@theglitchking/semantic-memory 1.0.0 → 1.1.0

package/dist/{chunk-CXTRTCIK.js → chunk-XBAN7GRT.js}

@@ -689,13 +689,17 @@ function patchByHeadingInMemory(content, heading, newContent) {
 // src/core/synthesize.ts
 import { basename as basename3 } from "path";
 function buildSynthesizeChangeSet(input) {
-  const path = input.suggested_path.endsWith(".md") ? input.suggested_path : input.suggested_path + ".md";
-  const title = input.topic.trim();
   const today = (/* @__PURE__ */ new Date()).toISOString().slice(0, 10);
+  const title = input.topic.trim();
+  const canonicalPath = input.suggested_path.endsWith(".md") ? input.suggested_path : input.suggested_path + ".md";
+  const isProposal = input.proposal === true;
+  const subdir = (input.proposal_subdir ?? "proposals").replace(/\/+$/, "");
+  const slug = slugForTopic(title);
+  const path = isProposal ? `${subdir}/${today}-${slug}.md` : canonicalPath;
   const frontmatter = {
     title,
     type: input.type ?? "note",
-    status: input.status ?? "active",
+    status: isProposal ? "proposal" : input.status ?? "active",
     last_verified: today,
     confidence: input.confidence ?? "medium",
     ...input.sources && input.sources.length > 0 && { sources: input.sources },
@@ -703,12 +707,21 @@ function buildSynthesizeChangeSet(input) {
     ...input.decision_maker && { decision_maker: input.decision_maker },
     ...input.decided_on && { decided_on: input.decided_on },
     ...input.severity && { severity: input.severity },
+    ...isProposal && { proposed_target: canonicalPath },
     ...input.extra_frontmatter ?? {}
   };
   const body = buildBody(title, input.answer, input.related_notes ?? []);
   const create = { path, content: body, frontmatter };
   const changeset = { creates: [create] };
-  return { changeset, path, title };
+  return {
+    changeset,
+    path,
+    title,
+    ...isProposal && { is_proposal: true, proposed_target: canonicalPath }
+  };
+}
+function slugForTopic(topic) {
+  return topic.toLowerCase().replace(/[^a-z0-9]+/g, "-").replace(/^-+|-+$/g, "").slice(0, 60) || "untitled";
 }
 function buildBody(title, answer, relatedNotes) {
   let body = `# ${title}
@@ -745,6 +758,361 @@ function wikilinkName(pathOrName) {
   const base = basename3(pathOrName).replace(/\.md$/, "");
   return base;
 }
+function buildPromoteChangeSet(input) {
+  const fm = { ...input.frontmatter };
+  const target = input.target_path ?? (typeof fm.proposed_target === "string" ? fm.proposed_target : void 0);
+  if (!target) {
+    throw new Error(
+      `Cannot promote ${input.proposal_path}: no target_path provided and no 'proposed_target' frontmatter on the proposal.`
+    );
+  }
+  if (fm.status === "proposal") fm.status = "active";
+  delete fm.proposed_target;
+  const create = {
+    path: target,
+    content: input.body,
+    frontmatter: fm
+  };
+  const changeset = {
+    creates: [create],
+    deletes: [{ path: input.proposal_path }]
+  };
+  return { changeset, from: input.proposal_path, to: target };
+}
+
+// src/core/agents-contract.ts
+import { readFile as readFile5, writeFile as writeFile5 } from "fs/promises";
+import { existsSync as existsSync4 } from "fs";
+import { join as join5 } from "path";
+var BEGIN_MARKER = "<!-- semantic-memory:begin contract -->";
+var END_MARKER = "<!-- semantic-memory:end contract -->";
+var LOCAL_NOTES_HEADING = "## Local Notes";
+async function regenerateAgentsContract(opts) {
+  const path = join5(opts.projectRoot, "AGENTS.md");
+  const generatedBlock = buildManagedBlock(opts);
+  const generatedFull = buildFullDocument(opts, generatedBlock);
+  if (!existsSync4(path)) {
+    await writeFile5(path, generatedFull, "utf-8");
+    return { path, written: true };
+  }
+  const existing = await readFile5(path, "utf-8");
+  const beginIdx = existing.indexOf(BEGIN_MARKER);
+  const endIdx = existing.indexOf(END_MARKER);
+  if (beginIdx === -1 || endIdx === -1 || endIdx < beginIdx) {
+    return {
+      path,
+      written: false,
+      reason: "AGENTS.md exists but does not contain the semantic-memory managed-block markers. Move your existing content into a Local Notes section outside the managed block, or delete AGENTS.md and re-run to bootstrap from scratch."
+    };
+  }
+  const existingBlock = existing.slice(beginIdx, endIdx + END_MARKER.length);
+  const localTail = extractLocalTail(existing, endIdx + END_MARKER.length);
+  if (!opts.force && hasHandEdits(existingBlock, generatedBlock)) {
+    return {
+      path,
+      written: false,
+      hand_edit_detected: true,
+      reason: "Managed-block content has been hand-edited. Move your changes to the Local Notes section (outside the managed block) and re-run, or pass force=true to overwrite."
+    };
+  }
+  const newPrefix = buildPrefix(opts);
+  const newDoc = newPrefix + generatedBlock + localTail;
+  await writeFile5(path, newDoc, "utf-8");
+  return {
+    path,
+    written: true,
+    preserved_local_notes_chars: localTail.length
+  };
+}
+function buildPrefix(opts) {
+  return [
+    "---",
+    `generated_by: semantic-memory`,
+    `version: ${opts.pluginVersion}`,
+    `last_generated: ${opts.nowIso ?? (/* @__PURE__ */ new Date()).toISOString()}`,
+    "---",
+    "",
+    "# Project Agent Contract",
+    ""
+  ].join("\n");
+}
+function buildFullDocument(opts, managedBlock) {
+  const localNotes = `
+
+${LOCAL_NOTES_HEADING}
+
+_User-authored content lives here. Preserved across \`regenerate_contract\` runs._
+`;
+  return buildPrefix(opts) + managedBlock + localNotes;
+}
+function buildManagedBlock(opts) {
+  const lines = [BEGIN_MARKER, ""];
+  lines.push("## Active Modes", "");
+  const modes = opts.modes ?? defaultModes();
+  for (const m of modes) {
+    const tag = m.isDefault ? " (default)" : "";
+    lines.push(`- **${m.name}**${tag} \u2014 ${m.description}`);
+  }
+  lines.push("");
+  lines.push("## Required Workflow", "");
+  lines.push("1. For multi-step work that needs verification, open a session: `session_start({task})`.");
+  lines.push("2. Use mode-aware retrieval: `search_hybrid`, `read_note`, `list_notes`, `backlinks`/`forwardlinks`.");
+  lines.push("3. Make durable updates via `apply_patch` or `synthesize_note` \u2014 never bypass the patch layer for multi-note edits.");
+  lines.push("4. Run verification commands inside a session: `session_run({cmd})`.");
+  lines.push("5. Close with `session_finish({summary})` \u2014 refused without verification unless explicitly waived.");
+  lines.push("6. Lint regularly: `lint_vault({checks: ['schema','provenance','stale','broken_links']})`.");
+  lines.push("");
+  lines.push("## Tool Surface", "");
+  const live = opts.tools.filter((t) => !t.deprecated);
+  const deprecated = opts.tools.filter((t) => t.deprecated);
+  for (const t of live) {
+    lines.push(`- \`${t.name}\` \u2014 ${stripDeprecationPrefix(t.description)}`);
+  }
+  if (deprecated.length > 0) {
+    lines.push("");
+    lines.push("### Deprecated (removed in v2.0.0)", "");
+    for (const t of deprecated) {
+      lines.push(`- \`${t.name}\` \u2014 ${stripDeprecationPrefix(t.description)}`);
+    }
+  }
+  lines.push("");
+  lines.push("## Memory Policy", "");
+  lines.push("- Markdown is canonical. The vault under `.claude/.vault/` (or wherever `--notes` points) is the source of truth.");
+  lines.push("- Indexes (vector / graph / FTS) are derived state \u2014 rebuildable via `reindex` without losing knowledge.");
+  lines.push("- Provenance frontmatter is required for `note`/`decision`/`gotcha` types \u2014 `sources` (external) or `derived_from` (internal).");
+  lines.push("- Mode router lives at `.claude/.sidekick-mode`; explicit `/mode` is ground truth.");
+  lines.push("");
+  lines.push(END_MARKER);
+  return lines.join("\n");
+}
+function defaultModes() {
+  return [
+    { name: "vault-first", description: "Project-scoped prose questions trigger vault consultation with cite-or-deflect.", isDefault: true },
+    { name: "research", description: "Every source introduced is filed via `ingest_source`; mandatory `synthesize_note` on exit." },
+    { name: "outage-silence", description: "No proactive vault search. Terse responses. Postmortem `synthesize_note` on exit." }
+  ];
+}
+function stripDeprecationPrefix(description) {
+  return description.replace(/^\[DEPRECATED[^\]]*\]\s*/, "(deprecated) ");
+}
+function extractLocalTail(existing, afterEndIdx) {
+  const tail = existing.slice(afterEndIdx);
+  return tail;
+}
+function hasHandEdits(existingBlock, generatedBlock) {
+  return existingBlock.trim() !== generatedBlock.trim();
+}
+async function inspectAgentsContract(projectRoot) {
+  const path = join5(projectRoot, "AGENTS.md");
+  if (!existsSync4(path)) {
+    return { path, exists: false, has_managed_block: false, local_notes_chars: 0 };
+  }
+  const raw = await readFile5(path, "utf-8");
+  const beginIdx = raw.indexOf(BEGIN_MARKER);
+  const endIdx = raw.indexOf(END_MARKER);
+  if (beginIdx === -1 || endIdx === -1) {
+    return { path, exists: true, has_managed_block: false, local_notes_chars: 0 };
+  }
+  const localTail = raw.slice(endIdx + END_MARKER.length).trim();
+  return { path, exists: true, has_managed_block: true, local_notes_chars: localTail.length };
+}
+
+// src/core/session.ts
+import { mkdir as mkdir3, readFile as readFile6, writeFile as writeFile6, rm } from "fs/promises";
+import { existsSync as existsSync5 } from "fs";
+import { join as join6 } from "path";
+import { spawn } from "child_process";
+var STALE_THRESHOLD_MS = 24 * 60 * 60 * 1e3;
+var DEFAULT_TIMEOUT_MS = 5 * 60 * 1e3;
+var TAIL_BYTES = 4096;
+var SessionManager = class {
+  constructor(sessionDir) {
+    this.sessionDir = sessionDir;
+  }
+  sessionDir;
+  get sessionPath() {
+    return join6(this.sessionDir, "session.json");
+  }
+  async start(task, opts = {}) {
+    if (!task || task.trim().length === 0) {
+      return { ok: false, error: "session_start requires a non-empty task." };
+    }
+    await mkdir3(this.sessionDir, { recursive: true });
+    const existing = await this.read();
+    if (existing && !existing.closed_at) {
+      const reuseSameTask = opts.reuseSameTask !== false;
+      if (reuseSameTask && existing.task === task) {
+        return { ok: true, id: existing.id, reused: true };
+      }
+      return {
+        ok: false,
+        error: `Session already open: id=${existing.id}, task=${JSON.stringify(existing.task)}. Close it with session_finish first.`
+      };
+    }
+    const now = (/* @__PURE__ */ new Date()).toISOString();
+    const id = `ses_${now.replace(/[:.]/g, "-")}`;
+    const state = {
+      id,
+      task: task.trim(),
+      started_at: now,
+      last_activity_at: now,
+      verifications: [],
+      notes_touched: []
+    };
+    await writeFile6(this.sessionPath, JSON.stringify(state, null, 2), "utf-8");
+    return { ok: true, id };
+  }
+  async status() {
+    const state = await this.read();
+    if (!state || state.closed_at) return { state: "no_session" };
+    const age = Date.now() - new Date(state.last_activity_at).getTime();
+    const label = age > STALE_THRESHOLD_MS ? "stale" : "active";
+    return { ...state, state: label };
+  }
+  async run(cmd, timeoutMs) {
+    const state = await this.read();
+    if (!state || state.closed_at) {
+      return { ok: false, error: "No active session. Run session_start first." };
+    }
+    if (!cmd || cmd.trim().length === 0) {
+      return { ok: false, error: "session_run requires a non-empty command." };
+    }
+    const start = Date.now();
+    const record = await this.spawnAndCapture(cmd, timeoutMs ?? DEFAULT_TIMEOUT_MS);
+    record.duration_ms = Date.now() - start;
+    state.verifications.push(record);
+    state.last_activity_at = (/* @__PURE__ */ new Date()).toISOString();
+    await writeFile6(this.sessionPath, JSON.stringify(state, null, 2), "utf-8");
+    return { ok: true, record };
+  }
+  async finish(input) {
+    const state = await this.read();
+    if (!state || state.closed_at) {
+      return { ok: false, error: "No active session to finish." };
+    }
+    const explicitWaiver = input.verified === false;
+    if (!explicitWaiver && state.verifications.length === 0) {
+      return {
+        ok: false,
+        error: "session_finish refused: no verification commands recorded. Run session_run with a real verification command (tests, lint, etc.) first, OR pass verified=false with a reason to waive verification (e.g. for doc-only edits)."
+      };
+    }
+    if (explicitWaiver && (!input.reason || input.reason.trim().length === 0)) {
+      return {
+        ok: false,
+        error: "session_finish refused: verified=false requires a non-empty `reason` explaining why verification is not applicable to this task."
+      };
+    }
+    if (!input.summary || input.summary.trim().length === 0) {
+      return { ok: false, error: "session_finish requires a non-empty `summary`." };
+    }
+    const closed = {
+      ...state,
+      closed_at: (/* @__PURE__ */ new Date()).toISOString(),
+      closed_summary: input.summary.trim(),
+      ...explicitWaiver && {
+        closed_verified_waived: true,
+        closed_waiver_reason: input.reason.trim()
+      }
+    };
+    await rm(this.sessionPath, { force: true });
+    return { ok: true, closed };
+  }
+  /**
+   * Append paths to notes_touched on the active session, deduplicating. No-op when no
+   * session is active. Used by patch tools to record what the session edited.
+   */
+  async recordNotesTouched(paths) {
+    if (paths.length === 0) return;
+    const state = await this.read();
+    if (!state || state.closed_at) return;
+    const set = new Set(state.notes_touched);
+    for (const p of paths) set.add(p);
+    state.notes_touched = Array.from(set);
+    state.last_activity_at = (/* @__PURE__ */ new Date()).toISOString();
+    await writeFile6(this.sessionPath, JSON.stringify(state, null, 2), "utf-8");
+  }
+  /**
+   * Read the active session WITHOUT computing the stale label. Returns null when no
+   * session is active or when the file is unparseable.
+   */
+  async readActive() {
+    const state = await this.read();
+    if (!state || state.closed_at) return null;
+    return state;
+  }
+  async read() {
+    if (!existsSync5(this.sessionPath)) return null;
+    try {
+      const raw = await readFile6(this.sessionPath, "utf-8");
+      const parsed = JSON.parse(raw);
+      if (typeof parsed?.id !== "string") return null;
+      return parsed;
+    } catch {
+      return null;
+    }
+  }
+  spawnAndCapture(cmd, timeoutMs) {
+    return new Promise((resolve) => {
+      const proc = spawn(cmd, { shell: true });
+      let buf = "";
+      let killedByTimeout = false;
+      const timer = setTimeout(() => {
+        killedByTimeout = true;
+        proc.kill("SIGTERM");
+        setTimeout(() => {
+          try {
+            proc.kill("SIGKILL");
+          } catch {
+          }
+        }, 1e3).unref();
+      }, timeoutMs);
+      const onData = (chunk) => {
+        buf += chunk.toString("utf-8");
+        if (buf.length > TAIL_BYTES * 4) {
+          buf = buf.slice(buf.length - TAIL_BYTES * 2);
+        }
+      };
+      proc.stdout?.on("data", onData);
+      proc.stderr?.on("data", onData);
+      proc.on("close", (code, signal) => {
+        clearTimeout(timer);
+        const tail = buf.slice(-TAIL_BYTES);
+        resolve({
+          cmd,
+          exit: killedByTimeout ? null : code,
+          signal: killedByTimeout ? "SIGTERM (timeout)" : signal ?? null,
+          duration_ms: 0,
+          tail,
+          at: (/* @__PURE__ */ new Date()).toISOString()
+        });
+      });
+      proc.on("error", (err) => {
+        clearTimeout(timer);
+        const tail = buf + `
+[spawn error: ${err.message}]`;
+        resolve({
+          cmd,
+          exit: null,
+          signal: null,
+          duration_ms: 0,
+          tail: tail.slice(-TAIL_BYTES),
+          at: (/* @__PURE__ */ new Date()).toISOString()
+        });
+      });
+    });
+  }
+};
+function deriveProjectRoot(notesPath) {
+  const norm = notesPath.replace(/[\\/]+$/, "");
+  if (norm.endsWith("/.claude/.vault") || norm.endsWith("\\.claude\\.vault")) {
+    return norm.slice(0, -".claude/.vault".length).replace(/[\\/]+$/, "");
+  }
+  return norm;
+}
+function deriveSessionDir(notesPath) {
+  return join6(deriveProjectRoot(notesPath), ".claude", ".semantic-memory");
+}
 
 export {
   NoteCrud,
@@ -757,6 +1125,12 @@ export {
   regenDirectoryIndex,
   regenIndexesForPaths,
   applyPatch,
-  buildSynthesizeChangeSet
+  buildSynthesizeChangeSet,
+  buildPromoteChangeSet,
+  regenerateAgentsContract,
+  inspectAgentsContract,
+  SessionManager,
+  deriveProjectRoot,
+  deriveSessionDir
 };
-//# sourceMappingURL=chunk-CXTRTCIK.js.map
+//# sourceMappingURL=chunk-XBAN7GRT.js.map

package/dist/chunk-XBAN7GRT.js.map

@@ -0,0 +1 @@
+{"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","../src/core/agents-contract.ts","../src/core/session.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   * When true, the resulting note is filed under `proposals/<date>-<slug>.md` with\n   * `status: proposal` frontmatter, regardless of `suggested_path`. The original path\n   * is preserved as `proposed_target` in frontmatter so `synthesize_promote` knows\n   * where to move it on acceptance.\n   */\n  proposal?: boolean;\n  /**\n   * When provided alongside `proposal: true`, used as the proposal subdirectory name.\n   * Defaults to \"proposals\". Useful for callers that want to segregate by source\n   * (e.g. \"proposals/research\", \"proposals/outage\").\n   */\n  proposal_subdir?: string;\n}\n\nexport interface SynthesizePreview {\n  changeset: ChangeSet;\n  path: string;\n  title: string;\n  /** True when the preview is a proposal — caller (or `synthesize_promote`) must move it later. */\n  is_proposal?: boolean;\n  /** When `is_proposal` is true, the canonical path that `synthesize_promote` should move it to. */\n  proposed_target?: 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 *\n * Proposal mode: when `proposal: true`, the path is rewritten to\n * `<proposal_subdir>/<YYYY-MM-DD>-<slug>.md`, the `status` is forced to `proposal`,\n * and `proposed_target` records the original suggested path. `synthesize_promote`\n * later moves the file to that target and clears the proposal frontmatter.\n */\nexport function buildSynthesizeChangeSet(input: SynthesizeNoteInput): SynthesizePreview {\n  const today = new Date().toISOString().slice(0, 10);\n  const title = input.topic.trim();\n  const canonicalPath = input.suggested_path.endsWith(\".md\") ? input.suggested_path : input.suggested_path + \".md\";\n\n  const isProposal = input.proposal === true;\n  const subdir = (input.proposal_subdir ?? \"proposals\").replace(/\\/+$/, \"\");\n  const slug = slugForTopic(title);\n  const path = isProposal ? `${subdir}/${today}-${slug}.md` : canonicalPath;\n\n  const frontmatter: Record<string, unknown> = {\n    title,\n    type: input.type ?? \"note\",\n    status: isProposal ? \"proposal\" : (input.status ?? \"active\"),\n    last_verified: today,\n    confidence: input.confidence ?? \"medium\",\n    ...(input.sources && input.sources.length > 0 && { sources: input.sources }),\n    ...(input.derived_from && input.derived_from.length > 0 && { derived_from: input.derived_from }),\n    ...(input.decision_maker && { decision_maker: input.decision_maker }),\n    ...(input.decided_on && { decided_on: input.decided_on }),\n    ...(input.severity && { severity: input.severity }),\n    ...(isProposal && { proposed_target: canonicalPath }),\n    ...(input.extra_frontmatter ?? {}),\n  };\n\n  const body = buildBody(title, input.answer, input.related_notes ?? []);\n\n  const create: PatchCreate = { path, content: body, frontmatter };\n  const changeset: ChangeSet = { creates: [create] };\n\n  return {\n    changeset,\n    path,\n    title,\n    ...(isProposal && { is_proposal: true, proposed_target: canonicalPath }),\n  };\n}\n\nfunction slugForTopic(topic: string): string {\n  return topic\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, \"-\")\n    .replace(/^-+|-+$/g, \"\")\n    .slice(0, 60) || \"untitled\";\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 base;\n}\n\nexport interface PromoteInput {\n  /**\n   * Path to the proposal note (relative to vault root). Must have `status: proposal` frontmatter\n   * AND `proposed_target` frontmatter, both written by `buildSynthesizeChangeSet` in proposal mode.\n   */\n  proposal_path: string;\n  /**\n   * Optional override for the destination path. When omitted, the proposal's own\n   * `proposed_target` frontmatter is used.\n   */\n  target_path?: string;\n}\n\nexport interface PromotePreview {\n  changeset: ChangeSet;\n  from: string;\n  to: string;\n}\n\n/**\n * Promote a reviewed proposal to its canonical destination.\n *\n * Reads the proposal's existing content + frontmatter, strips `status: proposal` and\n * `proposed_target` keys, restores the original status (default \"active\"), and returns\n * a ChangeSet that:\n *   - creates the canonical path with the cleaned frontmatter + body\n *   - deletes the proposal path\n *\n * The caller (the MCP tool) reads the proposal file, runs this builder, and applies the\n * resulting changeset via applyPatch — preserving atomicity and rollback semantics.\n */\nexport function buildPromoteChangeSet(input: {\n  proposal_path: string;\n  target_path?: string;\n  body: string;\n  frontmatter: Record<string, unknown>;\n}): PromotePreview {\n  const fm = { ...input.frontmatter };\n  const target = input.target_path ?? (typeof fm.proposed_target === \"string\" ? fm.proposed_target : undefined);\n  if (!target) {\n    throw new Error(\n      `Cannot promote ${input.proposal_path}: no target_path provided and no 'proposed_target' frontmatter on the proposal.`\n    );\n  }\n  // Restore canonical status (default \"active\") and strip proposal markers.\n  if (fm.status === \"proposal\") fm.status = \"active\";\n  delete fm.proposed_target;\n\n  const create: PatchCreate = {\n    path: target,\n    content: input.body,\n    frontmatter: fm,\n  };\n  const changeset: ChangeSet = {\n    creates: [create],\n    deletes: [{ path: input.proposal_path }],\n  };\n\n  return { changeset, from: input.proposal_path, to: target };\n}\n","import { readFile, writeFile } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { join } from \"node:path\";\n\nconst BEGIN_MARKER = \"<!-- semantic-memory:begin contract -->\";\nconst END_MARKER = \"<!-- semantic-memory:end contract -->\";\nconst LOCAL_NOTES_HEADING = \"## Local Notes\";\n\nexport interface ToolSummary {\n  name: string;\n  description: string;\n  deprecated?: boolean;\n}\n\nexport interface ModeSummary {\n  name: string;\n  description: string;\n  isDefault?: boolean;\n}\n\nexport interface RegenerateContractOptions {\n  projectRoot: string;\n  pluginVersion: string;\n  tools: ToolSummary[];\n  modes?: ModeSummary[];\n  /** When true, overwrite hand-edited managed blocks. Default false → fails loudly on detected hand-edits. */\n  force?: boolean;\n  /** Override \"now\" — used by tests for deterministic timestamps. */\n  nowIso?: string;\n}\n\nexport interface RegenerateContractResult {\n  path: string;\n  written: boolean;\n  reason?: string;\n  hand_edit_detected?: boolean;\n  preserved_local_notes_chars?: number;\n}\n\n/**\n * Generate or refresh AGENTS.md at the project root.\n *\n * Behavior:\n *  - If AGENTS.md is absent, write the full contract + an empty Local Notes section.\n *  - If AGENTS.md exists and contains the managed block markers:\n *      * Regenerate the content INSIDE the markers from the current tool/mode inventory.\n *      * Preserve everything OUTSIDE the markers (Local Notes tail, custom sections, frontmatter the\n *        user added).\n *      * If `force` is false and the inside-block content differs from a freshly-generated block AND\n *        the difference is not just a regenerable timestamp/version, fail with hand_edit_detected.\n *  - If AGENTS.md exists without managed-block markers, refuse and report — the user has a custom\n *    AGENTS.md and we should not silently take it over.\n */\nexport async function regenerateAgentsContract(opts: RegenerateContractOptions): Promise<RegenerateContractResult> {\n  const path = join(opts.projectRoot, \"AGENTS.md\");\n  const generatedBlock = buildManagedBlock(opts);\n  const generatedFull = buildFullDocument(opts, generatedBlock);\n\n  if (!existsSync(path)) {\n    await writeFile(path, generatedFull, \"utf-8\");\n    return { path, written: true };\n  }\n\n  const existing = await readFile(path, \"utf-8\");\n  const beginIdx = existing.indexOf(BEGIN_MARKER);\n  const endIdx = existing.indexOf(END_MARKER);\n\n  if (beginIdx === -1 || endIdx === -1 || endIdx < beginIdx) {\n    return {\n      path,\n      written: false,\n      reason:\n        \"AGENTS.md exists but does not contain the semantic-memory managed-block markers. Move your existing content into a Local Notes section outside the managed block, or delete AGENTS.md and re-run to bootstrap from scratch.\",\n    };\n  }\n\n  const existingBlock = existing.slice(beginIdx, endIdx + END_MARKER.length);\n  const localTail = extractLocalTail(existing, endIdx + END_MARKER.length);\n\n  if (!opts.force && hasHandEdits(existingBlock, generatedBlock)) {\n    return {\n      path,\n      written: false,\n      hand_edit_detected: true,\n      reason:\n        \"Managed-block content has been hand-edited. Move your changes to the Local Notes section (outside the managed block) and re-run, or pass force=true to overwrite.\",\n    };\n  }\n\n  // Refresh the entire pre-block prefix (frontmatter + title) so timestamp/version\n  // stamps reflect the current regeneration. Keep the managed block fresh and the\n  // Local Notes tail untouched.\n  const newPrefix = buildPrefix(opts);\n  const newDoc = newPrefix + generatedBlock + localTail;\n  await writeFile(path, newDoc, \"utf-8\");\n  return {\n    path,\n    written: true,\n    preserved_local_notes_chars: localTail.length,\n  };\n}\n\nfunction buildPrefix(opts: RegenerateContractOptions): string {\n  return [\n    \"---\",\n    `generated_by: semantic-memory`,\n    `version: ${opts.pluginVersion}`,\n    `last_generated: ${opts.nowIso ?? new Date().toISOString()}`,\n    \"---\",\n    \"\",\n    \"# Project Agent Contract\",\n    \"\",\n  ].join(\"\\n\");\n}\n\nfunction buildFullDocument(opts: RegenerateContractOptions, managedBlock: string): string {\n  const localNotes = `\\n\\n${LOCAL_NOTES_HEADING}\\n\\n_User-authored content lives here. Preserved across \\`regenerate_contract\\` runs._\\n`;\n  return buildPrefix(opts) + managedBlock + localNotes;\n}\n\nfunction buildManagedBlock(opts: RegenerateContractOptions): string {\n  const lines: string[] = [BEGIN_MARKER, \"\"];\n\n  lines.push(\"## Active Modes\", \"\");\n  const modes = opts.modes ?? defaultModes();\n  for (const m of modes) {\n    const tag = m.isDefault ? \" (default)\" : \"\";\n    lines.push(`- **${m.name}**${tag} — ${m.description}`);\n  }\n  lines.push(\"\");\n\n  lines.push(\"## Required Workflow\", \"\");\n  lines.push(\"1. For multi-step work that needs verification, open a session: `session_start({task})`.\");\n  lines.push(\"2. Use mode-aware retrieval: `search_hybrid`, `read_note`, `list_notes`, `backlinks`/`forwardlinks`.\");\n  lines.push(\"3. Make durable updates via `apply_patch` or `synthesize_note` — never bypass the patch layer for multi-note edits.\");\n  lines.push(\"4. Run verification commands inside a session: `session_run({cmd})`.\");\n  lines.push(\"5. Close with `session_finish({summary})` — refused without verification unless explicitly waived.\");\n  lines.push(\"6. Lint regularly: `lint_vault({checks: ['schema','provenance','stale','broken_links']})`.\");\n  lines.push(\"\");\n\n  lines.push(\"## Tool Surface\", \"\");\n  const live = opts.tools.filter((t) => !t.deprecated);\n  const deprecated = opts.tools.filter((t) => t.deprecated);\n  for (const t of live) {\n    lines.push(`- \\`${t.name}\\` — ${stripDeprecationPrefix(t.description)}`);\n  }\n  if (deprecated.length > 0) {\n    lines.push(\"\");\n    lines.push(\"### Deprecated (removed in v2.0.0)\", \"\");\n    for (const t of deprecated) {\n      lines.push(`- \\`${t.name}\\` — ${stripDeprecationPrefix(t.description)}`);\n    }\n  }\n  lines.push(\"\");\n\n  lines.push(\"## Memory Policy\", \"\");\n  lines.push(\"- Markdown is canonical. The vault under `.claude/.vault/` (or wherever `--notes` points) is the source of truth.\");\n  lines.push(\"- Indexes (vector / graph / FTS) are derived state — rebuildable via `reindex` without losing knowledge.\");\n  lines.push(\"- Provenance frontmatter is required for `note`/`decision`/`gotcha` types — `sources` (external) or `derived_from` (internal).\");\n  lines.push(\"- Mode router lives at `.claude/.sidekick-mode`; explicit `/mode` is ground truth.\");\n  lines.push(\"\");\n\n  lines.push(END_MARKER);\n  return lines.join(\"\\n\");\n}\n\nfunction defaultModes(): ModeSummary[] {\n  return [\n    { name: \"vault-first\", description: \"Project-scoped prose questions trigger vault consultation with cite-or-deflect.\", isDefault: true },\n    { name: \"research\", description: \"Every source introduced is filed via `ingest_source`; mandatory `synthesize_note` on exit.\" },\n    { name: \"outage-silence\", description: \"No proactive vault search. Terse responses. Postmortem `synthesize_note` on exit.\" },\n  ];\n}\n\nfunction stripDeprecationPrefix(description: string): string {\n  return description.replace(/^\\[DEPRECATED[^\\]]*\\]\\s*/, \"(deprecated) \");\n}\n\nfunction extractLocalTail(existing: string, afterEndIdx: number): string {\n  const tail = existing.slice(afterEndIdx);\n  // Trim a single leading blank-line-then-newline if present so we don't double-space across regenerations.\n  return tail;\n}\n\n/**\n * Detect hand-edits by comparing semantic content of the managed block, ignoring lines that are\n * regenerable (currently no per-block timestamps live inside the block — they're in frontmatter).\n * Returns true if the existing block diverges from what we'd generate now.\n */\nfunction hasHandEdits(existingBlock: string, generatedBlock: string): boolean {\n  return existingBlock.trim() !== generatedBlock.trim();\n}\n\n/**\n * Inspect AGENTS.md without modifying it. Returns whether the file exists, whether it has managed\n * markers, and how many characters of Local Notes tail are preserved.\n */\nexport async function inspectAgentsContract(projectRoot: string): Promise<{\n  path: string;\n  exists: boolean;\n  has_managed_block: boolean;\n  local_notes_chars: number;\n}> {\n  const path = join(projectRoot, \"AGENTS.md\");\n  if (!existsSync(path)) {\n    return { path, exists: false, has_managed_block: false, local_notes_chars: 0 };\n  }\n  const raw = await readFile(path, \"utf-8\");\n  const beginIdx = raw.indexOf(BEGIN_MARKER);\n  const endIdx = raw.indexOf(END_MARKER);\n  if (beginIdx === -1 || endIdx === -1) {\n    return { path, exists: true, has_managed_block: false, local_notes_chars: 0 };\n  }\n  const localTail = raw.slice(endIdx + END_MARKER.length).trim();\n  return { path, exists: true, has_managed_block: true, local_notes_chars: localTail.length };\n}\n","import { mkdir, readFile, writeFile, rm } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { join } from \"node:path\";\nimport { spawn } from \"node:child_process\";\n\nexport interface VerificationRecord {\n  cmd: string;\n  exit: number | null;\n  signal: string | null;\n  duration_ms: number;\n  tail: string;\n  at: string;\n}\n\nexport interface SessionState {\n  id: string;\n  task: string;\n  started_at: string;\n  last_activity_at: string;\n  verifications: VerificationRecord[];\n  notes_touched: string[];\n  closed_at?: string;\n  closed_summary?: string;\n  closed_verified_waived?: boolean;\n  closed_waiver_reason?: string;\n}\n\nexport type SessionStatus =\n  | { state: \"no_session\" }\n  | (SessionState & { state: \"active\" | \"stale\" });\n\nexport interface SessionStartOptions {\n  /** When true and a session for the same task is already open, return the existing id rather than failing. Defaults to true. */\n  reuseSameTask?: boolean;\n}\n\nexport interface SessionFinishInput {\n  summary: string;\n  /**\n   * When false, the caller is explicitly waiving verification (e.g. for doc-only edits).\n   * Requires a non-empty `reason`. When true (default) and no verifications have been\n   * recorded, the call is refused.\n   */\n  verified?: boolean;\n  reason?: string;\n}\n\nconst STALE_THRESHOLD_MS = 24 * 60 * 60 * 1000;\nconst DEFAULT_TIMEOUT_MS = 5 * 60 * 1000;\nconst TAIL_BYTES = 4096;\n\n/**\n * SessionManager owns a single session.json file at `<sessionDir>/session.json`.\n *\n * State is durable across MCP server restarts (the file persists). At most one session\n * is active per project at a time — concurrent sessions are explicitly out of scope\n * for v1.1; brain has the same constraint.\n *\n * Hard gates:\n *  - session_finish refuses without verifications unless verified=false + reason\n *  - session_run refuses without an open session\n *  - session_start refuses if another session is open with a different task\n *\n * Stale detection: a session whose last_activity_at is >24h old is reported as\n * state:\"stale\" by status(). Stale sessions can still be finished or extended; the\n * label is informational so callers can decide whether to abandon (rm + start new) or\n * resume.\n */\nexport class SessionManager {\n  constructor(private sessionDir: string) {}\n\n  get sessionPath(): string {\n    return join(this.sessionDir, \"session.json\");\n  }\n\n  async start(task: string, opts: SessionStartOptions = {}): Promise<{ ok: true; id: string; reused?: boolean } | { ok: false; error: string }> {\n    if (!task || task.trim().length === 0) {\n      return { ok: false, error: \"session_start requires a non-empty task.\" };\n    }\n    await mkdir(this.sessionDir, { recursive: true });\n    const existing = await this.read();\n    if (existing && !existing.closed_at) {\n      const reuseSameTask = opts.reuseSameTask !== false;\n      if (reuseSameTask && existing.task === task) {\n        return { ok: true, id: existing.id, reused: true };\n      }\n      return {\n        ok: false,\n        error: `Session already open: id=${existing.id}, task=${JSON.stringify(existing.task)}. 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DEFAULT_TIMEOUT_MS);\n    record.duration_ms = Date.now() - start;\n    state.verifications.push(record);\n    state.last_activity_at = new Date().toISOString();\n    await writeFile(this.sessionPath, JSON.stringify(state, null, 2), \"utf-8\");\n    return { ok: true, record };\n  }\n\n  async finish(input: SessionFinishInput): Promise<{ ok: true; closed: SessionState } | { ok: false; error: string }> {\n    const state = await this.read();\n    if (!state || state.closed_at) {\n      return { ok: false, error: \"No active session to finish.\" };\n    }\n    const explicitWaiver = input.verified === false;\n    if (!explicitWaiver && state.verifications.length === 0) {\n      return {\n        ok: false,\n        error:\n          \"session_finish refused: no verification commands recorded. Run session_run with a real verification command (tests, lint, etc.) first, OR pass verified=false with a reason to waive verification (e.g. for doc-only edits).\",\n      };\n    }\n    if (explicitWaiver && (!input.reason || input.reason.trim().length === 0)) {\n      return {\n        ok: false,\n        error: \"session_finish refused: verified=false requires a non-empty `reason` explaining why verification is not applicable to this task.\",\n      };\n    }\n    if (!input.summary || input.summary.trim().length === 0) {\n      return { ok: false, error: \"session_finish requires a non-empty `summary`.\" };\n    }\n    const closed: SessionState = {\n      ...state,\n      closed_at: new Date().toISOString(),\n      closed_summary: input.summary.trim(),\n      ...(explicitWaiver && {\n        closed_verified_waived: true,\n        closed_waiver_reason: input.reason!.trim(),\n      }),\n    };\n    // Sessions are ephemeral runtime state — finished sessions are removed from disk.\n    // Durable artifacts (synthesize_note proposals, log entries) capture what mattered.\n    await rm(this.sessionPath, { force: true });\n    return { ok: true, closed };\n  }\n\n  /**\n   * Append paths to notes_touched on the active session, deduplicating. No-op when no\n   * session is active. Used by patch tools to record what the session edited.\n   */\n  async recordNotesTouched(paths: string[]): Promise<void> {\n    if (paths.length === 0) return;\n    const state = await this.read();\n    if (!state || state.closed_at) return;\n    const set = new Set(state.notes_touched);\n    for (const p of paths) set.add(p);\n    state.notes_touched = Array.from(set);\n    state.last_activity_at = new Date().toISOString();\n    await writeFile(this.sessionPath, JSON.stringify(state, null, 2), \"utf-8\");\n  }\n\n  /**\n   * Read the active session WITHOUT computing the stale label. Returns null when no\n   * session is active or when the file is unparseable.\n   */\n  async readActive(): Promise<SessionState | null> {\n    const state = await this.read();\n    if (!state || state.closed_at) return null;\n    return state;\n  }\n\n  private async read(): Promise<SessionState | null> {\n    if (!existsSync(this.sessionPath)) return null;\n    try {\n      const raw = await readFile(this.sessionPath, \"utf-8\");\n      const parsed = JSON.parse(raw);\n      if (typeof parsed?.id !== \"string\") return null;\n      return parsed as SessionState;\n    } catch {\n      return null;\n    }\n  }\n\n  private spawnAndCapture(cmd: string, timeoutMs: number): Promise<VerificationRecord> {\n    return new Promise((resolve) => {\n      const proc = spawn(cmd, { shell: true });\n      let buf = \"\";\n      let killedByTimeout = false;\n      const timer = setTimeout(() => {\n        killedByTimeout = true;\n        proc.kill(\"SIGTERM\");\n        setTimeout(() => {\n          try { proc.kill(\"SIGKILL\"); } catch { /* already gone */ }\n        }, 1000).unref();\n      }, timeoutMs);\n\n      const onData = (chunk: Buffer) => {\n        buf += chunk.toString(\"utf-8\");\n        if (buf.length > TAIL_BYTES * 4) {\n          buf = buf.slice(buf.length - TAIL_BYTES * 2);\n        }\n      };\n      proc.stdout?.on(\"data\", onData);\n      proc.stderr?.on(\"data\", onData);\n\n      proc.on(\"close\", (code, signal) => {\n        clearTimeout(timer);\n        const tail = buf.slice(-TAIL_BYTES);\n        resolve({\n          cmd,\n          exit: killedByTimeout ? null : code,\n          signal: killedByTimeout ? \"SIGTERM (timeout)\" : (signal ?? null),\n          duration_ms: 0,\n          tail,\n          at: new Date().toISOString(),\n        });\n      });\n\n      proc.on(\"error\", (err) => {\n        clearTimeout(timer);\n        const tail = buf + `\\n[spawn error: ${err.message}]`;\n        resolve({\n          cmd,\n          exit: null,\n          signal: null,\n          duration_ms: 0,\n          tail: tail.slice(-TAIL_BYTES),\n          at: new Date().toISOString(),\n        });\n      });\n    });\n  }\n}\n\n/**\n * Heuristic: derive the project root from the vault path. If the vault path ends in\n * `.claude/.vault`, the project root is two levels up. Otherwise the vault path is\n * treated as the project root.\n */\nexport function deriveProjectRoot(notesPath: string): string {\n  const norm = notesPath.replace(/[\\\\/]+$/, \"\");\n  if (norm.endsWith(\"/.claude/.vault\") || norm.endsWith(\"\\\\.claude\\\\.vault\")) {\n    return norm.slice(0, -\".claude/.vault\".length).replace(/[\\\\/]+$/, \"\");\n  }\n  return norm;\n}\n\nexport function deriveSessionDir(notesPath: string): string {\n  return join(deriveProjectRoot(notesPath), \".claude\", 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