memorix 1.1.7 → 1.1.9

package/dist/cli/index.js

@@ -3212,7 +3212,7 @@ ${import_picocolors.default.gray(m3)}  ${s2}
 
 // src/cli/version.ts
 function getCliVersion() {
-  return true ? "1.1.7" : pkg.version;
+  return true ? "1.1.9" : pkg.version;
 }
 var init_version = __esm({
   "src/cli/version.ts"() {
@@ -8145,12 +8145,12 @@ async function removeMultipleAsync(orama, ids, batchSize, language, skipHooks) {
   if (!skipHooks) {
     await runMultipleHook(orama.beforeRemoveMultiple, orama, docIdsForHooks);
   }
-  await new Promise((resolve3, reject) => {
+  await new Promise((resolve4, reject) => {
     let i2 = 0;
     async function _removeMultiple() {
       const batch = ids.slice(i2 * batchSize, ++i2 * batchSize);
       if (!batch.length) {
-        return resolve3();
+        return resolve4();
       }
       for (const doc of batch) {
         try {
@@ -12429,6 +12429,7 @@ function loadYamlConfig(projectRoot) {
     agent: { ...userConfig.agent, ...projectConfig.agent },
     embedding: { ...userConfig.embedding, ...projectConfig.embedding },
     git: { ...userConfig.git, ...projectConfig.git },
+    codegraph: { ...userConfig.codegraph, ...projectConfig.codegraph },
     behavior: { ...userConfig.behavior, ...projectConfig.behavior },
     server: { ...userConfig.server, ...projectConfig.server },
     team: { ...userConfig.team, ...projectConfig.team }
@@ -12531,6 +12532,7 @@ function mergeTomlConfig(base, override) {
     embedding: { ...base.embedding, ...override.embedding },
     hooks: { ...base.hooks, ...override.hooks },
     git: { ...base.git, ...override.git },
+    codegraph: { ...base.codegraph, ...override.codegraph },
     server: { ...base.server, ...override.server }
   };
 }
@@ -13154,6 +13156,9 @@ function getResolvedConfig(options2 = {}) {
       excludePatterns: firstArray(toml.git?.exclude_patterns, yaml4.git?.excludePatterns),
       noiseKeywords: firstArray(toml.git?.noise_keywords, yaml4.git?.noiseKeywords)
     },
+    codegraph: {
+      excludePatterns: firstArray(toml.codegraph?.exclude_patterns, yaml4.codegraph?.excludePatterns)
+    },
     server: {
       transport: first(toml.server?.transport, yaml4.server?.transport),
       dashboard: firstBool(toml.server?.dashboard, yaml4.server?.dashboard),
@@ -13762,7 +13767,7 @@ async function fetchWithRetry(url, apiKey, body, attempt = 0) {
     const retryAfter = response.headers.get("retry-after");
     const waitMs = retryAfter ? parseInt(retryAfter, 10) * 1e3 : delay;
     console.error(`[memorix] Embedding API ${response.status}, retry ${attempt + 1}/${MAX_RETRIES} in ${waitMs}ms`);
-    await new Promise((resolve3) => setTimeout(resolve3, waitMs));
+    await new Promise((resolve4) => setTimeout(resolve4, waitMs));
     return fetchWithRetry(url, apiKey, body, attempt + 1);
   }
   const errorText = await response.text().catch(() => "unknown error");
@@ -15701,8 +15706,12 @@ function makeEntryKey(projectId, observationId) {
   return `${projectId ?? ""}::${observationId}`;
 }
 function rememberObservationDoc(doc) {
-  if (!doc.projectId || typeof doc.observationId !== "number") return;
-  docByObservationKey.set(makeEntryKey(doc.projectId, doc.observationId), doc);
+  const publicDoc = { ...doc };
+  delete publicDoc.embedding;
+  if (doc.projectId && typeof doc.observationId === "number") {
+    docByObservationKey.set(makeEntryKey(doc.projectId, doc.observationId), publicDoc);
+  }
+  return publicDoc;
 }
 function isCommandLikeQuery(query) {
   return COMMAND_LIKE_QUERY2.test(query);
@@ -15804,14 +15813,14 @@ async function batchGenerateEmbeddings(texts) {
 }
 async function hydrateIndex(observations2) {
   const database = await getDb();
-  const currentCount = await count2(database);
-  if (currentCount > 0) return 0;
   let inserted = 0;
   for (const obs of observations2) {
     if (!obs || !obs.id || !obs.projectId) continue;
     try {
+      const id = makeOramaObservationId(obs.projectId, obs.id);
+      if (getByID(database, id)) continue;
       const doc = {
-        id: makeOramaObservationId(obs.projectId, obs.id),
+        id,
         observationId: obs.id,
         entityName: obs.entityName || "",
         type: obs.type || "discovery",
@@ -15905,6 +15914,7 @@ async function searchObservations(options2) {
   let searchParams = {
     term: originalQuery,
     limit: requestLimit,
+    includeVectors: true,
     ...Object.keys(filters).length > 0 ? { where: filters } : {},
     // Search specific fields (not tokens, accessCount, etc.)
     properties: ["title", "entityName", "narrative", "facts", "concepts", "filesModified"],
@@ -15976,6 +15986,7 @@ async function searchObservations(options2) {
       const vectorOnlyParams = {
         term: "",
         limit: requestLimit,
+        includeVectors: true,
         ...Object.keys(filters).length > 0 ? { where: filters } : {},
         mode: "vector",
         vector: {
@@ -16274,6 +16285,7 @@ async function getObservationsByIds(ids, projectId) {
     }
     const searchResult = await search2(database, {
       term: "",
+      includeVectors: true,
       where: {
         observationId: { eq: id },
         ...projectId ? { projectId } : {}
@@ -16281,7 +16293,7 @@ async function getObservationsByIds(ids, projectId) {
       limit: 1
     });
     if (searchResult.hits.length > 0) {
-      results.push(searchResult.hits[0].document);
+      results.push(rememberObservationDoc(searchResult.hits[0].document));
     }
   }
   return results;
@@ -20793,7 +20805,7 @@ var init_official_skills = __esm({
           "",
           "## Search Rules",
           "",
-          "- Use `memorix_project_context` before broad continuation work, unfamiliar code changes, ad-hoc file reads, or dev-log reads. Pass the user's actual task so Memorix can choose a bugfix, feature, release, onboarding, refactor, docs, test, or general brief. Start by reading its suggested files.",
+          "- Default first step for non-trivial coding work: call `memorix_project_context` before progress files, dev-log reads, ad-hoc file reads, or git archaeology. Pass the user's actual task so Memorix can choose a bugfix, feature, release, onboarding, refactor, docs, test, or general brief. Start by reading its suggested files.",
           "- In Claude Code headless/print-mode, an initial MCP `pending` status is not a failure by itself. Prefer MCP first: use the client's tool discovery/dynamic loading to find `memorix_project_context` when it is not in the first visible tool list.",
           '- Run `memorix context --task "<task>"` from the shell only after MCP is unavailable, disabled, or not discoverable, and pass the user\'s real task text. Do not skip memory, wait indefinitely on `pending`, or hand-write tool-call syntax.',
           "- Use `memorix_search` for a specific decision, bug, file, or prior change that the project context did not answer.",
@@ -21104,6 +21116,7 @@ var init_audit = __esm({
 var installers_exports = {};
 __export(installers_exports, {
   detectInstalledAgents: () => detectInstalledAgents,
+  getAgentRulesPath: () => getAgentRulesPath,
   getGlobalConfigPath: () => getGlobalConfigPath,
   getHookStatus: () => getHookStatus,
   getProjectConfigPath: () => getProjectConfigPath,
@@ -21728,8 +21741,8 @@ async function installHooks(agent, projectRoot, global2 = false) {
       try {
         const { access: access3, unlink: unlink2 } = await import("fs/promises");
         await access3(entry.path);
-        const basename4 = path13.basename(entry.path);
-        if (basename4 === "AGENTS.md" || basename4 === "GEMINI.md" || basename4 === "CONTEXT.md") {
+        const basename5 = path13.basename(entry.path);
+        if (basename5 === "AGENTS.md" || basename5 === "GEMINI.md" || basename5 === "CONTEXT.md") {
           continue;
         }
         await unlink2(entry.path);
@@ -21970,7 +21983,7 @@ function getAgentRulesContent(agent, scope = "project") {
   let frontmatter = "";
   const contextNoun = scope === "global" ? "workspace" : "project";
   const title = scope === "global" ? "# Memorix \u2014 Memory Tools for Active Workspaces" : "# Memorix \u2014 Project Memory Tools";
-  const intro = scope === "global" ? "Use Memorix when the active workspace has Memorix tools available and prior context would materially help. Do not assume every workspace is configured for Memorix." : "This repository is configured to use Memorix for persistent cross-session memory. Memory tools are available when you need context from prior sessions or when you learn something worth saving.";
+  const intro = scope === "global" ? "Use Memorix when the active workspace has Memorix tools available and prior context would materially help. For non-trivial coding work, Memory Autopilot is the default entry point before local progress notes or broad file exploration. Do not assume every workspace is configured for Memorix." : "This repository is configured to use Memorix for persistent cross-session memory. For non-trivial coding work, Memory Autopilot is the default entry point before local progress notes or broad file exploration.";
   if (agent === "windsurf") {
     frontmatter = "---\ntrigger: always_on\n---\n\n";
   } else if (agent === "cursor") {
@@ -21988,7 +22001,7 @@ alwaysApply: true
     "",
     "## Start with Memory Autopilot",
     "",
-    `For starting or continuing code work, use \`memorix_project_context\` with the user's actual task before ad-hoc file reads, dev-log reads, or git archaeology. Memorix will choose a task-lensed brief (bugfix, feature, release, onboarding, refactor, docs, test, or general). Treat its "Start here" files as the first ${contextNoun} files to inspect.`,
+    `Default first step for non-trivial coding work: call \`memorix_project_context\` with the user's actual task before progress files, dev-log reads, ad-hoc file reads, or git archaeology. Memorix will choose a task-lensed brief (bugfix, feature, release, onboarding, refactor, docs, test, or general). Treat its "Start here" files as the first ${contextNoun} files to inspect.`,
     "",
     'If the MCP tool is not visible yet but the client supports tool discovery or dynamic loading, search/select `memorix_project_context` first. Run `memorix context --task "<task>"` only after MCP is unavailable, disabled, or not discoverable, and pass the user\'s real task text. Do not skip memory, wait indefinitely on MCP startup, or hand-write tool-call syntax.',
     "",
@@ -22082,8 +22095,8 @@ async function uninstallHooks(agent, projectRoot, global2 = false) {
     const agentFiles = prevFiles.filter((e3) => e3.agent === agent);
     for (const entry of agentFiles) {
       try {
-        const basename4 = path13.basename(entry.path);
-        if (basename4 === "AGENTS.md" || basename4 === "GEMINI.md" || basename4 === "CONTEXT.md") {
+        const basename5 = path13.basename(entry.path);
+        if (basename5 === "AGENTS.md" || basename5 === "GEMINI.md" || basename5 === "CONTEXT.md") {
           try {
             const content = await fs9.readFile(entry.path, "utf-8");
             const memorixStart = content.indexOf("# Memorix");
@@ -22209,8 +22222,10 @@ var init_installers = __esm({
 // src/cli/commands/setup.ts
 var setup_exports = {};
 __export(setup_exports, {
+  buildMemorixServer: () => buildMemorixServer,
   buildSetupPlan: () => buildSetupPlan,
   default: () => setup_default,
+  getMcpAdapter: () => getMcpAdapter,
   getSetupAgentTargets: () => getSetupAgentTargets,
   getSetupIntegrationRows: () => getSetupIntegrationRows2,
   installAntigravityPluginPackage: () => installAntigravityPluginPackage,
@@ -23255,11 +23270,17 @@ __export(config_get_exports, {
 function readDotted(source, key) {
   let cursor = source;
   for (const part of key.split(".")) {
-    if (!cursor || typeof cursor !== "object" || !(part in cursor)) return void 0;
-    cursor = cursor[part];
+    if (!cursor || typeof cursor !== "object") return void 0;
+    const record2 = cursor;
+    const normalizedPart = part in record2 ? part : snakeToCamel(part);
+    if (!(normalizedPart in record2)) return void 0;
+    cursor = record2[normalizedPart];
   }
   return cursor;
 }
+function snakeToCamel(value) {
+  return value.replace(/_([a-z])/g, (_4, char) => char.toUpperCase());
+}
 function formatValue(value, key) {
   if (typeof value === "string") return shouldRedactKey(key) ? "<redacted>" : value;
   if (typeof value === "number" || typeof value === "boolean") return String(value);
@@ -26286,6 +26307,58 @@ var init_current_facts = __esm({
   }
 });
 
+// src/codegraph/exclude.ts
+function normalizeCodeGraphExcludePatterns(exclude) {
+  return [.../* @__PURE__ */ new Set([
+    ...DEFAULT_CODEGRAPH_EXCLUDES,
+    ...(exclude ?? []).map((pattern) => pattern.trim()).filter(Boolean)
+  ])];
+}
+function isCodeGraphExcludedPath(path29, exclude) {
+  const normalized = normalizeCodePath2(path29);
+  return normalizeCodeGraphExcludePatterns(exclude).some((pattern) => matchesPattern(normalized, normalizeCodePath2(pattern)));
+}
+function normalizeCodePath2(path29) {
+  return path29.replace(/\\/g, "/").replace(/^\.\/+/, "");
+}
+function matchesPattern(path29, pattern) {
+  if (pattern.endsWith("/**")) {
+    const base = pattern.slice(0, -3);
+    if (base.startsWith("**/")) {
+      const suffix = base.slice(3);
+      return path29 === suffix || path29.endsWith(`/${suffix}`) || path29.includes(`/${suffix}/`);
+    }
+    if (!base.includes("/")) {
+      return path29 === base || path29.startsWith(`${base}/`) || path29.includes(`/${base}/`);
+    }
+    return path29 === base || path29.startsWith(`${base}/`);
+  }
+  if (pattern.startsWith("**/")) {
+    const suffix = pattern.slice(3);
+    return path29 === suffix || path29.endsWith(`/${suffix}`);
+  }
+  return path29 === pattern || path29.startsWith(`${pattern}/`);
+}
+var DEFAULT_CODEGRAPH_EXCLUDES;
+var init_exclude = __esm({
+  "src/codegraph/exclude.ts"() {
+    "use strict";
+    init_esm_shims();
+    DEFAULT_CODEGRAPH_EXCLUDES = [
+      "node_modules/**",
+      "dist/**",
+      "build/**",
+      "coverage/**",
+      ".next/**",
+      ".turbo/**",
+      ".git/**",
+      ".tmp/**",
+      ".worktrees/**",
+      ".claude/worktrees/**"
+    ];
+  }
+});
+
 // src/codegraph/lite-provider.ts
 import { createHash as createHash4 } from "crypto";
 import { readdirSync as readdirSync2, readFileSync as readFileSync8, statSync as statSync2 } from "fs";
@@ -26301,18 +26374,6 @@ function languageForPath(path29) {
   const ext = extension(path29);
   return LANGUAGE_BY_EXTENSION.get(ext) ?? "unknown";
 }
-function isExcluded(path29, exclude) {
-  const normalized = normalizeCodePath(path29);
-  return exclude.some((pattern) => {
-    const p2 = normalizeCodePath(pattern);
-    if (p2.endsWith("/**")) {
-      const base = p2.slice(0, -3);
-      return normalized === base || normalized.startsWith(`${base}/`);
-    }
-    if (p2.startsWith("**/")) return normalized.endsWith(p2.slice(3));
-    return normalized === p2 || normalized.startsWith(`${p2}/`);
-  });
-}
 function walk(root, exclude, maxFiles) {
   const out = [];
   const visit = (dir) => {
@@ -26326,9 +26387,10 @@ function walk(root, exclude, maxFiles) {
     for (const entry of entries) {
       const abs = join20(dir, entry.name);
       const rel = normalizeCodePath(relative(root, abs));
-      if (isExcluded(rel, exclude)) continue;
+      if (isCodeGraphExcludedPath(rel, exclude)) continue;
       if (entry.isDirectory()) {
-        if (entry.name === ".git" || entry.name === "node_modules") continue;
+        if (entry.name === ".git" || entry.name === ".worktrees" || entry.name === ".tmp" || entry.name === "node_modules") continue;
+        if (rel === ".claude/worktrees" || rel.startsWith(".claude/worktrees/")) continue;
         visit(abs);
         if (out.length >= maxFiles) return;
         continue;
@@ -26413,15 +26475,7 @@ function extractImportEdges(projectId, file, text, indexedAt) {
   return edges;
 }
 async function indexProjectLite(options2) {
-  const exclude = options2.exclude ?? [
-    "node_modules/**",
-    "dist/**",
-    "build/**",
-    "coverage/**",
-    ".next/**",
-    ".turbo/**",
-    ".git/**"
-  ];
+  const exclude = normalizeCodeGraphExcludePatterns(options2.exclude);
   const maxFiles = options2.maxFiles ?? 5e3;
   const indexedAt = (/* @__PURE__ */ new Date()).toISOString();
   const paths = walk(options2.projectRoot, exclude, maxFiles);
@@ -26460,6 +26514,7 @@ var init_lite_provider = __esm({
     "use strict";
     init_esm_shims();
     init_ids();
+    init_exclude();
     LANGUAGE_BY_EXTENSION = /* @__PURE__ */ new Map([
       [".ts", "typescript"],
       [".tsx", "typescript"],
@@ -26636,23 +26691,17 @@ function countLanguages(files) {
   }
   return [...counts.entries()].map(([language, files2]) => ({ language, files: files2 })).sort((a3, b3) => a3.language.localeCompare(b3.language));
 }
-function normalizePath2(path29) {
-  return path29.replace(/\\/g, "/");
-}
-function isGeneratedPath(path29) {
-  return /(^|\/)(dist|build|coverage|\.next|\.turbo|node_modules)\//i.test(normalizePath2(path29));
-}
 function suggestedReadRank(path29) {
-  const normalized = normalizePath2(path29);
+  const normalized = path29.replace(/\\/g, "/");
   if (normalized.startsWith("src/")) return 0;
   if (normalized.startsWith("tests/") || normalized.startsWith("test/")) return 0;
   if (normalized.startsWith("packages/") && normalized.includes("/src/")) return 2;
   return 3;
 }
-function compactSuggestedReads(paths, limit = 8) {
-  return uniq(paths).filter((path29) => !isGeneratedPath(path29)).sort((a3, b3) => suggestedReadRank(a3) - suggestedReadRank(b3)).slice(0, limit);
+function compactSuggestedReads(paths, limit = 8, exclude) {
+  return uniq(paths).filter((path29) => !isCodeGraphExcludedPath(path29, exclude)).sort((a3, b3) => suggestedReadRank(a3) - suggestedReadRank(b3)).slice(0, limit);
 }
-function collectGraph(store2, projectId, observations2) {
+function collectGraph(store2, projectId, observations2, exclude) {
   const files = store2.listFiles(projectId);
   const symbols = files.flatMap((file) => store2.listSymbolsForFile(file.id));
   const filesById = new Map(files.map((file) => [file.id, file]));
@@ -26674,7 +26723,9 @@ function collectGraph(store2, projectId, observations2) {
     freshness[result.status] += 1;
     const observation = observationsById.get(ref.observationId);
     if (!observation) continue;
-    if (result.status === "current" && file) suggestedReads.push(file.path);
+    const excluded = file ? isCodeGraphExcludedPath(file.path, exclude) : false;
+    if (result.status === "current" && file && !excluded) suggestedReads.push(file.path);
+    if (excluded) continue;
     sources.push({
       observationId: observation.id,
       title: observation.title,
@@ -26691,12 +26742,12 @@ function collectGraph(store2, projectId, observations2) {
     refs,
     freshness,
     sources,
-    suggestedReads: compactSuggestedReads(suggestedReads)
+    suggestedReads: compactSuggestedReads(suggestedReads, 8, exclude)
   };
 }
 function buildProjectContextOverview(input) {
   const active = activeObservations(input.observations, input.project.id);
-  const graph = collectGraph(input.store, input.project.id, active);
+  const graph = collectGraph(input.store, input.project.id, active, input.exclude);
   const status = input.store.status(input.project.id);
   return {
     project: input.project,
@@ -26720,7 +26771,7 @@ function buildProjectContextOverview(input) {
 function buildProjectContextExplain(input) {
   const overview = buildProjectContextOverview(input);
   const active = activeObservations(input.observations, input.project.id);
-  const graph = collectGraph(input.store, input.project.id, active);
+  const graph = collectGraph(input.store, input.project.id, active, input.exclude);
   return {
     project: input.project,
     sources: graph.sources.sort((a3, b3) => a3.observationId - b3.observationId || (a3.path ?? "").localeCompare(b3.path ?? "")),
@@ -26774,11 +26825,12 @@ var init_project_context = __esm({
     "use strict";
     init_esm_shims();
     init_freshness2();
+    init_exclude();
   }
 });
 
 // src/codegraph/task-lens.ts
-function normalizePath3(path29) {
+function normalizePath2(path29) {
   return path29.replace(/\\/g, "/");
 }
 function tokenize3(text) {
@@ -26808,7 +26860,7 @@ function resolveTaskLens(task) {
   return best.score > 0 ? LENSES[best.id] : LENSES.general;
 }
 function pathKindScore(path29, lens) {
-  const normalized = normalizePath3(path29).toLowerCase();
+  const normalized = normalizePath2(path29).toLowerCase();
   const name = normalized.split("/").pop() ?? normalized;
   const inDocs = normalized.startsWith("docs/") || name === "readme.md" || name.includes("readme");
   const isTest = /(^|\/)(tests?|__tests__|spec|fixtures?)\//.test(normalized) || /\.(test|spec)\.[cm]?[jt]sx?$/.test(normalized) || /\.(test|spec)\.py$/.test(normalized);
@@ -26857,7 +26909,7 @@ function sourceTaskMatchScore(source, task) {
   return 0;
 }
 function fallbackPathRank(path29) {
-  const normalized = normalizePath3(path29);
+  const normalized = normalizePath2(path29);
   if (normalized.startsWith("src/")) return 0;
   if (normalized.startsWith("tests/") || normalized.startsWith("test/")) return 1;
   if (normalized.startsWith("packages/") && normalized.includes("/src/")) return 2;
@@ -26866,7 +26918,7 @@ function fallbackPathRank(path29) {
 }
 function rankLensPaths(paths, lens, task) {
   const tokens = tokenize3(task ?? "");
-  return [...new Set(paths.map(normalizePath3))].map((path29, index) => ({
+  return [...new Set(paths.map(normalizePath2))].map((path29, index) => ({
     path: path29,
     index,
     score: pathKindScore(path29, lens) + tokenScore(path29, tokens),
@@ -27120,6 +27172,7 @@ async function buildAutoProjectContext(input) {
   const now = input.now ?? /* @__PURE__ */ new Date();
   const task = input.task?.trim();
   const lens = resolveTaskLens(task);
+  const exclude = input.exclude ?? getResolvedConfig({ projectRoot: input.project.rootPath }).codegraph.excludePatterns;
   const store2 = new CodeGraphStore();
   await store2.init(input.dataDir);
   const initialStatus = store2.status(input.project.id);
@@ -27137,7 +27190,8 @@ async function buildAutoProjectContext(input) {
     try {
       const indexed = await indexProjectLite({
         projectId: input.project.id,
-        projectRoot: input.project.rootPath
+        projectRoot: input.project.rootPath,
+        exclude
       });
       store2.replaceProjectIndex(input.project.id, indexed);
       const backfill = await backfillMissingObservationCodeRefs(
@@ -27157,12 +27211,14 @@ async function buildAutoProjectContext(input) {
   const overview = buildProjectContextOverview({
     project: input.project,
     store: store2,
-    observations: input.observations
+    observations: input.observations,
+    exclude
   });
   const explain = buildProjectContextExplain({
     project: input.project,
     store: store2,
-    observations: input.observations
+    observations: input.observations,
+    exclude
   });
   return {
     project: input.project,
@@ -27372,6 +27428,7 @@ var init_auto_context = __esm({
   "src/codegraph/auto-context.ts"() {
     "use strict";
     init_esm_shims();
+    init_resolved_config();
     init_binder();
     init_current_facts();
     init_lite_provider();
@@ -27508,9 +27565,6 @@ function tokenize4(text) {
 function timestampOf(observation) {
   return Date.parse(observation.updatedAt ?? observation.createdAt ?? "") || 0;
 }
-function isGeneratedPath2(path29) {
-  return /(^|\/)(dist|build|coverage|\.next|\.turbo|node_modules)\//i.test(path29.replace(/\\/g, "/"));
-}
 function relevanceScore(observation, taskTokens) {
   if (taskTokens.length === 0) return 0;
   const title = observation.title.toLowerCase();
@@ -27561,7 +27615,8 @@ function assembleContextPackForTask(input) {
     refs,
     files,
     symbols,
-    suggestedVerification: input.suggestedVerification
+    suggestedVerification: input.suggestedVerification,
+    exclude: input.exclude
   });
 }
 function assembleContextPack(input) {
@@ -27580,6 +27635,7 @@ function assembleContextPack(input) {
     observationIdsWithRefs.add(ref.observationId);
     const file = ref.fileId ? files.get(ref.fileId) : void 0;
     const symbol = ref.symbolId ? symbols.get(ref.symbolId) : void 0;
+    if (file && isCodeGraphExcludedPath(file.path, input.exclude)) continue;
     const freshness = evaluateCodeRefFreshness(ref, file, symbol);
     if (freshness.status === "current") {
       const memoryKey = `${observation.id}:${freshness.status}`;
@@ -27645,8 +27701,8 @@ function buildContextPackPrompt(pack) {
   const reliableMemories = pack.memories.filter((memory) => memory.status === "current");
   const unboundMemories = pack.memories.filter((memory) => memory.status === "unbound");
   const lines = ["## Task", pack.task, "", "## Reliable Memories"];
-  const visibleCodeFacts = pack.codeFacts.filter((fact) => !isGeneratedPath2(fact.path)).slice(0, 5);
-  const visibleSuggestedReads = pack.suggestedReads.filter((path29) => !isGeneratedPath2(path29)).slice(0, 5);
+  const visibleCodeFacts = pack.codeFacts.filter((fact) => !isCodeGraphExcludedPath(fact.path)).slice(0, 5);
+  const visibleSuggestedReads = pack.suggestedReads.filter((path29) => !isCodeGraphExcludedPath(path29)).slice(0, 5);
   if (reliableMemories.length === 0) lines.push("- none");
   for (const memory of reliableMemories) {
     lines.push(`- #${memory.id} ${memory.status}: [${memory.type}] ${memory.title} (${memory.reason})`);
@@ -27681,6 +27737,7 @@ var init_context_pack = __esm({
     "use strict";
     init_esm_shims();
     init_freshness2();
+    init_exclude();
   }
 });
 
@@ -27719,6 +27776,7 @@ var init_codegraph = __esm({
     init_lite_provider();
     init_context_pack();
     init_binder();
+    init_resolved_config();
     init_observations();
     init_operator_shared();
     codegraph_default = defineCommand({
@@ -27741,6 +27799,7 @@ var init_codegraph = __esm({
           const store2 = new CodeGraphStore();
           await store2.init(dataDir);
           const explicitAction = Boolean(positional[0] || args.action);
+          const exclude = getResolvedConfig({ projectRoot: project.rootPath }).codegraph.excludePatterns;
           switch (action) {
             case "status": {
               const status = store2.status(project.id);
@@ -27753,7 +27812,8 @@ ${formatUsageHint()}`;
             case "refresh": {
               const indexed = await indexProjectLite({
                 projectId: project.id,
-                projectRoot: project.rootPath
+                projectRoot: project.rootPath,
+                exclude
               });
               store2.replaceProjectIndex(project.id, indexed);
               const activeObservations2 = getAllObservations().filter((obs) => obs.projectId === project.id && (obs.status ?? "active") === "active");
@@ -27784,7 +27844,8 @@ ${formatUsageHint()}`;
                 projectId: project.id,
                 task,
                 observations: observations2,
-                limit
+                limit,
+                exclude
               });
               emitResult({ project, pack }, buildContextPackPrompt(pack), asJson);
               return;
@@ -43369,12 +43430,12 @@ var init_stdio2 = __esm({
         this.onclose?.();
       }
       send(message) {
-        return new Promise((resolve3) => {
+        return new Promise((resolve4) => {
           const json = serializeMessage(message);
           if (this._stdout.write(json)) {
-            resolve3();
+            resolve4();
           } else {
-            this._stdout.once("drain", resolve3);
+            this._stdout.once("drain", resolve4);
           }
         });
       }
@@ -45907,7 +45968,7 @@ var init_protocol = __esm({
               return;
             }
             const pollInterval = task2.pollInterval ?? this._options?.defaultTaskPollInterval ?? 1e3;
-            await new Promise((resolve3) => setTimeout(resolve3, pollInterval));
+            await new Promise((resolve4) => setTimeout(resolve4, pollInterval));
             options2?.signal?.throwIfAborted();
           }
         } catch (error2) {
@@ -45924,7 +45985,7 @@ var init_protocol = __esm({
        */
       request(request, resultSchema, options2) {
         const { relatedRequestId, resumptionToken, onresumptiontoken, task, relatedTask } = options2 ?? {};
-        return new Promise((resolve3, reject) => {
+        return new Promise((resolve4, reject) => {
           const earlyReject = (error2) => {
             reject(error2);
           };
@@ -46002,7 +46063,7 @@ var init_protocol = __esm({
               if (!parseResult.success) {
                 reject(parseResult.error);
               } else {
-                resolve3(parseResult.data);
+                resolve4(parseResult.data);
               }
             } catch (error2) {
               reject(error2);
@@ -46263,12 +46324,12 @@ var init_protocol = __esm({
           }
         } catch {
         }
-        return new Promise((resolve3, reject) => {
+        return new Promise((resolve4, reject) => {
           if (signal.aborted) {
             reject(new McpError(ErrorCode.InvalidRequest, "Request cancelled"));
             return;
           }
-          const timeoutId = setTimeout(resolve3, interval);
+          const timeoutId = setTimeout(resolve4, interval);
           signal.addEventListener("abort", () => {
             clearTimeout(timeoutId);
             reject(new McpError(ErrorCode.InvalidRequest, "Request cancelled"));
@@ -49316,7 +49377,7 @@ var require_compile = __commonJS({
       const schOrFunc = root.refs[ref];
       if (schOrFunc)
         return schOrFunc;
-      let _sch = resolve3.call(this, root, ref);
+      let _sch = resolve4.call(this, root, ref);
       if (_sch === void 0) {
         const schema = (_a = root.localRefs) === null || _a === void 0 ? void 0 : _a[ref];
         const { schemaId } = this.opts;
@@ -49343,7 +49404,7 @@ var require_compile = __commonJS({
     function sameSchemaEnv(s1, s2) {
       return s1.schema === s2.schema && s1.root === s2.root && s1.baseId === s2.baseId;
     }
-    function resolve3(root, ref) {
+    function resolve4(root, ref) {
       let sch;
       while (typeof (sch = this.refs[ref]) == "string")
         ref = sch;
@@ -49977,7 +50038,7 @@ var require_fast_uri = __commonJS({
       }
       return uri;
     }
-    function resolve3(baseURI, relativeURI, options2) {
+    function resolve4(baseURI, relativeURI, options2) {
       const schemelessOptions = options2 ? Object.assign({ scheme: "null" }, options2) : { scheme: "null" };
       const resolved = resolveComponent(parse5(baseURI, schemelessOptions), parse5(relativeURI, schemelessOptions), schemelessOptions, true);
       schemelessOptions.skipEscape = true;
@@ -50235,7 +50296,7 @@ var require_fast_uri = __commonJS({
     var fastUri = {
       SCHEMES,
       normalize,
-      resolve: resolve3,
+      resolve: resolve4,
       resolveComponent,
       equal,
       serialize,
@@ -54417,7 +54478,7 @@ var init_mcp = __esm({
         let task = createTaskResult.task;
         const pollInterval = task.pollInterval ?? 5e3;
         while (task.status !== "completed" && task.status !== "failed" && task.status !== "cancelled") {
-          await new Promise((resolve3) => setTimeout(resolve3, pollInterval));
+          await new Promise((resolve4) => setTimeout(resolve4, pollInterval));
           const updatedTask = await extra.taskStore.getTask(taskId);
           if (!updatedTask) {
             throw new McpError(ErrorCode.InternalError, `Task ${taskId} not found during polling`);
@@ -54961,9 +55022,9 @@ async function createAutoRelations(obs, extracted, graphManager) {
     }
   }
   for (const file of obs.filesModified) {
-    const basename4 = file.split("/").pop()?.replace(/\.\w+$/, "") ?? "";
-    if (basename4.length < 3 || basename4.toLowerCase() === selfName) continue;
-    const matchedEntity = graphManager.findEntityByName(basename4);
+    const basename5 = file.split("/").pop()?.replace(/\.\w+$/, "") ?? "";
+    if (basename5.length < 3 || basename5.toLowerCase() === selfName) continue;
+    const matchedEntity = graphManager.findEntityByName(basename5);
     if (matchedEntity) {
       relations.push({
         from: obs.entityName,
@@ -54973,12 +55034,12 @@ async function createAutoRelations(obs, extracted, graphManager) {
     }
   }
   if (relations.length === 0) return 0;
-  const unique = relations.filter(
+  const unique2 = relations.filter(
     (r4, i2, arr) => arr.findIndex(
       (o3) => o3.from === r4.from && o3.to === r4.to && o3.relationType === r4.relationType
     ) === i2
   );
-  const created = await graphManager.createRelations(unique);
+  const created = await graphManager.createRelations(unique2);
   return created.length;
 }
 var init_auto_relations = __esm({
@@ -56506,7 +56567,6 @@ var require_loader = __commonJS({
       this.legacy = options2["legacy"] || false;
       this.json = options2["json"] || false;
       this.listener = options2["listener"] || null;
-      this.maxTotalMergeKeys = typeof options2["maxTotalMergeKeys"] === "number" ? options2["maxTotalMergeKeys"] : 1e4;
       this.implicitTypes = this.schema.compiledImplicit;
       this.typeMap = this.schema.compiledTypeMap;
       this.length = input.length;
@@ -56514,7 +56574,6 @@ var require_loader = __commonJS({
       this.line = 0;
       this.lineStart = 0;
       this.lineIndent = 0;
-      this.totalMergeKeys = 0;
       this.documents = [];
     }
     function generateError(state, message) {
@@ -56599,9 +56658,6 @@ var require_loader = __commonJS({
       sourceKeys = Object.keys(source);
       for (index = 0, quantity = sourceKeys.length; index < quantity; index += 1) {
         key = sourceKeys[index];
-        if (state.maxTotalMergeKeys !== -1 && ++state.totalMergeKeys > state.maxTotalMergeKeys) {
-          throwError(state, "merge keys exceeded maxTotalMergeKeys (" + state.maxTotalMergeKeys + ")");
-        }
         if (!_hasOwnProperty.call(destination, key)) {
           setProperty(destination, key, source[key]);
           overridableKeys[key] = true;
@@ -60918,7 +60974,7 @@ async function handleApi(req, res, dataDir, projectId, projectName, baseDir, pro
       }
       case "/config": {
         const os5 = await import("os");
-        const { existsSync: existsSync25 } = await import("fs");
+        const { existsSync: existsSync26 } = await import("fs");
         const { join: join32 } = await import("path");
         let yml = {};
         const configProjectRoot = effectiveProjectRoot;
@@ -60954,7 +61010,7 @@ async function handleApi(req, res, dataDir, projectId, projectName, baseDir, pro
             if (fpath === null) {
               files[key] = { exists: false, path: "unavailable", unavailable: true };
             } else {
-              files[key] = { exists: existsSync25(fpath), path: fpath };
+              files[key] = { exists: existsSync26(fpath), path: fpath };
             }
           }
         } catch {
@@ -61329,10 +61385,10 @@ async function buildTeamSnapshot(dataDir, projectId, scope, mode) {
   }
 }
 function readBody(req) {
-  return new Promise((resolve3, reject) => {
+  return new Promise((resolve4, reject) => {
     const chunks = [];
     req.on("data", (c5) => chunks.push(c5));
-    req.on("end", () => resolve3(Buffer.concat(chunks).toString("utf-8")));
+    req.on("end", () => resolve4(Buffer.concat(chunks).toString("utf-8")));
     req.on("error", reject);
   });
 }
@@ -61420,7 +61476,7 @@ async function startDashboard(dataDir, port, staticDir, projectId, projectName,
       await serveStatic(req, res, resolvedStaticDir);
     }
   });
-  return new Promise((resolve3, reject) => {
+  return new Promise((resolve4, reject) => {
     server.on("error", (err) => {
       if (err.code === "EADDRINUSE") {
         console.error(`Port ${port} is already in use. Try: memorix dashboard --port ${port + 1}`);
@@ -61444,7 +61500,7 @@ async function startDashboard(dataDir, port, staticDir, projectId, projectName,
   Press Ctrl+C to stop
 `);
       if (autoOpen) openBrowser(url);
-      resolve3();
+      resolve4();
     });
   });
 }
@@ -61960,7 +62016,7 @@ The path should point to a directory containing a .git folder.`
   };
   const server = existingServer ?? new McpServer({
     name: "memorix",
-    version: true ? "1.1.7" : "1.0.1"
+    version: true ? "1.1.9" : "1.0.1"
   });
   const originalRegisterTool = server.registerTool.bind(server);
   server.registerTool = ((name, ...args) => {
@@ -62662,15 +62718,18 @@ _Search mode: ${getLastSearchMode2(project.id)}_`;
       return withFreshIndex(async () => {
         const { CodeGraphStore: CodeGraphStore2 } = await Promise.resolve().then(() => (init_store(), store_exports));
         const { assembleContextPackForTask: assembleContextPackForTask2, buildContextPackPrompt: buildContextPackPrompt2 } = await Promise.resolve().then(() => (init_context_pack(), context_pack_exports));
+        const { getResolvedConfig: getResolvedConfig2 } = await Promise.resolve().then(() => (init_resolved_config(), resolved_config_exports));
         const store2 = new CodeGraphStore2();
         await store2.init(projectDir2);
+        const exclude = getResolvedConfig2({ projectRoot: project.rootPath }).codegraph.excludePatterns;
         const observations2 = getAllObservations().filter((obs) => obs.projectId === project.id && (obs.status ?? "active") === "active").reverse();
         const pack = assembleContextPackForTask2({
           store: store2,
           projectId: project.id,
           task,
           observations: observations2,
-          limit: typeof limit === "number" ? limit : 20
+          limit: typeof limit === "number" ? limit : 20,
+          exclude
         });
         const text = buildContextPackPrompt2(pack);
         return {
@@ -62969,12 +63028,12 @@ Run with dryRun=false to apply.`
           }]
         };
       }
-      const unique = [...new Set(toResolve)];
-      await resolveObservations2(unique, "resolved");
+      const unique2 = [...new Set(toResolve)];
+      await resolveObservations2(unique2, "resolved");
       return {
         content: [{
           type: "text",
-          text: `[CLEANUP] Deduplicated: resolved ${unique.length} memory(ies)
+          text: `[CLEANUP] Deduplicated: resolved ${unique2.length} memory(ies)
 
 ${actions.join("\n")}`
         }]
@@ -63299,10 +63358,10 @@ Archived memories are hidden from default search but can be found with status: "
   );
   let enableKG = isToolInProfile("create_entities", toolProfile);
   try {
-    const { homedir: homedir33 } = await import("os");
+    const { homedir: homedir34 } = await import("os");
     const { join: join32 } = await import("path");
-    const { readFile: readFile7 } = await import("fs/promises");
-    const raw = await readFile7(join32(homedir33(), ".memorix", "settings.json"), "utf-8");
+    const { readFile: readFile8 } = await import("fs/promises");
+    const raw = await readFile8(join32(homedir34(), ".memorix", "settings.json"), "utf-8");
     const s2 = JSON.parse(raw);
     if (s2.knowledgeGraph === true) enableKG = true;
   } catch {
@@ -64220,15 +64279,15 @@ ${json}
       if (inControlPlane) {
         const http = await import("http");
         const postData = JSON.stringify({ projectId: project.id, projectName: project.name });
-        await new Promise((resolve3) => {
+        await new Promise((resolve4) => {
           const req = http.request({
             hostname: "127.0.0.1",
             port: portNum,
             path: "/api/set-current-project",
             method: "POST",
             headers: { "Content-Type": "application/json", "Content-Length": Buffer.byteLength(postData) }
-          }, () => resolve3());
-          req.on("error", () => resolve3());
+          }, () => resolve4());
+          req.on("error", () => resolve4());
           req.write(postData);
           req.end();
         });
@@ -64253,33 +64312,33 @@ ${json}
       }
       if (dashboardRunning) {
         const { createConnection } = await import("net");
-        const isAlive = await new Promise((resolve3) => {
+        const isAlive = await new Promise((resolve4) => {
           const sock = createConnection(portNum, "127.0.0.1");
           sock.once("connect", () => {
             sock.destroy();
-            resolve3(true);
+            resolve4(true);
           });
           sock.once("error", () => {
             sock.destroy();
-            resolve3(false);
+            resolve4(false);
           });
           setTimeout(() => {
             sock.destroy();
-            resolve3(false);
+            resolve4(false);
           }, 1e3);
         });
         if (isAlive) {
           const http = await import("http");
           const postData = JSON.stringify({ projectId: project.id, projectName: project.name });
-          await new Promise((resolve3) => {
+          await new Promise((resolve4) => {
             const req = http.request({
               hostname: "127.0.0.1",
               port: portNum,
               path: "/api/set-current-project",
               method: "POST",
               headers: { "Content-Type": "application/json", "Content-Length": Buffer.byteLength(postData) }
-            }, () => resolve3());
-            req.on("error", () => resolve3());
+            }, () => resolve4());
+            req.on("error", () => resolve4());
             req.write(postData);
             req.end();
           });
@@ -64325,18 +64384,18 @@ ${json}
           dashboardRunning = false;
         });
         const { createConnection } = await import("net");
-        await new Promise((resolve3) => {
+        await new Promise((resolve4) => {
           const deadline = Date.now() + 5e3;
           const tryConnect = () => {
             const sock = createConnection(portNum, "127.0.0.1");
             sock.once("connect", () => {
               sock.destroy();
-              resolve3();
+              resolve4();
             });
             sock.once("error", () => {
               sock.destroy();
               if (Date.now() < deadline) setTimeout(tryConnect, 100);
-              else resolve3();
+              else resolve4();
             });
           };
           tryConnect();
@@ -64898,10 +64957,10 @@ Preview: ${analysis.description.slice(0, 300)}${analysis.description.length > 30
         const { ensureHooksDir: ensureHooksDir2 } = await Promise.resolve().then(() => (init_hooks_path(), hooks_path_exports));
         const resolved = ensureHooksDir2(project.rootPath);
         if (resolved) {
-          const { existsSync: existsSync25, readFileSync: readFileSync22, writeFileSync: writeFileSync11, chmodSync: chmodSync2 } = await import("fs");
+          const { existsSync: existsSync26, readFileSync: readFileSync22, writeFileSync: writeFileSync11, chmodSync: chmodSync2 } = await import("fs");
           const { hookPath } = resolved;
           const HOOK_MARKER3 = "# [memorix-git-hook]";
-          const needsInstall = !existsSync25(hookPath) || !readFileSync22(hookPath, "utf-8").includes(HOOK_MARKER3);
+          const needsInstall = !existsSync26(hookPath) || !readFileSync22(hookPath, "utf-8").includes(HOOK_MARKER3);
           if (needsInstall) {
             const hookScript = `#!/bin/sh
 ${HOOK_MARKER3}
@@ -64910,7 +64969,7 @@ if command -v memorix >/dev/null 2>&1; then
   memorix ingest commit --auto >/dev/null 2>&1 &
 fi
 `;
-            if (existsSync25(hookPath)) {
+            if (existsSync26(hookPath)) {
               const existing = readFileSync22(hookPath, "utf-8");
               writeFileSync11(hookPath, existing.trimEnd() + `
 
@@ -65362,10 +65421,10 @@ function describeAutoUpdateFailure(error2, timeoutMs) {
 async function fetchLatestVersion() {
   try {
     const { default: https } = await import("https");
-    return new Promise((resolve3) => {
+    return new Promise((resolve4) => {
       const req = https.get(REGISTRY_URL, { timeout: 5e3 }, (res) => {
         if (res.statusCode !== 200) {
-          resolve3(null);
+          resolve4(null);
           return;
         }
         let body = "";
@@ -65375,16 +65434,16 @@ async function fetchLatestVersion() {
         res.on("end", () => {
           try {
             const data = JSON.parse(body);
-            resolve3(data.version ?? null);
+            resolve4(data.version ?? null);
           } catch {
-            resolve3(null);
+            resolve4(null);
           }
         });
       });
-      req.on("error", () => resolve3(null));
+      req.on("error", () => resolve4(null));
       req.on("timeout", () => {
         req.destroy();
-        resolve3(null);
+        resolve4(null);
       });
     });
   } catch {
@@ -65533,7 +65592,7 @@ var init_serve = __esm({
         const { StdioServerTransport: StdioServerTransport2 } = await Promise.resolve().then(() => (init_stdio2(), stdio_exports));
         const { createMemorixServer: createMemorixServer2 } = await Promise.resolve().then(() => (init_server4(), server_exports2));
         const { detectProject: detectProject2, findGitInSubdirs: findGitInSubdirs2, isSystemDirectory: isSystemDirectory2 } = await Promise.resolve().then(() => (init_detector(), detector_exports));
-        const { homedir: homedir33 } = await import("os");
+        const { homedir: homedir34 } = await import("os");
         const { resolveServeProject: resolveServeProject2 } = await Promise.resolve().then(() => (init_serve_shared(), serve_shared_exports));
         process.stdin.on("end", () => {
           console.error("[memorix] stdin closed \u2014 exiting");
@@ -65543,16 +65602,16 @@ var init_serve = __esm({
         try {
           safeCwd = process.cwd();
         } catch {
-          safeCwd = homedir33();
+          safeCwd = homedir34();
         }
-        const { existsSync: existsSync25, readFileSync: readFileSync22 } = await import("fs");
+        const { existsSync: existsSync26, readFileSync: readFileSync22 } = await import("fs");
         const path29 = await import("path");
-        const lastRootFile = path29.join(homedir33(), ".memorix", "last-project-root");
+        const lastRootFile = path29.join(homedir34(), ".memorix", "last-project-root");
         let lastKnownProjectRoot;
-        if (existsSync25(lastRootFile)) {
+        if (existsSync26(lastRootFile)) {
           try {
             const lastRoot = readFileSync22(lastRootFile, "utf-8").trim();
-            if (lastRoot && existsSync25(lastRoot)) {
+            if (lastRoot && existsSync26(lastRoot)) {
               lastKnownProjectRoot = lastRoot;
             }
           } catch {
@@ -65564,7 +65623,7 @@ var init_serve = __esm({
             envProjectRoot: process.env.MEMORIX_PROJECT_ROOT,
             initCwd: process.env.INIT_CWD,
             processCwd: safeCwd,
-            homeDir: homedir33(),
+            homeDir: homedir34(),
             lastKnownProjectRoot
           },
           { detectProject: detectProject2, findGitInSubdirs: findGitInSubdirs2, isSystemDirectory: isSystemDirectory2 }
@@ -65582,7 +65641,7 @@ var init_serve = __esm({
         if (detected) {
           try {
             const { writeFileSync: writeFileSync11, mkdirSync: mkdirSync11 } = await import("fs");
-            const memorixDir = path29.join(homedir33(), ".memorix");
+            const memorixDir = path29.join(homedir34(), ".memorix");
             mkdirSync11(memorixDir, { recursive: true });
             writeFileSync11(path29.join(memorixDir, "last-project-root"), detected.rootPath, "utf-8");
           } catch {
@@ -65600,7 +65659,7 @@ var init_serve = __esm({
           try {
             const { writeFileSync: writeFileSync11, mkdirSync: mkdirSync11 } = await import("fs");
             const pathMod = await import("path");
-            const memorixDir = pathMod.join(homedir33(), ".memorix");
+            const memorixDir = pathMod.join(homedir34(), ".memorix");
             mkdirSync11(memorixDir, { recursive: true });
             writeFileSync11(pathMod.join(memorixDir, "last-project-root"), rootPath, "utf-8");
           } catch {
@@ -66156,7 +66215,7 @@ var init_dist5 = __esm({
             });
             if (!chunk) {
               if (i2 === 1) {
-                await new Promise((resolve3) => setTimeout(resolve3));
+                await new Promise((resolve4) => setTimeout(resolve4));
                 maxReadCount = 3;
                 continue;
               }
@@ -66664,9 +66723,9 @@ data:
           const initRequest = messages.find((m4) => isInitializeRequest(m4));
           const clientProtocolVersion = initRequest ? initRequest.params.protocolVersion : req.headers.get("mcp-protocol-version") ?? DEFAULT_NEGOTIATED_PROTOCOL_VERSION;
           if (this._enableJsonResponse) {
-            return new Promise((resolve3) => {
+            return new Promise((resolve4) => {
               this._streamMapping.set(streamId, {
-                resolveJson: resolve3,
+                resolveJson: resolve4,
                 cleanup: () => {
                   this._streamMapping.delete(streamId);
                 }
@@ -67068,8 +67127,8 @@ var init_serve_http = __esm({
         const { isInitializeRequest: isInitializeRequest2 } = await Promise.resolve().then(() => (init_types4(), types_exports));
         const { createMemorixServer: createMemorixServer2 } = await Promise.resolve().then(() => (init_server4(), server_exports2));
         const { findGitInSubdirs: findGitInSubdirs2, detectProjectWithDiagnostics: detectProjectWithDiagnostics2 } = await Promise.resolve().then(() => (init_detector(), detector_exports));
-        const { existsSync: existsSync25, readFileSync: readFileSync22, writeFileSync: writeFileSync11, mkdirSync: mkdirSync11 } = await import("fs");
-        const { homedir: homedir33 } = await import("os");
+        const { existsSync: existsSync26, readFileSync: readFileSync22, writeFileSync: writeFileSync11, mkdirSync: mkdirSync11 } = await import("fs");
+        const { homedir: homedir34 } = await import("os");
         const earlyPath = await import("path");
         const port = parseInt(args.port || "3211", 10);
         const host = args.host || "127.0.0.1";
@@ -67078,15 +67137,15 @@ var init_serve_http = __esm({
         try {
           safeCwd = process.cwd();
         } catch {
-          safeCwd = homedir33();
+          safeCwd = homedir34();
         }
         let projectRoot = args.cwd || process.env.MEMORIX_PROJECT_ROOT || safeCwd;
-        const lastRootFile = earlyPath.join(homedir33(), ".memorix", "last-project-root");
+        const lastRootFile = earlyPath.join(homedir34(), ".memorix", "last-project-root");
         const initialCheck = detectProjectWithDiagnostics2(projectRoot);
-        if (!initialCheck.project && existsSync25(lastRootFile)) {
+        if (!initialCheck.project && existsSync26(lastRootFile)) {
           try {
             const lastRoot = readFileSync22(lastRootFile, "utf-8").trim();
-            if (lastRoot && existsSync25(lastRoot)) {
+            if (lastRoot && existsSync26(lastRoot)) {
               const lastCheck = detectProjectWithDiagnostics2(lastRoot);
               if (lastCheck.project) {
                 console.error(`[memorix] No git at "${projectRoot}", restored last known project: ${lastRoot}`);
@@ -67129,13 +67188,13 @@ var init_serve_http = __esm({
           }
         }
         function parseBody(req) {
-          return new Promise((resolve3, reject) => {
+          return new Promise((resolve4, reject) => {
             const chunks = [];
             req.on("data", (chunk) => chunks.push(chunk));
             req.on("end", () => {
               try {
                 const body = Buffer.concat(chunks).toString("utf-8");
-                resolve3(body ? JSON.parse(body) : void 0);
+                resolve4(body ? JSON.parse(body) : void 0);
               } catch (err) {
                 reject(err);
               }
@@ -67294,8 +67353,8 @@ var init_serve_http = __esm({
               try {
                 const { writeFileSync: writeFileSync12, mkdirSync: mkdirSync12 } = await import("fs");
                 const pathMod = await import("path");
-                const { homedir: homedir34 } = await import("os");
-                const memorixDir = pathMod.join(homedir34(), ".memorix");
+                const { homedir: homedir35 } = await import("os");
+                const memorixDir = pathMod.join(homedir35(), ".memorix");
                 mkdirSync12(memorixDir, { recursive: true });
                 writeFileSync12(pathMod.join(memorixDir, "last-project-root"), rootPath, "utf-8");
               } catch {
@@ -67785,7 +67844,7 @@ var init_serve_http = __esm({
             if (apiPath === "/config") {
               const { projectId: configProjectId } = await resolveRequestProject(url);
               const os5 = await import("os");
-              const { existsSync: existsSync26 } = await import("fs");
+              const { existsSync: existsSync27 } = await import("fs");
               const { join: join32 } = await import("path");
               const { loadYamlConfig: loadYamlConfig2 } = await Promise.resolve().then(() => (init_yaml_loader(), yaml_loader_exports));
               const { loadFileConfig: loadFileConfig2, loadDotenv: loadDotenv2, getLoadedEnvFiles: getLoadedEnvFiles2 } = await Promise.resolve().then(() => (init_config(), config_exports));
@@ -67807,7 +67866,7 @@ var init_serve_http = __esm({
                   "legacy config.json": join32(home, ".memorix", "config.json")
                 };
                 for (const [key, fpath] of Object.entries(paths)) {
-                  files[key] = { exists: existsSync26(fpath), path: fpath };
+                  files[key] = { exists: existsSync27(fpath), path: fpath };
                 }
               } else {
                 files["project memorix.yml"] = { exists: false, path: "unavailable", unavailable: true };
@@ -67818,7 +67877,7 @@ var init_serve_http = __esm({
                   "legacy config.json": join32(home, ".memorix", "config.json")
                 };
                 for (const [key, fpath] of Object.entries(userPaths)) {
-                  files[key] = { exists: existsSync26(fpath), path: fpath };
+                  files[key] = { exists: existsSync27(fpath), path: fpath };
                 }
               }
               const values = [];
@@ -68300,7 +68359,7 @@ var init_status = __esm({
         const { getProjectDataDir: getProjectDataDir2 } = await Promise.resolve().then(() => (init_persistence(), persistence_exports));
         const { getEmbeddingProvider: getEmbeddingProvider2 } = await Promise.resolve().then(() => (init_provider(), provider_exports));
         const { getResolvedConfig: getResolvedConfig2, getResolvedAgentLane: getResolvedAgentLane2 } = await Promise.resolve().then(() => (init_resolved_config(), resolved_config_exports));
-        const { existsSync: existsSync25, readFileSync: readFileSync22 } = await import("fs");
+        const { existsSync: existsSync26, readFileSync: readFileSync22 } = await import("fs");
         we("memorix status");
         const project = detectProject2();
         if (!project) {
@@ -68386,7 +68445,7 @@ Embedding: ${embeddingStatus}${embeddingHint}`,
           try {
             const { resolveHooksDir: resolveHooksDir2 } = await Promise.resolve().then(() => (init_hooks_path(), hooks_path_exports));
             const resolved2 = resolveHooksDir2(project.rootPath);
-            if (resolved2 && existsSync25(resolved2.hookPath)) {
+            if (resolved2 && existsSync26(resolved2.hookPath)) {
               const hookContent = readFileSync22(resolved2.hookPath, "utf-8");
               if (hookContent.includes("# [memorix-git-hook]")) {
                 diagLines.push(`  Git hook:      installed [OK]`);
@@ -69828,9 +69887,9 @@ async function handleHookEvent(input) {
   };
 }
 async function runHook(agentOverride, eventOverride) {
-  const rawInput = await new Promise((resolve3) => {
+  const rawInput = await new Promise((resolve4) => {
     const chunks = [];
-    const finish = () => resolve3(Buffer.concat(chunks).toString("utf-8").trim());
+    const finish = () => resolve4(Buffer.concat(chunks).toString("utf-8").trim());
     const timer = setTimeout(() => {
       process.stdin.removeAllListeners("data");
       process.stdin.removeAllListeners("end");
@@ -71466,7 +71525,7 @@ function getMemorixDir() {
   const home = process.env.HOME || process.env.USERPROFILE || "";
   return home.replace(/\\/g, "/") + "/.memorix";
 }
-function normalizePath4(p2) {
+function normalizePath3(p2) {
   return process.platform === "win32" ? p2.replace(/\//g, "\\") : p2;
 }
 function getStateFilePath() {
@@ -71632,7 +71691,7 @@ async function doStart(port) {
     `  Port:       ${port}`,
     `  Dashboard:  http://127.0.0.1:${port}/`,
     `  MCP:        http://127.0.0.1:${port}/mcp`,
-    `  Logs:       ${normalizePath4(logFile)}`,
+    `  Logs:       ${normalizePath3(logFile)}`,
     ""
   ].join("\n");
   process.stderr.write(startMsg + "\n");
@@ -71646,7 +71705,7 @@ async function doStart(port) {
     }
     if (!isProcessRunning(pid)) {
       console.error("[ERROR] Background process exited unexpectedly.");
-      console.error(`  Check logs: ${normalizePath4(logFile)}`);
+      console.error(`  Check logs: ${normalizePath3(logFile)}`);
       clearState();
       process.exitCode = 1;
       return;
@@ -71784,7 +71843,7 @@ async function doStatus() {
   if (state.instanceToken) console.log(`  Instance:   ${state.instanceToken.slice(0, 8)}\u2026`);
   console.log(`  Dashboard:  http://127.0.0.1:${state.port}/`);
   console.log(`  MCP:        http://127.0.0.1:${state.port}/mcp`);
-  console.log(`  Logs:       ${normalizePath4(state.logFile)}`);
+  console.log(`  Logs:       ${normalizePath3(state.logFile)}`);
   if (health.ok && health.data) {
     const d3 = health.data;
     console.log("");
@@ -71974,6 +72033,492 @@ var init_background = __esm({
   }
 });
 
+// src/cli/commands/agent-integrations.ts
+var agent_integrations_exports = {};
+__export(agent_integrations_exports, {
+  formatAgentIntegrationReport: () => formatAgentIntegrationReport,
+  formatAgentRepairResult: () => formatAgentRepairResult,
+  inspectAgentIntegrations: () => inspectAgentIntegrations,
+  repairAgentIntegrations: () => repairAgentIntegrations
+});
+import { existsSync as existsSync21 } from "fs";
+import { mkdir as mkdir7, readFile as readFile7, writeFile as writeFile7 } from "fs/promises";
+import { basename as basename3, dirname as dirname7, resolve as resolve2 } from "path";
+import { homedir as homedir32 } from "os";
+function requestedAgents(agent) {
+  const all = getSetupAgentTargets();
+  if (!agent || agent === "all") return all;
+  return all.includes(agent) ? [agent] : [];
+}
+function requestedMcpScopes(agent, scope) {
+  if (scope === "local") return agent === "claude" ? ["local"] : [];
+  if (scope === "project" || scope === "global") return [scope];
+  return agent === "claude" ? ["local", "project", "global"] : ["project", "global"];
+}
+function requestedGuidanceScopes(scope) {
+  if (scope === "project" || scope === "global") return [scope];
+  if (scope === "local") return [];
+  return ["project", "global"];
+}
+function unique(values) {
+  return [...new Set(values)];
+}
+function worstStatus(statuses) {
+  if (statuses.includes("repairable")) return "repairable";
+  if (statuses.includes("missing")) return "missing";
+  if (statuses.includes("ok")) return "ok";
+  return "skipped";
+}
+function isMcpConfigAgent(agent) {
+  return agent !== "pi";
+}
+function isActionableMcpRepairIssue(issue2) {
+  return issue2 !== "memorix-server-missing";
+}
+function aggregateMcpStatus(checks) {
+  const actionableRepair = checks.some(
+    (check2) => check2.status === "repairable" && check2.issues.some(isActionableMcpRepairIssue)
+  );
+  if (actionableRepair) return "repairable";
+  if (checks.some((check2) => check2.status === "ok")) return "ok";
+  if (checks.some((check2) => check2.status === "repairable")) return "repairable";
+  if (checks.some((check2) => check2.status === "missing")) return "missing";
+  return "skipped";
+}
+function aggregateMcpIssues(checks) {
+  const status = aggregateMcpStatus(checks);
+  if (status === "repairable") {
+    return unique(checks.filter((check2) => check2.status === "repairable").flatMap((check2) => check2.issues.filter(isActionableMcpRepairIssue)));
+  }
+  if (status === "missing") {
+    return unique(checks.filter((check2) => check2.status === "missing").flatMap((check2) => check2.issues));
+  }
+  return [];
+}
+function aggregateGuidanceStatus(checks) {
+  const projectCheck = checks.find((check2) => check2.scope === "project");
+  if (projectCheck?.status === "repairable") return "repairable";
+  if (checks.some((check2) => check2.status === "ok")) return "ok";
+  if (checks.some((check2) => check2.status === "repairable")) return "repairable";
+  if (checks.some((check2) => check2.status === "missing")) return "missing";
+  return "skipped";
+}
+function aggregateGuidanceIssues(checks) {
+  const status = aggregateGuidanceStatus(checks);
+  if (status === "repairable") {
+    const projectCheck = checks.find((check2) => check2.scope === "project");
+    if (projectCheck?.status === "repairable") return projectCheck.issues;
+    return unique(checks.filter((check2) => check2.status === "repairable").flatMap((check2) => check2.issues));
+  }
+  if (status === "missing") {
+    return unique(checks.filter((check2) => check2.status === "missing").flatMap((check2) => check2.issues));
+  }
+  return [];
+}
+function asRecord2(value) {
+  return value && typeof value === "object" && !Array.isArray(value) ? value : null;
+}
+function looksLikeStaleMemorixCommand(server) {
+  const text = [server.command, ...server.args ?? []].join(" ");
+  return /[\\/]\.worktrees[\\/]/i.test(text) || /[\\/]dist[\\/]cli[\\/]index\.js/i.test(text);
+}
+function isRecommendedStdioServer(server) {
+  const commandBase = basename3(server.command).toLowerCase().replace(/\.(cmd|ps1|exe)$/i, "");
+  return commandBase === "memorix" && server.args?.[0] === "serve";
+}
+function sanitizeServer(server) {
+  if (server.url) {
+    return {
+      transport: "http",
+      url: server.url,
+      envKeys: server.env ? Object.keys(server.env) : void 0
+    };
+  }
+  return {
+    transport: "stdio",
+    command: server.command,
+    args: server.args ?? [],
+    alwaysLoad: server.alwaysLoad,
+    envKeys: server.env ? Object.keys(server.env) : void 0
+  };
+}
+function normalizeProjectKey(projectRoot) {
+  return resolve2(projectRoot).replace(/\\/g, "/").toLowerCase();
+}
+function defaultClaudeProjectKey(projectRoot) {
+  return resolve2(projectRoot).replace(/\\/g, "/");
+}
+function getClaudeLocalConfigPath() {
+  return `${homedir32()}/.claude.json`;
+}
+function coerceClaudeLocalServer(name, value) {
+  const entry = asRecord2(value);
+  if (!entry) return null;
+  const args = Array.isArray(entry.args) ? entry.args.map(String) : [];
+  return {
+    name,
+    command: typeof entry.command === "string" ? entry.command : "",
+    args,
+    ...asRecord2(entry.env) ? { env: entry.env } : {},
+    ...typeof entry.url === "string" ? { url: entry.url } : {},
+    ...entry.alwaysLoad === true ? { alwaysLoad: true } : {}
+  };
+}
+function findClaudeLocalProject(config2, projectRoot) {
+  const projects = asRecord2(config2.projects);
+  if (!projects) return null;
+  const target = normalizeProjectKey(projectRoot);
+  for (const [key, value] of Object.entries(projects)) {
+    if (normalizeProjectKey(key) !== target) continue;
+    const project = asRecord2(value);
+    return project ? { key, project } : null;
+  }
+  return null;
+}
+async function inspectClaudeLocalMcp(projectRoot) {
+  const configPath = getClaudeLocalConfigPath();
+  if (!existsSync21(configPath)) {
+    return {
+      scope: "local",
+      path: configPath,
+      exists: false,
+      status: "missing",
+      issues: ["mcp-config-missing"]
+    };
+  }
+  let config2 = {};
+  try {
+    config2 = JSON.parse(await readFile7(configPath, "utf-8"));
+  } catch {
+    return {
+      scope: "local",
+      path: configPath,
+      exists: true,
+      status: "repairable",
+      issues: ["mcp-config-unreadable"]
+    };
+  }
+  const localProject = findClaudeLocalProject(config2, projectRoot);
+  const pathLabel = localProject ? `${configPath}#projects[${localProject.key}]` : configPath;
+  if (!localProject) {
+    return {
+      scope: "local",
+      path: pathLabel,
+      exists: true,
+      status: "missing",
+      issues: ["mcp-config-missing"]
+    };
+  }
+  const servers = asRecord2(localProject.project.mcpServers);
+  const server = coerceClaudeLocalServer("memorix", servers?.memorix);
+  if (!server) {
+    return {
+      scope: "local",
+      path: pathLabel,
+      exists: true,
+      status: "repairable",
+      issues: ["memorix-server-missing"]
+    };
+  }
+  const issues = [];
+  if (!server.url && looksLikeStaleMemorixCommand(server)) issues.push("stale-command-path");
+  if (!server.url && !isRecommendedStdioServer(server)) issues.push("nonstandard-mcp-command");
+  if (server.alwaysLoad !== true) issues.push("claude-always-load-missing");
+  return {
+    scope: "local",
+    path: pathLabel,
+    exists: true,
+    status: issues.length > 0 ? "repairable" : "ok",
+    issues,
+    server: sanitizeServer(server)
+  };
+}
+async function installClaudeLocalMcpConfig(projectRoot) {
+  const configPath = getClaudeLocalConfigPath();
+  let config2 = {};
+  try {
+    config2 = JSON.parse(await readFile7(configPath, "utf-8"));
+  } catch {
+    config2 = {};
+  }
+  const projects = asRecord2(config2.projects) ?? {};
+  const existing = findClaudeLocalProject({ ...config2, projects }, projectRoot);
+  const projectKey = existing?.key ?? defaultClaudeProjectKey(projectRoot);
+  const project = existing?.project ?? asRecord2(projects[projectKey]) ?? {};
+  const mcpServers = asRecord2(project.mcpServers) ?? {};
+  const server = buildMemorixServer("stdio");
+  server.alwaysLoad = true;
+  mcpServers.memorix = {
+    type: "stdio",
+    command: server.command,
+    args: server.args,
+    alwaysLoad: true
+  };
+  project.mcpServers = mcpServers;
+  projects[projectKey] = project;
+  config2.projects = projects;
+  await mkdir7(dirname7(configPath), { recursive: true });
+  await writeFile7(configPath, `${JSON.stringify(config2, null, 2)}
+`, "utf-8");
+}
+async function inspectMcp(agent, projectRoot, scope) {
+  if (!isMcpConfigAgent(agent)) {
+    return { status: "skipped", issues: ["mcp-managed-by-package"], checks: [] };
+  }
+  const adapter = getMcpAdapter(agent);
+  const checks = [];
+  for (const targetScope of requestedMcpScopes(agent, scope)) {
+    if (agent === "claude" && targetScope === "local") {
+      checks.push(await inspectClaudeLocalMcp(projectRoot));
+      continue;
+    }
+    const configPath = adapter.getConfigPath(targetScope === "project" ? projectRoot : void 0);
+    if (targetScope === "global" && configPath === adapter.getConfigPath(projectRoot)) continue;
+    if (!existsSync21(configPath)) {
+      checks.push({
+        scope: targetScope,
+        path: configPath,
+        exists: false,
+        status: "missing",
+        issues: ["mcp-config-missing"]
+      });
+      continue;
+    }
+    const content = await readFile7(configPath, "utf-8");
+    if (agent === "claude" && targetScope === "global") {
+      try {
+        const parsed = JSON.parse(content);
+        if (asRecord2(parsed.projects) && !asRecord2(parsed.mcpServers)) {
+          checks.push({
+            scope: targetScope,
+            path: configPath,
+            exists: true,
+            status: "missing",
+            issues: ["mcp-config-missing"]
+          });
+          continue;
+        }
+      } catch {
+        checks.push({
+          scope: targetScope,
+          path: configPath,
+          exists: true,
+          status: "repairable",
+          issues: ["mcp-config-unreadable"]
+        });
+        continue;
+      }
+    }
+    const servers = adapter.parse(content);
+    const server = servers.find((entry) => entry.name === "memorix");
+    if (!server) {
+      checks.push({
+        scope: targetScope,
+        path: configPath,
+        exists: true,
+        status: "repairable",
+        issues: ["memorix-server-missing"]
+      });
+      continue;
+    }
+    const issues = [];
+    if (!server.url && looksLikeStaleMemorixCommand(server)) issues.push("stale-command-path");
+    if (!server.url && !isRecommendedStdioServer(server)) issues.push("nonstandard-mcp-command");
+    if (agent === "claude" && server.alwaysLoad !== true) issues.push("claude-always-load-missing");
+    checks.push({
+      scope: targetScope,
+      path: configPath,
+      exists: true,
+      status: issues.length > 0 ? "repairable" : "ok",
+      issues,
+      server: sanitizeServer(server)
+    });
+  }
+  return {
+    status: aggregateMcpStatus(checks),
+    issues: aggregateMcpIssues(checks),
+    checks
+  };
+}
+function isCurrentGuidance(content) {
+  return content.includes("Memory Autopilot") && content.includes("Default first step for non-trivial coding work") && content.includes("memorix_project_context");
+}
+async function inspectGuidance(agent, projectRoot, scope) {
+  if (!GUIDANCE_AGENTS.has(agent)) {
+    return { status: "skipped", issues: ["guidance-managed-by-package"], checks: [] };
+  }
+  const checks = [];
+  for (const targetScope of requestedGuidanceScopes(scope)) {
+    const root = targetScope === "project" ? projectRoot : homedir32();
+    const rulesPath = getAgentRulesPath(agent, root, targetScope === "global");
+    if (!existsSync21(rulesPath)) {
+      checks.push({
+        scope: targetScope,
+        path: rulesPath,
+        exists: false,
+        status: "missing",
+        issues: ["guidance-missing"]
+      });
+      continue;
+    }
+    const content = await readFile7(rulesPath, "utf-8");
+    const issues = isCurrentGuidance(content) ? [] : ["guidance-outdated"];
+    checks.push({
+      scope: targetScope,
+      path: rulesPath,
+      exists: true,
+      status: issues.length > 0 ? "repairable" : "ok",
+      issues
+    });
+  }
+  return {
+    status: aggregateGuidanceStatus(checks),
+    issues: aggregateGuidanceIssues(checks),
+    checks
+  };
+}
+async function inspectAgentIntegrations(options2 = {}) {
+  const projectRoot = options2.projectRoot ?? process.cwd();
+  const scope = options2.scope === "local" || options2.scope === "project" || options2.scope === "global" || options2.scope === "all" ? options2.scope : "all";
+  const agents = requestedAgents(options2.agent);
+  const entries = [];
+  for (const agent of agents) {
+    entries.push({
+      agent,
+      mcp: await inspectMcp(agent, projectRoot, scope),
+      guidance: await inspectGuidance(agent, projectRoot, scope)
+    });
+  }
+  const entryStatuses = entries.map((entry) => worstStatus([entry.mcp.status, entry.guidance.status]));
+  return {
+    projectRoot,
+    scope,
+    entries,
+    summary: {
+      checked: entries.length,
+      ok: entryStatuses.filter((status) => status === "ok").length,
+      missing: entryStatuses.filter((status) => status === "missing").length,
+      repairable: entryStatuses.filter((status) => status === "repairable").length
+    },
+    repairCommand: `memorix repair agents${options2.agent ? ` --agent ${options2.agent}` : ""}${scope === "all" ? "" : ` --scope ${scope}`}`
+  };
+}
+function formatAgentIntegrationReport(report) {
+  const lines = [
+    "Memorix Agent Doctor",
+    `Project: ${report.projectRoot}`,
+    `Scope: ${report.scope}`,
+    ""
+  ];
+  for (const entry of report.entries) {
+    const status = worstStatus([entry.mcp.status, entry.guidance.status]);
+    lines.push(`${entry.agent}: ${status}`);
+    if (entry.mcp.issues.length > 0) lines.push(`  MCP: ${entry.mcp.issues.join(", ")}`);
+    if (entry.guidance.issues.length > 0) lines.push(`  Guidance: ${entry.guidance.issues.join(", ")}`);
+  }
+  lines.push("");
+  lines.push(`Repair: ${report.repairCommand}`);
+  return lines.join("\n");
+}
+async function repairAgentIntegrations(options2 = {}) {
+  const projectRoot = options2.projectRoot ?? process.cwd();
+  const scope = options2.scope === "local" || options2.scope === "project" || options2.scope === "global" || options2.scope === "all" ? options2.scope : "all";
+  const before = await inspectAgentIntegrations({ projectRoot, agent: options2.agent, scope });
+  const changed = [];
+  const skipped = [];
+  const canInstallMissing = Boolean(options2.agent && scope !== "all");
+  for (const entry of before.entries) {
+    if (isMcpConfigAgent(entry.agent)) {
+      for (const check2 of entry.mcp.checks) {
+        if (check2.status === "ok" || check2.status === "skipped") continue;
+        if (check2.status === "missing" && !canInstallMissing) {
+          skipped.push(`${entry.agent}:mcp:${check2.scope}:missing`);
+          continue;
+        }
+        if (!options2.dry) {
+          if (entry.agent === "claude" && check2.scope === "local") {
+            await installClaudeLocalMcpConfig(projectRoot);
+          } else {
+            await installMcpConfig({
+              agent: entry.agent,
+              projectRoot,
+              global: check2.scope === "global",
+              mcp: "stdio"
+            });
+          }
+        }
+        changed.push(`${entry.agent}:mcp:${check2.scope}`);
+      }
+    } else {
+      skipped.push(`${entry.agent}:mcp`);
+    }
+    if (GUIDANCE_AGENTS.has(entry.agent)) {
+      for (const check2 of entry.guidance.checks) {
+        if (check2.status === "ok" || check2.status === "skipped") continue;
+        if (check2.status === "missing" && !canInstallMissing) {
+          skipped.push(`${entry.agent}:guidance:${check2.scope}:missing`);
+          continue;
+        }
+        if (!options2.dry) {
+          await installAgentGuidance(entry.agent, projectRoot, check2.scope === "global");
+        }
+        changed.push(`${entry.agent}:guidance:${check2.scope}`);
+      }
+    } else {
+      skipped.push(`${entry.agent}:guidance`);
+    }
+  }
+  return {
+    projectRoot,
+    scope,
+    changed,
+    skipped,
+    before,
+    after: options2.dry ? void 0 : await inspectAgentIntegrations({ projectRoot, agent: options2.agent, scope })
+  };
+}
+function formatAgentRepairResult(result) {
+  const lines = [
+    "Memorix Agent Repair",
+    `Project: ${result.projectRoot}`,
+    `Scope: ${result.scope}`,
+    ""
+  ];
+  if (result.changed.length === 0) {
+    lines.push("No repairable agent integration issues found.");
+  } else {
+    lines.push("Changed:");
+    for (const item of result.changed) lines.push(`- ${item}`);
+  }
+  if (result.skipped.length > 0) {
+    lines.push("");
+    lines.push("Skipped:");
+    for (const item of result.skipped) lines.push(`- ${item}`);
+  }
+  return lines.join("\n");
+}
+var GUIDANCE_AGENTS;
+var init_agent_integrations = __esm({
+  "src/cli/commands/agent-integrations.ts"() {
+    "use strict";
+    init_esm_shims();
+    init_installers();
+    init_setup();
+    GUIDANCE_AGENTS = /* @__PURE__ */ new Set([
+      "claude",
+      "codex",
+      "cursor",
+      "windsurf",
+      "copilot",
+      "gemini-cli",
+      "antigravity",
+      "kiro",
+      "opencode",
+      "trae"
+    ]);
+  }
+});
+
 // src/cli/commands/doctor.ts
 var doctor_exports = {};
 __export(doctor_exports, {
@@ -71991,6 +72536,14 @@ var init_doctor = __esm({
         description: "Diagnose Memorix health \u2014 project identity, embedding, data, conflicts"
       },
       args: {
+        agent: {
+          type: "string",
+          description: 'Agent to inspect for "doctor agents" (default: all)'
+        },
+        scope: {
+          type: "string",
+          description: 'Scope for "doctor agents": local, project, global, or all'
+        },
         json: {
           type: "boolean",
           description: "Output as JSON instead of human-readable text",
@@ -72003,9 +72556,23 @@ var init_doctor = __esm({
         }
       },
       run: async ({ args }) => {
-        const { existsSync: existsSync25, readFileSync: readFileSync22 } = await import("fs");
-        const { join: join32, basename: basename4 } = await import("path");
-        const { homedir: homedir33 } = await import("os");
+        const positional = args._ ?? [];
+        if (positional[0] === "agents") {
+          const { inspectAgentIntegrations: inspectAgentIntegrations2, formatAgentIntegrationReport: formatAgentIntegrationReport2 } = await Promise.resolve().then(() => (init_agent_integrations(), agent_integrations_exports));
+          const report2 = await inspectAgentIntegrations2({
+            agent: args.agent,
+            scope: args.scope
+          });
+          if (args.json) {
+            console.log(JSON.stringify({ agents: report2 }, null, 2));
+          } else {
+            console.log(formatAgentIntegrationReport2(report2));
+          }
+          return;
+        }
+        const { existsSync: existsSync26, readFileSync: readFileSync22 } = await import("fs");
+        const { join: join32, basename: basename5 } = await import("path");
+        const { homedir: homedir34 } = await import("os");
         const { execSync: execSync11 } = await import("child_process");
         const report = {};
         const issues = [];
@@ -72067,13 +72634,13 @@ var init_doctor = __esm({
         }
         lines.push("");
         lines.push("\u250C\u2500 Runtime Mode \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500");
-        const memorixDir = join32(homedir33(), ".memorix");
+        const memorixDir = join32(homedir34(), ".memorix");
         const bgStatePath = join32(memorixDir, "background.json");
         let bgRunning = false;
         let bgPort = 0;
         let bgPid = 0;
         try {
-          if (existsSync25(bgStatePath)) {
+          if (existsSync26(bgStatePath)) {
             const bgState = JSON.parse(readFileSync22(bgStatePath, "utf-8"));
             bgPid = bgState.pid;
             bgPort = bgState.port;
@@ -72089,15 +72656,15 @@ var init_doctor = __esm({
           lines.push(ok(`Background control plane running (PID ${bgPid}, port ${bgPort})`));
           try {
             const http = await import("http");
-            const healthy = await new Promise((resolve3) => {
+            const healthy = await new Promise((resolve4) => {
               const req = http.request({ hostname: "127.0.0.1", port: bgPort, path: "/api/team", timeout: 3e3 }, (res) => {
                 res.resume();
-                resolve3(res.statusCode === 200);
+                resolve4(res.statusCode === 200);
               });
-              req.on("error", () => resolve3(false));
+              req.on("error", () => resolve4(false));
               req.on("timeout", () => {
                 req.destroy();
-                resolve3(false);
+                resolve4(false);
               });
               req.end();
             });
@@ -72120,15 +72687,15 @@ var init_doctor = __esm({
         if (!bgRunning) {
           try {
             const http = await import("http");
-            const portUsed = await new Promise((resolve3) => {
+            const portUsed = await new Promise((resolve4) => {
               const req = http.request({ hostname: "127.0.0.1", port: 3211, path: "/api/team", timeout: 2e3 }, (res) => {
                 res.resume();
-                resolve3(res.statusCode === 200);
+                resolve4(res.statusCode === 200);
               });
-              req.on("error", () => resolve3(false));
+              req.on("error", () => resolve4(false));
               req.on("timeout", () => {
                 req.destroy();
-                resolve3(false);
+                resolve4(false);
               });
               req.end();
             });
@@ -72166,7 +72733,7 @@ var init_doctor = __esm({
             }
             try {
               const cachePath = join32(memorixDir, "embedding-cache.json");
-              if (existsSync25(cachePath)) {
+              if (existsSync26(cachePath)) {
                 const cache4 = JSON.parse(readFileSync22(cachePath, "utf-8"));
                 const cacheCount = Object.keys(cache4).length;
                 lines.push(info(`Cached embeddings: ${cacheCount}`));
@@ -72181,7 +72748,7 @@ var init_doctor = __esm({
         }
         lines.push("");
         lines.push("\u250C\u2500 Data Status \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500");
-        if (dataDir && existsSync25(dataDir)) {
+        if (dataDir && existsSync26(dataDir)) {
           let obsCount = 0;
           let activeCount = 0;
           let ranCount = 0;
@@ -72247,16 +72814,19 @@ var init_doctor = __esm({
           try {
             const { CodeGraphStore: CodeGraphStore2 } = await Promise.resolve().then(() => (init_store(), store_exports));
             const { buildProjectContextOverview: buildProjectContextOverview2 } = await Promise.resolve().then(() => (init_project_context(), project_context_exports));
+            const { getResolvedConfig: getResolvedConfig2 } = await Promise.resolve().then(() => (init_resolved_config(), resolved_config_exports));
             const codeStore = new CodeGraphStore2();
             await codeStore.init(dataDir);
+            const exclude = getResolvedConfig2({ projectRoot: projectRoot || process.cwd() }).codegraph.excludePatterns;
             const overview = buildProjectContextOverview2({
               project: {
                 id: projectId,
-                name: projectName || basename4(projectRoot || process.cwd()),
+                name: projectName || basename5(projectRoot || process.cwd()),
                 rootPath: projectRoot || process.cwd()
               },
               store: codeStore,
-              observations: projectObservations
+              observations: projectObservations,
+              exclude
             });
             const languageText = overview.code.languages.length > 0 ? overview.code.languages.map((item) => `${item.language} ${item.files}`).join(", ") : "none indexed yet";
             if (overview.code.files > 0) {
@@ -72297,7 +72867,7 @@ var init_doctor = __esm({
         let conflictsFound = false;
         if (dataDir) {
           const lockFile = join32(dataDir, ".memorix.lock");
-          if (existsSync25(lockFile)) {
+          if (existsSync26(lockFile)) {
             try {
               const lockData = JSON.parse(readFileSync22(lockFile, "utf-8"));
               const lockAge = Date.now() - lockData.time;
@@ -72412,6 +72982,71 @@ var init_doctor = __esm({
   }
 });
 
+// src/cli/commands/repair.ts
+var repair_exports = {};
+__export(repair_exports, {
+  default: () => repair_default
+});
+var repair_default;
+var init_repair = __esm({
+  "src/cli/commands/repair.ts"() {
+    "use strict";
+    init_esm_shims();
+    init_dist2();
+    repair_default = defineCommand({
+      meta: {
+        name: "repair",
+        description: "Repair Memorix-owned agent integration files"
+      },
+      args: {
+        agent: {
+          type: "string",
+          description: "Agent to repair (default: all detected repairable entries)"
+        },
+        scope: {
+          type: "string",
+          description: "Scope: local, project, global, or all"
+        },
+        dry: {
+          type: "boolean",
+          description: "Show what would be repaired without writing files",
+          default: false
+        },
+        json: {
+          type: "boolean",
+          description: "Emit machine-readable JSON output",
+          default: false
+        }
+      },
+      run: async ({ args }) => {
+        const positional = args._ ?? [];
+        const action = positional[0] || "agents";
+        if (action !== "agents") {
+          const message = "Usage: memorix repair agents [--agent <agent>] [--scope local|project|global|all] [--dry]";
+          if (args.json) {
+            console.log(JSON.stringify({ error: message }, null, 2));
+          } else {
+            console.log(message);
+          }
+          process.exitCode = 1;
+          return;
+        }
+        const { repairAgentIntegrations: repairAgentIntegrations2, formatAgentRepairResult: formatAgentRepairResult2 } = await Promise.resolve().then(() => (init_agent_integrations(), agent_integrations_exports));
+        const repair = await repairAgentIntegrations2({
+          agent: args.agent,
+          scope: args.scope,
+          dry: !!args.dry
+        });
+        if (args.json) {
+          console.log(JSON.stringify({ repair }, null, 2));
+        } else {
+          console.log(formatAgentRepairResult2(repair));
+        }
+      }
+    });
+  }
+});
+
 // src/cli/commands/dashboard.ts
 var dashboard_exports = {};
 __export(dashboard_exports, {
@@ -72582,14 +73217,14 @@ Project: ${projectName} (${projectId})
         const highQuality = projectObs.filter((o3) => !isLowQuality(o3.title ?? ""));
         const seen = /* @__PURE__ */ new Set();
         const duplicates = [];
-        const unique = [];
+        const unique2 = [];
         for (const obs of highQuality) {
           const key = `${obs.type}|${obs.title}|${obs.entityName}`;
           if (seen.has(key)) {
             duplicates.push(obs);
           } else {
             seen.add(key);
-            unique.push(obs);
+            unique2.push(obs);
           }
         }
         const noiseHits = [];
@@ -72604,7 +73239,7 @@ Project: ${projectName} (${projectId})
         const toArchive = noiseHits.map((h3) => h3.obs);
         console.log(`Analysis (active observations for ${projectId}):`);
         console.log(`   Total active:       ${projectObs.length}`);
-        console.log(`   High quality:       ${unique.length - toArchive.length}`);
+        console.log(`   High quality:       ${unique2.length - toArchive.length}`);
         console.log(`   Low quality:        ${lowQuality.length}`);
         console.log(`   Duplicates:         ${duplicates.length}`);
         if (args.noise) {
@@ -72651,8 +73286,8 @@ Project: ${projectName} (${projectId})
             toRemove.length > 0 ? `delete ${toRemove.length}` : "",
             toArchive.length > 0 ? `archive ${toArchive.length}` : ""
           ].filter(Boolean).join(" and ");
-          const answer = await new Promise((resolve3) => {
-            rl.question(`Proceed to ${desc} observations? (y/N) `, resolve3);
+          const answer = await new Promise((resolve4) => {
+            rl.question(`Proceed to ${desc} observations? (y/N) `, resolve4);
           });
           rl.close();
           if (answer.trim().toLowerCase() !== "y") {
@@ -72945,8 +73580,8 @@ async function confirm(description) {
   }
   const readline = await import("readline");
   const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
-  const answer = await new Promise((resolve3) => {
-    rl.question(`Proceed to ${description}? (y/N) `, resolve3);
+  const answer = await new Promise((resolve4) => {
+    rl.question(`Proceed to ${description}? (y/N) `, resolve4);
   });
   rl.close();
   return answer.trim().toLowerCase() === "y";
@@ -73258,8 +73893,8 @@ function spawnAgentWithStream(command, args, opts, stdinData, onStdoutLine, onCo
           if (done) {
             return Promise.resolve({ value: void 0, done: true });
           }
-          return new Promise((resolve3) => {
-            waiters.push({ resolve: resolve3 });
+          return new Promise((resolve4) => {
+            waiters.push({ resolve: resolve4 });
           });
         }
       };
@@ -73299,7 +73934,7 @@ function spawnAgentWithStream(command, args, opts, stdinData, onStdoutLine, onCo
       }, SIGKILL_GRACE_MS);
     }, timeoutMs);
   }
-  const completion = new Promise((resolve3) => {
+  const completion = new Promise((resolve4) => {
     let exitCode = null;
     let exitSignal = null;
     let exited = false;
@@ -73319,7 +73954,7 @@ function spawnAgentWithStream(command, args, opts, stdinData, onStdoutLine, onCo
       const tail = stdinError ? `${stdinError}
 ${ring.toString()}` : ring.toString();
       const baseResult = { exitCode, signal: exitSignal, tailOutput: tail, killed };
-      resolve3(onCompletion ? onCompletion(baseResult) : baseResult);
+      resolve4(onCompletion ? onCompletion(baseResult) : baseResult);
     }
     child.on("exit", (code, signal) => {
       exited = true;
@@ -73346,7 +73981,7 @@ ${ring.toString()}` : ring.toString();
       closeStream();
       const tail = stdinError ? `${stdinError}
 ` : "";
-      resolve3({
+      resolve4({
         exitCode: null,
         signal: null,
         tailOutput: `${tail}spawn error: ${err.message}
@@ -74249,8 +74884,8 @@ function buildIdleReasons(available, dispatchedNames, config2, excludeAgents) {
   const excluded = excludeAgents ?? /* @__PURE__ */ new Set();
   for (const adapter of available) {
     if (dispatchedNames.has(adapter.name)) continue;
-    const isExcluded2 = excluded.has(adapter.name);
-    if (isExcluded2) {
+    const isExcluded = excluded.has(adapter.name);
+    if (isExcluded) {
       result.push({ name: adapter.name, reason: "excluded due to prior failure" });
     } else {
       const inAnyPref = Object.values(DEFAULT_ROLE_PREFERENCES).some((prefs) => prefs.includes(adapter.name));
@@ -74349,8 +74984,8 @@ var init_pipeline_trace = __esm({
 
 // src/orchestrate/worktree.ts
 import { execSync as execSync7 } from "child_process";
-import { existsSync as existsSync22, rmSync as rmSync2 } from "fs";
-import { join as join30, basename as basename3 } from "path";
+import { existsSync as existsSync23, rmSync as rmSync2 } from "fs";
+import { join as join30, basename as basename4 } from "path";
 function createWorktree(projectDir2, taskId, pipelineId) {
   const shortId2 = taskId.slice(0, 8);
   const shortPipeline = pipelineId.slice(0, 8);
@@ -74410,7 +75045,7 @@ function removeWorktree(projectDir2, worktreePath, branch) {
       timeout: 1e4
     });
   } catch {
-    if (existsSync22(worktreePath)) {
+    if (existsSync23(worktreePath)) {
       try {
         rmSync2(worktreePath, { recursive: true, force: true });
       } catch {
@@ -74458,7 +75093,7 @@ function listWorktrees(projectDir2) {
   }
 }
 function extractTaskIdFromPath(worktreePath) {
-  const name = basename3(worktreePath);
+  const name = basename4(worktreePath);
   const match = name.match(/^task-([a-f0-9]+)$/);
   return match ? match[1] : null;
 }
@@ -74488,7 +75123,7 @@ var init_worktree = __esm({
 import { spawn as spawn2, execSync as execSync8 } from "child_process";
 function runGate(gate, command, cwd, timeoutMs, outputBudget = DEFAULT_OUTPUT_BUDGET) {
   const start = Date.now();
-  return new Promise((resolve3) => {
+  return new Promise((resolve4) => {
     const chunks = [];
     let totalBytes = 0;
     const proc = spawn2(command, {
@@ -74531,7 +75166,7 @@ function runGate(gate, command, cwd, timeoutMs, outputBudget = DEFAULT_OUTPUT_BU
       const output = Buffer.concat(chunks).toString("utf-8");
       const durationMs = Date.now() - start;
       if (killed) {
-        resolve3({
+        resolve4({
           gate,
           passed: false,
           output: output + `
@@ -74541,7 +75176,7 @@ function runGate(gate, command, cwd, timeoutMs, outputBudget = DEFAULT_OUTPUT_BU
         });
         return;
       }
-      resolve3({
+      resolve4({
         gate,
         passed: code === 0,
         output,
@@ -74551,7 +75186,7 @@ function runGate(gate, command, cwd, timeoutMs, outputBudget = DEFAULT_OUTPUT_BU
     });
     proc.on("error", (err) => {
       clearTimeout(timer);
-      resolve3({
+      resolve4({
         gate,
         passed: false,
         output: `[ERROR] Failed to spawn gate command: ${err.message}`,
@@ -75181,7 +75816,7 @@ function hashErrorPattern(errorOutput) {
   return createHash8("sha256").update(sanitized).digest("hex").slice(0, 12);
 }
 function sleep2(ms) {
-  return new Promise((resolve3) => setTimeout(() => resolve3([]), ms));
+  return new Promise((resolve4) => setTimeout(() => resolve4([]), ms));
 }
 var DEFAULT_BRIDGE_CONFIG, _storeObservation, _searchObservations;
 var init_memorix_bridge = __esm({
@@ -76142,7 +76777,7 @@ ${formatCostSummary(costSummary)}`);
   }
 }
 function sleep3(ms) {
-  return new Promise((resolve3) => setTimeout(resolve3, ms));
+  return new Promise((resolve4) => setTimeout(resolve4, ms));
 }
 function isGitRepository(projectDir2) {
   try {
@@ -80312,10 +80947,10 @@ function WorkbenchApp({ version: version2, onExitForInteractive }) {
           }
           try {
             const { resolveHooksDir: resolveHooksDir2 } = await Promise.resolve().then(() => (init_hooks_path(), hooks_path_exports));
-            const { existsSync: existsSync25, readFileSync: readFileSync22, writeFileSync: writeFileSync11, unlinkSync: unlinkSync4 } = await import("fs");
+            const { existsSync: existsSync26, readFileSync: readFileSync22, writeFileSync: writeFileSync11, unlinkSync: unlinkSync4 } = await import("fs");
             const resolved = resolveHooksDir2(proj.rootPath);
             const hookMarker = "# [memorix-git-hook]";
-            if (!resolved || !existsSync25(resolved.hookPath)) {
+            if (!resolved || !existsSync26(resolved.hookPath)) {
               setActionStatus("No post-commit hook found.");
               return;
             }
@@ -80470,7 +81105,7 @@ function WorkbenchApp({ version: version2, onExitForInteractive }) {
           break;
         }
         case "3": {
-          const { existsSync: existsSync25, readFileSync: readFileSync22, writeFileSync: writeFileSync11, chmodSync: chmodSync2 } = await import("fs");
+          const { existsSync: existsSync26, readFileSync: readFileSync22, writeFileSync: writeFileSync11, chmodSync: chmodSync2 } = await import("fs");
           const { ensureHooksDir: ensureHooksDir2 } = await Promise.resolve().then(() => (init_hooks_path(), hooks_path_exports));
           const hookMarker = "# [memorix-git-hook]";
           const resolved = ensureHooksDir2(cwd);
@@ -80484,7 +81119,7 @@ if command -v memorix >/dev/null 2>&1; then
   memorix ingest commit --auto >/dev/null 2>&1 &
 fi
 `;
-          if (existsSync25(resolved.hookPath)) {
+          if (existsSync26(resolved.hookPath)) {
             if (readFileSync22(resolved.hookPath, "utf-8").includes(hookMarker)) {
               setActionStatus("Post-commit hook already installed.");
               break;
@@ -80504,11 +81139,11 @@ ${hookScript}`, "utf-8");
           break;
         }
         case "4": {
-          const { existsSync: existsSync25, readFileSync: readFileSync22, writeFileSync: writeFileSync11, unlinkSync: unlinkSync4 } = await import("fs");
+          const { existsSync: existsSync26, readFileSync: readFileSync22, writeFileSync: writeFileSync11, unlinkSync: unlinkSync4 } = await import("fs");
           const { resolveHooksDir: resolveHooksDir2 } = await Promise.resolve().then(() => (init_hooks_path(), hooks_path_exports));
           const hookMarker = "# [memorix-git-hook]";
           const resolved = resolveHooksDir2(cwd);
-          if (!resolved || !existsSync25(resolved.hookPath)) {
+          if (!resolved || !existsSync26(resolved.hookPath)) {
             setActionStatus("No post-commit hook found.");
             break;
           }
@@ -81268,14 +81903,14 @@ var main = defineCommand({
       async run({ args }) {
         let q3 = args.question || "";
         if (!q3 && !process.stdin.isTTY) {
-          q3 = await new Promise((resolve3) => {
+          q3 = await new Promise((resolve4) => {
             let data = "";
             process.stdin.setEncoding("utf-8");
             process.stdin.on("data", (chunk) => {
               data += chunk;
             });
-            process.stdin.on("end", () => resolve3(data.trim()));
-            process.stdin.on("error", () => resolve3(""));
+            process.stdin.on("end", () => resolve4(data.trim()));
+            process.stdin.on("error", () => resolve4(""));
           });
         }
         if (!q3) {
@@ -81356,6 +81991,7 @@ var main = defineCommand({
       }
     })),
     doctor: () => Promise.resolve().then(() => (init_doctor(), doctor_exports)).then((m4) => m4.default),
+    repair: () => Promise.resolve().then(() => (init_repair(), repair_exports)).then((m4) => m4.default),
     dashboard: () => Promise.resolve().then(() => (init_dashboard(), dashboard_exports)).then((m4) => m4.default),
     cleanup: () => Promise.resolve().then(() => (init_cleanup(), cleanup_exports)).then((m4) => m4.default),
     uninstall: () => Promise.resolve().then(() => (init_uninstall(), uninstall_exports)).then((m4) => m4.default),
@@ -81416,6 +82052,7 @@ var main = defineCommand({
       "bg",
       "bs",
       "doctor",
+      "repair",
       "dashboard",
       "cleanup",
       "uninstall",
@@ -81468,6 +82105,7 @@ var main = defineCommand({
       console.error("  serve      Start MCP server on stdio");
       console.error("  init       Create global defaults or project config");
       console.error("  setup      Install Memorix plugin/MCP/rules/hooks for an agent");
+      console.error("  repair     Repair Memorix-owned agent integration files");
       console.error("  config     Show TOML config paths and resolved values");
       console.error("  integrate  Install one IDE integration into the current repo");
       console.error("  status     Show project info + stats");