcp check threw: ${e.message}`); }
+
+  // hook registration
+  try {
+    const settings = join(projectRoot, ".claude", "settings.json");
+    if (existsSync(settings)) {
+      const data = JSON.parse(readFileSync(settings, "utf8"));
+      const hooks = (data && data.hooks) || {};
+      const required = ["SessionStart", "UserPromptSubmit", "Stop"];
+      const missing = required.filter((e) => !Array.isArray(hooks[e]) || hooks[e].length === 0);
+      if (missing.length > 0) findings.push({ check: "hook_registration", summary: `missing hook events: ${missing.join(", ")}` });
+    }
+  } catch (e) { debug(`hook check threw: ${e.message}`); }
+
+  // AGENTS.md managed-block (warn only when file exists but markers are absent)
+  try {
+    const agents = join(projectRoot, "AGENTS.md");
+    if (existsSync(agents)) {
+      const raw = readFileSync(agents, "utf8");
+      if (!raw.includes("<!-- semantic-memory:begin contract -->") || !raw.includes("<!-- semantic-memory:end contract -->")) {
+        findings.push({ check: "agents_contract", summary: "AGENTS.md exists but lacks managed-block markers" });
+      }
+    }
+  } catch (e) { debug(`agents check threw: ${e.message}`); }
+
+  // session staleness
+  try {
+    const sessPath = join(projectRoot, ".claude", ".semantic-memory", "session.json");
+    if (existsSync(sessPath)) {
+      const state = JSON.parse(readFileSync(sessPath, "utf8"));
+      if (state && !state.closed_at && typeof state.last_activity_at === "string") {
+        const ageMs = Date.now() - new Date(state.last_activity_at).getTime();
+        if (ageMs > 24 * 60 * 60 * 1000) {
+          findings.push({ check: "session_staleness", summary: `session ${state.id} stale (>${Math.round(ageMs / (60 * 60 * 1000))}h)` });
+        }
+      }
+    }
+  } catch (e) { debug(`session check threw: ${e.message}`); }
+
+  if (findings.length === 0) return "";
+
+  const lines = [
+    `<vault-drift count="${findings.length}">`,
+    `⚠️  semantic-memory: ${findings.length} drift issue${findings.length === 1 ? "" : "s"} detected`,
+  ];
+  for (const f of findings.slice(0, 5)) {
+    lines.push(`  ⚠ ${f.check}: ${f.summary}`);
+  }
+  if (findings.length > 5) lines.push(`  …and ${findings.length - 5} more`);
+  lines.push(`Run /healthcheck for details, or /healthcheck --fix to auto-fix safe items.`);
+  lines.push(`</vault-drift>`);
+  return lines.join("\n");
+}
+
 function formatStateDeltaBlock(sinceIso, entries) {
   if (!entries || entries.length === 0) {
     return `<vault-state-since date="${sinceIso}">\nNo logged activity in the last 14 days.\n</vault-state-since>`;
@@ -341,6 +435,19 @@ function emitStop(additionalContext, block) {
   process.stdout.write(JSON.stringify(out) + "\n");
 }
 
+function readActiveSession(projectRoot) {
+  const sessionPath = join(projectRoot, ".claude", ".semantic-memory", "session.json");
+  if (!existsSync(sessionPath)) return null;
+  try {
+    const state = JSON.parse(readFileSync(sessionPath, "utf8"));
+    if (state && typeof state.id === "string" && !state.closed_at) return state;
+    return null;
+  } catch (e) {
+    debug(`session.json parse failed: ${e.message}`);
+    return null;
+  }
+}
+
 async function handleStop(projectRoot) {
   const stopHookActive = process.env.CLAUDE_STOP_HOOK_ACTIVE === "1";
   if (stopHookActive) {
@@ -350,6 +457,34 @@ async function handleStop(projectRoot) {
     return;
   }
 
+  // Session-aware branch (Phase 5). When a session is open at Stop time, prompt the
+  // agent to close it via session_finish (with or without verification waiver). This
+  // takes precedence over mode-specific capture prompts because a session represents
+  // a verification-gated work boundary that must be explicitly closed.
+  const session = readActiveSession(projectRoot);
+  if (session) {
+    const verifs = Array.isArray(session.verifications) ? session.verifications : [];
+    const lines = [
+      `<vault-session-close id="${session.id}" task="${session.task}" verifications="${verifs.length}">`,
+      `Session ${session.id} is still open: task=${JSON.stringify(session.task)}, verifications=${verifs.length}.`,
+      "",
+    ];
+    if (verifs.length > 0) {
+      lines.push("Recent verifications:");
+      for (const v of verifs.slice(-3)) {
+        lines.push(`- \`${v.cmd}\` → exit=${v.exit ?? "(killed)"} in ${v.duration_ms}ms`);
+      }
+      lines.push("");
+      lines.push(`Before ending: call \`mcp__semantic-vault__session_finish\` with a one-line summary. Verification recorded — finish will succeed without a waiver.`);
+    } else {
+      lines.push(`Before ending: either run \`mcp__semantic-vault__session_run\` with at least one verification command (tests/lint), or call \`mcp__semantic-vault__session_finish\` with \`verified: false\` and a \`reason\` waiving verification (e.g. doc-only edits). session_finish refuses without one of these paths.`);
+    }
+    lines.push(`</vault-session-close>`);
+    resetCapturePending(projectRoot);
+    emitStop(lines.join("\n"), true);
+    return;
+  }
+
   const pending = readCapturePending(projectRoot);
   const mode = readMode(projectRoot);
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@theglitchking/semantic-memory",
-  "version": "1.0.1",
+  "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

@@ -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}`);
 }

package/dist/chunk-CXTRTCIK.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/core/crud.ts","../src/core/frontmatter.ts","../src/core/watcher.ts","../src/core/ingest.ts","../src/core/index-regen.ts","../src/core/patch.ts","../src/core/synthesize.ts"],"sourcesContent":["import { readFile, writeFile, unlink, rename, mkdir } from \"node:fs/promises\";\nimport { dirname, join, relative } from \"node:path\";\nimport { existsSync } from \"node:fs\";\nimport { glob } from \"glob\";\nimport matter from \"gray-matter\";\nimport type { UpdateNoteOptions } from \"./types.js\";\n\nexport class NoteCrud {\n  private notesPath: string;\n\n  constructor(notesPath: string) {\n    this.notesPath = notesPath;\n  }\n\n  async create(\n    relativePath: string,\n    content: string,\n    frontmatter?: Record<string, unknown>\n  ): Promise<string> {\n    const absPath = join(this.notesPath, relativePath);\n    if (existsSync(absPath)) {\n      throw new Error(`Note already exists: ${relativePath}`);\n    }\n\n    await mkdir(dirname(absPath), { recursive: true });\n\n    // Merge auto-stamps with caller-supplied frontmatter (caller wins on conflicts)\n    const stamps = computeStamps(content);\n    const merged = { ...stamps, ...(frontmatter ?? {}) };\n    const fileContent = matter.stringify(content, merged);\n\n    await writeFile(absPath, fileContent, \"utf-8\");\n    return relativePath;\n  }\n\n  async read(relativePath: string): Promise<string> {\n    const absPath = join(this.notesPath, relativePath);\n    return readFile(absPath, \"utf-8\");\n  }\n\n  async readMultiple(paths: string[]): Promise<Map<string, string>> {\n    const results = new Map<string, string>();\n    await Promise.all(\n      paths.map(async (p) => {\n        try {\n          const content = await this.read(p);\n          results.set(p, content);\n        } catch {\n          results.set(p, `[Error: could not read ${p}]`);\n        }\n      })\n    );\n    return results;\n  }\n\n  async update(\n    relativePath: string,\n    content: string,\n    options: UpdateNoteOptions\n  ): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    if (!existsSync(absPath)) {\n      throw new Error(`Note does not exist: ${relativePath}`);\n    }\n\n    const existing = await readFile(absPath, \"utf-8\");\n\n    let updated: string;\n\n    switch (options.mode) {\n      case \"overwrite\":\n        updated = content;\n        break;\n\n      case \"append\":\n        updated = existing + \"\\n\" + content;\n        break;\n\n      case \"prepend\": {\n        const { data, content: body } = matter(existing);\n        const newBody = content + \"\\n\" + body;\n        updated = Object.keys(data).length > 0 ? matter.stringify(newBody, data) : newBody;\n        break;\n      }\n\n      case \"patch-by-heading\": {\n        if (!options.heading) throw new Error(\"patch-by-heading requires a heading\");\n        updated = this.patchByHeading(existing, options.heading, content);\n        break;\n      }\n    }\n\n    // Re-parse the final content and inject updated stamps\n    // (preserves all existing frontmatter, only overwrites the three auto fields)\n    const { data: existingFm, content: body } = matter(updated);\n    const stamps = computeStamps(body);\n    const newFm = { ...existingFm, ...stamps };\n    await writeFile(absPath, matter.stringify(body, newFm), \"utf-8\");\n  }\n\n  async delete(relativePath: string): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    if (!existsSync(absPath)) {\n      throw new Error(`Note does not exist: ${relativePath}`);\n    }\n    await unlink(absPath);\n  }\n\n  async move(fromPath: string, toPath: string): Promise<void> {\n    const absFrom = join(this.notesPath, fromPath);\n    const absTo = join(this.notesPath, toPath);\n\n    if (!existsSync(absFrom)) {\n      throw new Error(`Note does not exist: ${fromPath}`);\n    }\n    if (existsSync(absTo)) {\n      throw new Error(`Destination already exists: ${toPath}`);\n    }\n\n    await mkdir(dirname(absTo), { recursive: true });\n    await rename(absFrom, absTo);\n\n    // Update wikilinks in other files that reference the old path\n    await this.updateWikilinksAfterMove(fromPath, toPath);\n  }\n\n  private async updateWikilinksAfterMove(\n    oldPath: string,\n    newPath: string\n  ): Promise<void> {\n    const oldName = oldPath.replace(/\\.md$/, \"\").split(\"/\").pop()!;\n    const newName = newPath.replace(/\\.md$/, \"\").split(\"/\").pop()!;\n\n    if (oldName === newName) return;\n\n    const files = await glob(\"**/*.md\", { cwd: this.notesPath });\n\n    for (const file of files) {\n      const absPath = join(this.notesPath, file);\n      const content = await readFile(absPath, \"utf-8\");\n\n      const pattern = new RegExp(`\\\\[\\\\[${escapeRegex(oldName)}(\\\\|[^\\\\]]*)?\\\\]\\\\]`, \"g\");\n      if (!pattern.test(content)) continue;\n\n      const updated = content.replace(pattern, `[[${newName}$1]]`);\n      await writeFile(absPath, updated, \"utf-8\");\n    }\n  }\n\n  private patchByHeading(\n    content: string,\n    heading: string,\n    newContent: string\n  ): string {\n    const lines = content.split(\"\\n\");\n    const headingPattern = new RegExp(`^#{1,6}\\\\s+${escapeRegex(heading)}\\\\s*$`, \"i\");\n\n    let headingIndex = -1;\n    let headingLevel = 0;\n\n    for (let i = 0; i < lines.length; i++) {\n      if (headingPattern.test(lines[i])) {\n        headingIndex = i;\n        const match = lines[i].match(/^(#{1,6})\\s+/);\n        headingLevel = match ? match[1].length : 1;\n        break;\n      }\n    }\n\n    if (headingIndex === -1) {\n      throw new Error(`Heading not found: ${heading}`);\n    }\n\n    // Find the end of this section (next heading of same or higher level)\n    let endIndex = lines.length;\n    for (let i = headingIndex + 1; i < lines.length; i++) {\n      const match = lines[i].match(/^(#{1,6})\\s+/);\n      if (match && match[1].length <= headingLevel) {\n        endIndex = i;\n        break;\n      }\n    }\n\n    const before = lines.slice(0, headingIndex + 1);\n    const after = lines.slice(endIndex);\n\n    return [...before, \"\", newContent, \"\", ...after].join(\"\\n\");\n  }\n}\n\nfunction escapeRegex(str: string): string {\n  return str.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n\n/**\n * Compute the three auto-stamp fields from note body text.\n * These are always factual/computable — no editorial judgment required.\n * - last_updated: today's date (YYYY-MM-DD)\n * - word_count: whitespace-separated token count\n * - estimated_read_time: assumes ~200 wpm average reading speed\n */\nfunction computeStamps(body: string): Record<string, unknown> {\n  const today = new Date().toISOString().slice(0, 10); // YYYY-MM-DD\n  const wordCount = body.trim() ? body.trim().split(/\\s+/).length : 0;\n  const minutes = Math.max(1, Math.ceil(wordCount / 200));\n  return {\n    last_updated: today,\n    word_count: wordCount,\n    estimated_read_time: `${minutes} min read`,\n  };\n}\n","import { readFile, writeFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport { glob } from \"glob\";\nimport matter from \"gray-matter\";\n\nexport class FrontmatterManager {\n  private notesPath: string;\n\n  constructor(notesPath: string) {\n    this.notesPath = notesPath;\n  }\n\n  async get(relativePath: string): Promise<Record<string, unknown>> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data } = matter(raw);\n    return data;\n  }\n\n  async update(\n    relativePath: string,\n    fields: Record<string, unknown>\n  ): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data, content } = matter(raw);\n\n    for (const [key, value] of Object.entries(fields)) {\n      if (value === null || value === undefined) {\n        delete data[key];\n      } else {\n        data[key] = value;\n      }\n    }\n\n    const updated = matter.stringify(content, data);\n    await writeFile(absPath, updated, \"utf-8\");\n  }\n}\n\nexport class TagManager {\n  private notesPath: string;\n\n  constructor(notesPath: string) {\n    this.notesPath = notesPath;\n  }\n\n  async list(relativePath: string): Promise<string[]> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data, content } = matter(raw);\n\n    const fmTags = Array.isArray(data.tags) ? (data.tags as string[]) : [];\n    const inlineTags = [...content.matchAll(/(?:^|\\s)#([a-zA-Z][\\w-/]*)/g)].map(\n      (m) => m[1]\n    );\n\n    return [...new Set([...fmTags, ...inlineTags])];\n  }\n\n  async add(relativePath: string, tags: string[]): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data, content } = matter(raw);\n\n    const existing = Array.isArray(data.tags) ? (data.tags as string[]) : [];\n    const merged = [...new Set([...existing, ...tags])];\n    data.tags = merged;\n\n    const updated = matter.stringify(content, data);\n    await writeFile(absPath, updated, \"utf-8\");\n  }\n\n  async remove(relativePath: string, tags: string[]): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data, content } = matter(raw);\n\n    // Remove from frontmatter\n    if (Array.isArray(data.tags)) {\n      data.tags = (data.tags as string[]).filter((t) => !tags.includes(t));\n    }\n\n    // Remove inline tags\n    let updatedContent = content;\n    for (const tag of tags) {\n      const pattern = new RegExp(`(^|\\\\s)#${escapeRegex(tag)}(?=\\\\s|$)`, \"g\");\n      updatedContent = updatedContent.replace(pattern, \"$1\");\n    }\n\n    const updated = matter.stringify(updatedContent, data);\n    await writeFile(absPath, updated, \"utf-8\");\n  }\n\n  async renameVaultWide(oldTag: string, newTag: string): Promise<number> {\n    const files = await glob(\"**/*.md\", { cwd: this.notesPath });\n    let count = 0;\n\n    for (const file of files) {\n      const absPath = join(this.notesPath, file);\n      const raw = await readFile(absPath, \"utf-8\");\n      const { data, content } = matter(raw);\n      let changed = false;\n\n      // Rename in frontmatter\n      if (Array.isArray(data.tags)) {\n        const idx = (data.tags as string[]).indexOf(oldTag);\n        if (idx >= 0) {\n          (data.tags as string[])[idx] = newTag;\n          changed = true;\n        }\n      }\n\n      // Rename inline tags\n      const pattern = new RegExp(`(^|\\\\s)#${escapeRegex(oldTag)}(?=\\\\s|$)`, \"g\");\n      const updatedContent = content.replace(pattern, `$1#${newTag}`);\n      if (updatedContent !== content) changed = true;\n\n      if (changed) {\n        const updated = matter.stringify(updatedContent, data);\n        await writeFile(absPath, updated, \"utf-8\");\n        count++;\n      }\n    }\n\n    return count;\n  }\n}\n\nfunction escapeRegex(str: string): string {\n  return str.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n","import { watch, type FSWatcher } from \"chokidar\";\nimport { EventEmitter } from \"node:events\";\n\nexport interface WatcherEvents {\n  changed: (paths: string[]) => void;\n  error: (error: Error) => void;\n}\n\nexport class Watcher extends EventEmitter {\n  private notesPath: string;\n  private fsWatcher: FSWatcher | null = null;\n  private debounceMs: number;\n  private pendingChanges = new Set<string>();\n  private debounceTimer: ReturnType<typeof setTimeout> | null = null;\n  private readyPromise: Promise<void> | null = null;\n  private usePolling: boolean;\n\n  constructor(notesPath: string, debounceMs: number = 500, usePolling: boolean = false) {\n    super();\n    this.notesPath = notesPath;\n    this.debounceMs = debounceMs;\n    this.usePolling = usePolling;\n  }\n\n  start(): void {\n    if (this.fsWatcher) return;\n\n    this.fsWatcher = watch(\"**/*.md\", {\n      cwd: this.notesPath,\n      ignoreInitial: true,\n      followSymlinks: true,\n      ignored: [\n        \"**/node_modules/**\",\n        \"**/.semantic-sidekick-index/**\",\n        \"**/.git/**\",\n      ],\n      ...(this.usePolling ? { usePolling: true, interval: 100 } : {}),\n    });\n\n    this.readyPromise = new Promise<void>((resolve) => {\n      this.fsWatcher!.on(\"ready\", resolve);\n    });\n\n    this.fsWatcher.on(\"add\", (path) => this.enqueue(path));\n    this.fsWatcher.on(\"change\", (path) => this.enqueue(path));\n    this.fsWatcher.on(\"unlink\", (path) => this.enqueue(path));\n    this.fsWatcher.on(\"error\", (err) => this.emit(\"error\", err));\n  }\n\n  async ready(): Promise<void> {\n    if (this.readyPromise) await this.readyPromise;\n  }\n\n  stop(): void {\n    if (this.debounceTimer) clearTimeout(this.debounceTimer);\n    this.fsWatcher?.close();\n    this.fsWatcher = null;\n    this.pendingChanges.clear();\n  }\n\n  private enqueue(path: string): void {\n    this.pendingChanges.add(path);\n\n    if (this.debounceTimer) clearTimeout(this.debounceTimer);\n    this.debounceTimer = setTimeout(() => {\n      const paths = [...this.pendingChanges];\n      this.pendingChanges.clear();\n      this.emit(\"changed\", paths);\n    }, this.debounceMs);\n  }\n}\n","import { basename } from \"node:path\";\nimport type { ChangeSet, PatchCreate } from \"./patch.js\";\n\nexport interface IngestSource {\n  /** Identifier of the source — URL, filesystem path, DOI, ISBN, etc. */\n  source_uri: string;\n  /** Human-readable title for the source-note's frontmatter */\n  source_title: string;\n  /** One of the schema types; typically \"source\" */\n  source_type?: string;\n  /** Path under the vault to write the source-note. Defaults to `sources/<slug>.md`. */\n  source_path?: string;\n  /** Free-form body for the source-note (summary, abstract, your notes on it) */\n  source_summary?: string;\n  /** Tags for the source-note */\n  source_tags?: string[];\n}\n\nexport interface IngestUnit {\n  /** Path under the vault where this extracted note should live */\n  path: string;\n  /** Note title — if absent, derived from basename */\n  title?: string;\n  /** Note body — markdown */\n  content: string;\n  /** Schema type. Default: \"note\". */\n  type?: string;\n  /** Additional wikilink-style derived_from targets beyond the source-note */\n  extra_derived_from?: string[];\n  /** Additional free-form frontmatter fields */\n  extra_frontmatter?: Record<string, unknown>;\n  /** Per-unit confidence override */\n  confidence?: string;\n}\n\nexport interface IngestInput {\n  source: IngestSource;\n  units: IngestUnit[];\n  /** If true, the existing source-note is updated if present; else an error is raised */\n  allow_existing_source?: boolean;\n}\n\nexport interface IngestPreview {\n  changeset: ChangeSet;\n  sourcePath: string;\n  unitPaths: string[];\n}\n\n/**\n * Build a ChangeSet for ingesting a source into the vault.\n *\n * Shape: one create for the source-note (type=source) + one create per unit,\n * each stamped with `derived_from: [<source-path>]` so lint.missing_provenance\n * is satisfied automatically and the graph reflects the provenance edge.\n *\n * Intentionally does NOT touch the filesystem — callers route the result\n * through applyPatch for atomicity, validation, and rollback.\n */\nexport function buildIngestChangeSet(input: IngestInput): IngestPreview {\n  const today = new Date().toISOString().slice(0, 10);\n  const sourcePath = input.source.source_path ?? defaultSourcePath(input.source);\n\n  const sourceNote: PatchCreate = {\n    path: sourcePath,\n    content: buildSourceBody(input.source),\n    frontmatter: {\n      title: input.source.source_title,\n      type: input.source.source_type ?? \"source\",\n      status: \"active\",\n      source: input.source.source_uri,\n      last_verified: today,\n      confidence: \"high\",\n      ...(input.source.source_tags && input.source.source_tags.length > 0 && { tags: input.source.source_tags }),\n    },\n  };\n\n  const unitCreates: PatchCreate[] = input.units.map((u) => {\n    const title = u.title ?? titleFromPath(u.path);\n    const derivedFrom = [sourcePath, ...(u.extra_derived_from ?? [])];\n    return {\n      path: u.path.endsWith(\".md\") ? u.path : u.path + \".md\",\n      content: u.content.startsWith(\"#\") ? u.content : `# ${title}\\n\\n${u.content.trim()}\\n`,\n      frontmatter: {\n        title,\n        type: u.type ?? \"note\",\n        status: \"active\",\n        derived_from: derivedFrom,\n        last_verified: today,\n        confidence: u.confidence ?? \"medium\",\n        ...(u.extra_frontmatter ?? {}),\n      },\n    };\n  });\n\n  return {\n    changeset: { creates: [sourceNote, ...unitCreates] },\n    sourcePath,\n    unitPaths: unitCreates.map((c) => c.path),\n  };\n}\n\nfunction buildSourceBody(source: IngestSource): string {\n  const lines = [`# ${source.source_title}`, \"\", `**Source:** ${source.source_uri}`, \"\"];\n  if (source.source_summary) {\n    lines.push(source.source_summary.trim(), \"\");\n  } else {\n    lines.push(\"_Summary not provided — fill in when referencing this source._\", \"\");\n  }\n  return lines.join(\"\\n\");\n}\n\nfunction defaultSourcePath(source: IngestSource): string {\n  const slug = slugify(source.source_title);\n  return `sources/${slug}.md`;\n}\n\nfunction titleFromPath(p: string): string {\n  return basename(p).replace(/\\.md$/, \"\").replace(/[-_]/g, \" \");\n}\n\nfunction slugify(s: string): string {\n  return s\n    .toLowerCase()\n    .replace(/[^\\w\\s-]/g, \"\")\n    .replace(/\\s+/g, \"-\")\n    .replace(/-+/g, \"-\")\n    .replace(/^-|-$/g, \"\")\n    .slice(0, 80);\n}\n","import { readdir, readFile, writeFile, stat } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { join, dirname, basename, sep } from \"node:path\";\nimport matter from \"gray-matter\";\n\nexport const INDEX_FILE = \"INDEX.md\";\nexport const INDEX_OVERFLOW_THRESHOLD = 100; // entries before we warn about splitting\n\nexport interface IndexEntry {\n  path: string; // relative to the directory\n  title: string;\n  summary?: string;\n}\n\nexport interface RegenResult {\n  directory: string;\n  indexPath: string;\n  entryCount: number;\n  overflowed: boolean;\n  wrote: boolean;\n}\n\n/**\n * Regenerate INDEX.md for a single vault directory.\n * Lists every *.md file in the directory (non-recursive, excluding the index itself)\n * with its title (frontmatter or first heading) and optional summary (from frontmatter\n * `purpose` or first non-heading paragraph).\n */\nexport async function regenDirectoryIndex(vaultPath: string, dirRel: string): Promise<RegenResult> {\n  const absDir = join(vaultPath, dirRel);\n  const indexPath = join(absDir, INDEX_FILE);\n  const relIndex = join(dirRel, INDEX_FILE);\n\n  if (!existsSync(absDir)) {\n    return { directory: dirRel, indexPath: relIndex, entryCount: 0, overflowed: false, wrote: false };\n  }\n\n  const files = (await readdir(absDir)).filter(\n    (f) => f.endsWith(\".md\") && f !== INDEX_FILE && f !== \"README.md\"\n  );\n\n  const entries: IndexEntry[] = [];\n  for (const f of files) {\n    const full = join(absDir, f);\n    try {\n      const st = await stat(full);\n      if (!st.isFile()) continue;\n      const raw = await readFile(full, \"utf-8\");\n      const { data, content } = matter(raw);\n      const title = typeof data.title === \"string\" ? data.title : firstHeading(content) ?? basenameNoExt(f);\n      const summary = typeof data.purpose === \"string\" ? data.purpose : firstParagraph(content);\n      entries.push({ path: f, title, summary });\n    } catch {\n      /* skip unreadable */\n    }\n  }\n\n  entries.sort((a, b) => a.title.localeCompare(b.title));\n  const body = renderIndex(dirRel, entries);\n  const overflowed = entries.length > INDEX_OVERFLOW_THRESHOLD;\n\n  let wrote = false;\n  if (existsSync(indexPath)) {\n    const current = await readFile(indexPath, \"utf-8\");\n    if (current !== body) {\n      await writeFile(indexPath, body, \"utf-8\");\n      wrote = true;\n    }\n  } else {\n    await writeFile(indexPath, body, \"utf-8\");\n    wrote = true;\n  }\n\n  return { directory: dirRel, indexPath: relIndex, entryCount: entries.length, overflowed, wrote };\n}\n\n/**\n * Regenerate indexes for every directory affected by a set of paths.\n * Walks up the parent chain for each input so a deep change at\n * `a/b/c/note.md` regenerates `a/b/c/INDEX.md`. Does NOT recurse further —\n * `a/b/INDEX.md` stays as-is unless a path under `a/b/` (not `a/b/c/`)\n * also changed.\n */\nexport async function regenIndexesForPaths(\n  vaultPath: string,\n  paths: string[]\n): Promise<RegenResult[]> {\n  const dirs = new Set<string>();\n  for (const p of paths) {\n    const d = dirname(p);\n    if (d === \".\" || d === \"/\") continue;\n    dirs.add(d);\n  }\n  const results: RegenResult[] = [];\n  for (const d of dirs) {\n    results.push(await regenDirectoryIndex(vaultPath, d));\n  }\n  return results;\n}\n\nfunction renderIndex(dirRel: string, entries: IndexEntry[]): string {\n  const header = `# ${toTitle(dirRel)} Index\\n\\n> Auto-generated by semantic-sidekick. Changes are overwritten on apply_patch. Add prose to per-note files, not here.\\n\\n`;\n  if (entries.length === 0) return header + \"_No notes in this directory yet._\\n\";\n  const overflowNote =\n    entries.length > INDEX_OVERFLOW_THRESHOLD\n      ? `> ⚠️  ${entries.length} entries — consider splitting this directory into subfolders (threshold: ${INDEX_OVERFLOW_THRESHOLD}).\\n\\n`\n      : \"\";\n  const lines = entries.map((e) => {\n    const linkText = e.title;\n    const target = e.path.replace(/\\.md$/, \"\");\n    const summary = e.summary ? ` — ${truncate(e.summary, 140)}` : \"\";\n    return `- [${linkText}](./${e.path}) — \\`[[${target}]]\\`${summary}`;\n  });\n  return header + overflowNote + lines.join(\"\\n\") + \"\\n\";\n}\n\nfunction toTitle(dirRel: string): string {\n  return dirRel\n    .split(sep)\n    .pop()!\n    .replace(/[-_]/g, \" \")\n    .replace(/\\b\\w/g, (c) => c.toUpperCase());\n}\n\nfunction basenameNoExt(p: string): string {\n  return basename(p).replace(/\\.md$/, \"\");\n}\n\nfunction firstHeading(content: string): string | null {\n  const m = content.match(/^\\s*#{1,6}\\s+(.+)$/m);\n  return m ? m[1].trim() : null;\n}\n\nfunction firstParagraph(content: string): string | undefined {\n  // Skip leading headings, then take the first line of non-heading text\n  const lines = content.split(\"\\n\");\n  for (const line of lines) {\n    const trimmed = line.trim();\n    if (!trimmed) continue;\n    if (trimmed.startsWith(\"#\")) continue;\n    if (trimmed.startsWith(\">\")) continue;\n    if (trimmed.startsWith(\"```\")) continue;\n    return trimmed.replace(/\\s+/g, \" \");\n  }\n  return undefined;\n}\n\nfunction truncate(s: string, n: number): string {\n  return s.length <= n ? s : s.slice(0, n - 1).trimEnd() + \"…\";\n}\n","import { readFile, writeFile, unlink, rename, mkdir } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { dirname, join } from \"node:path\";\nimport matter from \"gray-matter\";\nimport type { UpdateNoteOptions } from \"./types.js\";\nimport { NoteCrud } from \"./crud.js\";\nimport { loadSchema, validateNote, type LintFinding, type VaultSchema } from \"./schema.js\";\nimport { regenIndexesForPaths, type RegenResult } from \"./index-regen.js\";\n\nexport interface PatchCreate {\n  path: string;\n  content: string;\n  frontmatter?: Record<string, unknown>;\n}\n\nexport interface PatchUpdate {\n  path: string;\n  content: string;\n  mode: UpdateNoteOptions[\"mode\"];\n  heading?: string;\n}\n\nexport interface PatchDelete {\n  path: string;\n}\n\nexport interface PatchMove {\n  from: string;\n  to: string;\n}\n\nexport interface ChangeSet {\n  creates?: PatchCreate[];\n  updates?: PatchUpdate[];\n  deletes?: PatchDelete[];\n  moves?: PatchMove[];\n}\n\nexport interface ApplyPatchOptions {\n  dryRun?: boolean;\n  validate?: boolean;\n  allowLintWarnings?: boolean;\n  /** Regenerate INDEX.md in directories touched by this patch. Default: true. */\n  regenIndexes?: boolean;\n}\n\nexport interface AppliedOp {\n  op: \"create\" | \"update\" | \"delete\" | \"move\";\n  path: string;\n}\n\nexport interface ApplyPatchResult {\n  ok: boolean;\n  applied: AppliedOp[];\n  rolledBack: AppliedOp[];\n  lint: LintFinding[];\n  errors: string[];\n  /** Index files regenerated as a side-effect. Empty if regenIndexes=false or dry-run. */\n  indexes_regenerated?: RegenResult[];\n}\n\ninterface Snapshot {\n  op: \"create\" | \"update\" | \"delete\" | \"move\";\n  path: string;\n  absPath: string;\n  prevContent?: string; // for update/delete/move(from)\n  prevAbsPath?: string; // for move (prev location)\n}\n\n/**\n * Atomic multi-note patch with rollback. Applies creates → updates → moves → deletes\n * in that order. If any op fails, all successful ops before it are reverted in reverse.\n *\n * In dry-run mode, nothing is written; the result describes what would have happened,\n * including lint findings on the proposed state.\n */\nexport async function applyPatch(\n  notesPath: string,\n  changeset: ChangeSet,\n  options: ApplyPatchOptions = {}\n): Promise<ApplyPatchResult> {\n  const validate = options.validate !== false;\n  const dryRun = options.dryRun === true;\n  const allowWarn = options.allowLintWarnings !== false;\n\n  const errors: string[] = [];\n  const lint: LintFinding[] = [];\n  const applied: AppliedOp[] = [];\n  const snapshots: Snapshot[] = [];\n\n  const crud = new NoteCrud(notesPath);\n\n  let schema: VaultSchema | null = null;\n  if (validate) {\n    try {\n      schema = await loadSchema(notesPath);\n    } catch (e) {\n      errors.push(`failed to load schema: ${e instanceof Error ? e.message : String(e)}`);\n      return { ok: false, applied, rolledBack: [], lint, errors };\n    }\n  }\n\n  // Pre-check: collisions on creates, missing sources on updates/deletes/moves.\n  for (const c of changeset.creates ?? []) {\n    if (existsSync(join(notesPath, c.path))) {\n      errors.push(`create: already exists: ${c.path}`);\n    }\n  }\n  for (const u of changeset.updates ?? []) {\n    if (!existsSync(join(notesPath, u.path))) {\n      errors.push(`update: does not exist: ${u.path}`);\n    }\n  }\n  for (const d of changeset.deletes ?? []) {\n    if (!existsSync(join(notesPath, d.path))) {\n      errors.push(`delete: does not exist: ${d.path}`);\n    }\n  }\n  for (const m of changeset.moves ?? []) {\n    if (!existsSync(join(notesPath, m.from))) {\n      errors.push(`move: source does not exist: ${m.from}`);\n    }\n    if (existsSync(join(notesPath, m.to))) {\n      errors.push(`move: destination exists: ${m.to}`);\n    }\n  }\n\n  if (errors.length > 0) {\n    return { ok: false, applied, rolledBack: [], lint, errors };\n  }\n\n  // Lint pre-flight on proposed state. Simulate each create/update and validate.\n  if (validate && schema) {\n    for (const c of changeset.creates ?? []) {\n      const proposed = matter.stringify(c.content, c.frontmatter ?? {});\n      lint.push(...validateNote(c.path, proposed, schema));\n    }\n    for (const u of changeset.updates ?? 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[]) {\n      const abs = join(notesPath, c.path);\n      await crud.create(c.path, c.content, c.frontmatter);\n      snapshots.push({ op: \"create\", path: c.path, absPath: abs });\n      applied.push({ op: \"create\", path: c.path });\n    }\n    for (const u of changeset.updates ?? []) {\n      const abs = join(notesPath, u.path);\n      const prev = await readFile(abs, \"utf-8\");\n      await crud.update(u.path, u.content, { mode: u.mode, heading: u.heading } as UpdateNoteOptions);\n      snapshots.push({ op: \"update\", path: u.path, absPath: abs, prevContent: prev });\n      applied.push({ op: \"update\", path: u.path });\n    }\n    for (const m of changeset.moves ?? 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