@theglitchking/semantic-memory 1.0.1 → 1.1.0

package/hooks/vault-context.js

@@ -305,10 +305,98 @@ 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 +429,19 @@ 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 +451,34 @@ 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": "1.1.0",
   "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/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 ?? []) {\n      const abs = join(notesPath, u.path);\n      let proposed: string;\n      try {\n        const existing = await readFile(abs, \"utf-8\");\n        proposed = applyUpdateInMemory(existing, u);\n      } catch (e) {\n        errors.push(`update precheck: ${u.path}: ${e instanceof Error ? e.message : String(e)}`);\n        continue;\n      }\n      lint.push(...validateNote(u.path, proposed, schema));\n    }\n\n    const schemaErrors = lint.filter((f) => f.rule === \"schema_violations\" && f.severity === \"error\");\n    if (schemaErrors.length > 0) {\n      errors.push(`${schemaErrors.length} schema violation(s) blocked the patch`);\n    }\n    if (!allowWarn) {\n      const warns = lint.filter((f) => f.severity === \"warn\");\n      if (warns.length > 0) errors.push(`${warns.length} lint warning(s) blocked the patch (allowLintWarnings=false)`);\n    }\n  }\n\n  if (errors.length > 0 || dryRun) {\n    return { ok: errors.length === 0, applied, rolledBack: [], lint, errors };\n  }\n\n  // Execute — capture snapshots as we go so rollback can reverse.\n  try {\n    for (const c of changeset.creates ?? []) {\n      const abs = join(notesPath, c.path);\n      await crud.create(c.path, c.content, c.frontmatter);\n      snapshots.push({ op: \"create\", path: c.path, absPath: abs });\n      applied.push({ op: \"create\", path: c.path });\n    }\n    for (const u of changeset.updates ?? []) {\n      const abs = join(notesPath, u.path);\n      const prev = await readFile(abs, \"utf-8\");\n      await crud.update(u.path, u.content, { mode: u.mode, heading: u.heading } as UpdateNoteOptions);\n      snapshots.push({ op: \"update\", path: u.path, absPath: abs, prevContent: prev });\n      applied.push({ op: \"update\", path: u.path });\n    }\n    for (const m of changeset.moves ?? []) {\n      await crud.move(m.from, m.to);\n      snapshots.push({\n        op: \"move\",\n        path: m.to,\n        absPath: join(notesPath, m.to),\n        prevAbsPath: join(notesPath, m.from),\n      });\n      applied.push({ op: \"move\", path: `${m.from} -> ${m.to}` });\n    }\n    for (const d of changeset.deletes ?? []) {\n      const abs = join(notesPath, d.path);\n      const prev = await readFile(abs, \"utf-8\");\n      await crud.delete(d.path);\n      snapshots.push({ op: \"delete\", path: d.path, absPath: abs, prevContent: prev });\n      applied.push({ op: \"delete\", path: d.path });\n    }\n  } catch (e) {\n    errors.push(`op failed: ${e instanceof Error ? e.message : String(e)} — rolling back`);\n    const rolledBack = await rollback(snapshots);\n    return { ok: false, applied, rolledBack, lint, errors };\n  }\n\n  let indexes_regenerated: RegenResult[] = [];\n  if (options.regenIndexes !== false) {\n    const touched = [\n      ...(changeset.creates ?? []).map((c) => c.path),\n      ...(changeset.deletes ?? []).map((d) => d.path),\n      ...(changeset.moves ?? []).flatMap((m) => [m.from, m.to]),\n    ];\n    try {\n      indexes_regenerated = await regenIndexesForPaths(notesPath, touched);\n    } catch (e) {\n      // Non-fatal: patch succeeded; index regen is a best-effort side effect.\n      errors.push(`index regen failed (patch still applied): ${e instanceof Error ? e.message : String(e)}`);\n    }\n  }\n\n  return { ok: true, applied, rolledBack: [], lint, errors, indexes_regenerated };\n}\n\nasync function rollback(snapshots: Snapshot[]): Promise<AppliedOp[]> {\n  const reverted: AppliedOp[] = [];\n  for (const s of snapshots.slice().reverse()) {\n    try {\n      switch (s.op) {\n        case \"create\":\n          if (existsSync(s.absPath)) await unlink(s.absPath);\n          reverted.push({ op: \"create\", path: s.path });\n          break;\n        case \"update\":\n          if (s.prevContent !== undefined) {\n            await writeFile(s.absPath, s.prevContent, \"utf-8\");\n          }\n          reverted.push({ op: \"update\", path: s.path });\n          break;\n        case \"delete\":\n          if (s.prevContent !== undefined) {\n            await mkdir(dirname(s.absPath), { recursive: true });\n            await writeFile(s.absPath, s.prevContent, \"utf-8\");\n          }\n          reverted.push({ op: \"delete\", path: s.path });\n          break;\n        case \"move\":\n          if (s.prevAbsPath && existsSync(s.absPath)) {\n            await mkdir(dirname(s.prevAbsPath), { recursive: true });\n            await rename(s.absPath, s.prevAbsPath);\n          }\n          reverted.push({ op: \"move\", path: s.path });\n          break;\n      }\n    } catch {\n      // swallow — best-effort rollback\n    }\n  }\n  return reverted;\n}\n\nfunction applyUpdateInMemory(existing: string, u: PatchUpdate): string {\n  switch (u.mode) {\n    case \"overwrite\":\n      return u.content;\n    case \"append\":\n      return existing + \"\\n\" + u.content;\n    case \"prepend\": {\n      const { data, content: body } = matter(existing);\n      const newBody = u.content + \"\\n\" + body;\n      return Object.keys(data).length > 0 ? matter.stringify(newBody, data) : newBody;\n    }\n    case \"patch-by-heading\": {\n      if (!u.heading) throw new Error(\"patch-by-heading requires heading\");\n      return patchByHeadingInMemory(existing, u.heading, u.content);\n    }\n  }\n}\n\nfunction patchByHeadingInMemory(content: string, heading: string, newContent: string): string {\n  const lines = content.split(\"\\n\");\n  const re = new RegExp(`^#{1,6}\\\\s+${heading.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\")}\\\\s*$`, \"i\");\n  let idx = -1;\n  let level = 0;\n  for (let i = 0; i < lines.length; i++) {\n    if (re.test(lines[i])) {\n      idx = i;\n      const m = lines[i].match(/^(#{1,6})\\s+/);\n      level = m ? m[1].length : 1;\n      break;\n    }\n  }\n  if (idx === -1) throw new Error(`Heading not found: ${heading}`);\n  let end = lines.length;\n  for (let i = idx + 1; i < lines.length; i++) {\n    const m = lines[i].match(/^(#{1,6})\\s+/);\n    if (m && m[1].length <= level) {\n      end = i;\n      break;\n    }\n  }\n  return [...lines.slice(0, idx + 1), \"\", newContent, \"\", ...lines.slice(end)].join(\"\\n\");\n}\n","import { basename } from \"node:path\";\nimport type { ChangeSet, PatchCreate, PatchUpdate } from \"./patch.js\";\n\nexport interface SynthesizeNoteInput {\n  topic: string;\n  answer: string;\n  suggested_path: string;\n  type?: string;\n  sources?: string[];\n  derived_from?: string[];\n  related_notes?: string[];\n  status?: string;\n  confidence?: string;\n  decision_maker?: string;\n  decided_on?: string;\n  severity?: string;\n  extra_frontmatter?: Record<string, unknown>;\n}\n\nexport interface SynthesizePreview {\n  changeset: ChangeSet;\n  path: string;\n  title: string;\n}\n\n/**\n * Convert a query answer + provenance into a ChangeSet that can be fed to applyPatch.\n * The shaped note includes provenance frontmatter and auto-inserts [[wikilinks]] for\n * any related_notes that appear as bare titles in the body.\n *\n * Does NOT write to disk — always returns a ChangeSet. Callers pass it to applyPatch.\n */\nexport function buildSynthesizeChangeSet(input: SynthesizeNoteInput): SynthesizePreview {\n  const path = input.suggested_path.endsWith(\".md\") ? input.suggested_path : input.suggested_path + \".md\";\n  const title = input.topic.trim();\n  const today = new Date().toISOString().slice(0, 10);\n\n  const frontmatter: Record<string, unknown> = {\n    title,\n    type: input.type ?? \"note\",\n    status: input.status ?? \"active\",\n    last_verified: today,\n    confidence: input.confidence ?? \"medium\",\n    ...(input.sources && input.sources.length > 0 && { sources: input.sources }),\n    ...(input.derived_from && input.derived_from.length > 0 && { derived_from: input.derived_from }),\n    ...(input.decision_maker && { decision_maker: input.decision_maker }),\n    ...(input.decided_on && { decided_on: input.decided_on }),\n    ...(input.severity && { severity: input.severity }),\n    ...(input.extra_frontmatter ?? {}),\n  };\n\n  const body = buildBody(title, input.answer, input.related_notes ?? []);\n\n  const create: PatchCreate = { path, content: body, frontmatter };\n  const changeset: ChangeSet = { creates: [create] };\n\n  return { changeset, path, title };\n}\n\nfunction buildBody(title: string, answer: string, relatedNotes: string[]): string {\n  let body = `# ${title}\\n\\n${answer.trim()}\\n`;\n\n  if (relatedNotes.length > 0) {\n    body = autoWikilink(body, relatedNotes);\n    const links = relatedNotes.map((r) => `- [[${wikilinkName(r)}]]`).join(\"\\n\");\n    body += `\\n## Related\\n\\n${links}\\n`;\n  }\n\n  return body;\n}\n\n/**\n * For each related note, replace the first bare occurrence of its title in the body\n * with a [[wikilink]]. Conservative — only replaces whole-word matches outside code blocks.\n */\nfunction autoWikilink(body: string, relatedNotes: string[]): string {\n  // Skip content inside fenced code blocks\n  const parts = body.split(/(```[\\s\\S]*?```)/g);\n  return parts\n    .map((part, i) => {\n      if (i % 2 === 1) return part; // code block\n      let out = part;\n      for (const r of relatedNotes) {\n        const name = wikilinkName(r);\n        if (/[\\[\\]]/.test(out) && out.includes(`[[${name}]]`)) continue; // already linked\n        const escaped = name.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n        const re = new RegExp(`\\\\b${escaped}\\\\b`, \"i\");\n        out = out.replace(re, `[[${name}]]`);\n      }\n      return out;\n    })\n    .join(\"\");\n}\n\nfunction wikilinkName(pathOrName: string): string {\n  // \"decisions/auth-migration.md\" → \"auth-migration\"\n  // \"Auth Migration\" → \"Auth Migration\"\n  const base = basename(pathOrName).replace(/\\.md$/, \"\");\n  return 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