@cleocode/cleo 2026.3.46 → 2026.3.48

package/dist/mcp/index.js

@@ -34691,7 +34691,7 @@ function checkInjection2(projectRoot) {
       status: "warning",
       message: "AGENTS.md not found in project root",
       details: { path: agentsMdPath, exists: false },
-      fix: "cleo init --update-docs"
+      fix: "cleo upgrade"
     };
   }
   let content;
@@ -34716,7 +34716,7 @@ function checkInjection2(projectRoot) {
       status: "warning",
       message: "AGENTS.md exists but has no CAAMP markers",
       details: { path: agentsMdPath, hasCaampMarker: false },
-      fix: "cleo init --update-docs"
+      fix: "cleo upgrade"
     };
   }
   if (startCount !== endCount) {
@@ -34726,7 +34726,7 @@ function checkInjection2(projectRoot) {
       status: "warning",
       message: `CAAMP markers unbalanced: ${startCount} START vs ${endCount} END`,
       details: { path: agentsMdPath, startCount, endCount },
-      fix: "cleo init --update-docs"
+      fix: "cleo upgrade"
     };
   }
   const caampMatch = content.match(/<!-- CAAMP:START -->([\s\S]*?)<!-- CAAMP:END -->/);
@@ -34748,7 +34748,7 @@ function checkInjection2(projectRoot) {
         status: "warning",
         message: `Missing @ reference targets: ${missing.join(", ")}`,
         details: { path: agentsMdPath, missing, totalRefs: refs.length },
-        fix: "cleo init --update-docs"
+        fix: "cleo upgrade"
       };
     }
   }
@@ -34765,7 +34765,7 @@ function checkInjection2(projectRoot) {
           status: "warning",
           message: `CLAUDE.md CAAMP markers unbalanced: ${cStartCount} START vs ${cEndCount} END`,
           details: { file: "CLAUDE.md", startCount: cStartCount, endCount: cEndCount },
-          fix: "cleo init --update-docs"
+          fix: "cleo upgrade"
         };
       }
       if (cStartCount === 0) {
@@ -34775,7 +34775,7 @@ function checkInjection2(projectRoot) {
           status: "warning",
           message: "CLAUDE.md has no CAAMP markers",
           details: { file: "CLAUDE.md", hasCaampMarker: false },
-          fix: "cleo init --update-docs"
+          fix: "cleo upgrade"
         };
       }
     } catch {
@@ -34804,6 +34804,7 @@ __export(scaffold_exports, {
   CLEO_GITIGNORE_FALLBACK: () => CLEO_GITIGNORE_FALLBACK,
   REQUIRED_CLEO_SUBDIRS: () => REQUIRED_CLEO_SUBDIRS,
   REQUIRED_GLOBAL_SUBDIRS: () => REQUIRED_GLOBAL_SUBDIRS,
+  STALE_GLOBAL_ENTRIES: () => STALE_GLOBAL_ENTRIES,
   checkBrainDb: () => checkBrainDb,
   checkCleoGitRepo: () => checkCleoGitRepo,
   checkCleoStructure: () => checkCleoStructure,
@@ -34840,7 +34841,7 @@ __export(scaffold_exports, {
 import { execFile as execFile3 } from "node:child_process";
 import { randomUUID } from "node:crypto";
 import { existsSync as existsSync34, constants as fsConstants3, readFileSync as readFileSync22, statSync as statSync8 } from "node:fs";
-import { access as access3, mkdir as mkdir5, readFile as readFile6, writeFile as writeFile5 } from "node:fs/promises";
+import { access as access3, mkdir as mkdir5, readFile as readFile6, rm as rm2, writeFile as writeFile5 } from "node:fs/promises";
 import { dirname as dirname8, join as join37, resolve as resolve5 } from "node:path";
 import { fileURLToPath as fileURLToPath4 } from "node:url";
 import { promisify as promisify3 } from "node:util";
@@ -34855,7 +34856,7 @@ async function fileExists(path2) {
 async function stripCLEOBlocks(filePath) {
   if (!existsSync34(filePath)) return;
   const content = await readFile6(filePath, "utf8");
-  const stripped = content.replace(/\n?<!-- CLEO:START -->[\s\S]*?<!-- CLEO:END -->\n?/g, "");
+  const stripped = content.replace(/\n?<!-- CLEO:START[^>]*-->[\s\S]*?<!-- CLEO:END -->\n?/g, "");
   if (stripped !== content) await writeFile5(filePath, stripped, "utf8");
 }
 async function removeCleoFromRootGitignore(projectRoot) {
@@ -35538,6 +35539,19 @@ async function ensureGlobalHome() {
   for (const subdir of REQUIRED_GLOBAL_SUBDIRS) {
     await mkdir5(join37(cleoHome, subdir), { recursive: true });
   }
+  for (const stale of STALE_GLOBAL_ENTRIES) {
+    const stalePath = join37(cleoHome, stale);
+    if (existsSync34(stalePath)) {
+      try {
+        await rm2(stalePath, { recursive: true, force: true });
+        console.warn(`[CLEO] Removed stale global entry: ${stalePath}`);
+      } catch (err) {
+        console.warn(
+          `[CLEO] Could not remove stale global entry ${stalePath}: ${err instanceof Error ? err.message : String(err)}`
+        );
+      }
+    }
+  }
   return {
     action: alreadyExists ? "skipped" : "created",
     path: cleoHome,
@@ -35652,7 +35666,7 @@ function checkLogDir(projectRoot) {
     fix: null
   };
 }
-var execFileAsync3, REQUIRED_CLEO_SUBDIRS, CLEO_GITIGNORE_FALLBACK, REQUIRED_GLOBAL_SUBDIRS;
+var execFileAsync3, REQUIRED_CLEO_SUBDIRS, CLEO_GITIGNORE_FALLBACK, REQUIRED_GLOBAL_SUBDIRS, STALE_GLOBAL_ENTRIES;
 var init_scaffold = __esm({
   "packages/core/src/scaffold.ts"() {
     "use strict";
@@ -35710,6 +35724,20 @@ metrics/
 backups/
 `;
     REQUIRED_GLOBAL_SUBDIRS = ["logs", "templates"];
+    STALE_GLOBAL_ENTRIES = [
+      "adrs",
+      "rcasd",
+      "agent-outputs",
+      "backups",
+      "sandbox",
+      "tasks.db",
+      "tasks.db-shm",
+      "tasks.db-wal",
+      "brain-worker.pid",
+      "VERSION",
+      "schemas",
+      "bin"
+    ];
   }
 });
 
@@ -39445,8 +39473,8 @@ function parseTokenMetrics(inputFile, cwd) {
     const raw = JSON.parse(readFileSync28(file2, "utf-8"));
     if (raw.resourceMetrics) {
       const points = [];
-      for (const rm2 of raw.resourceMetrics ?? []) {
-        for (const sm of rm2.scopeMetrics ?? []) {
+      for (const rm3 of raw.resourceMetrics ?? []) {
+        for (const sm of rm3.scopeMetrics ?? []) {
           for (const metric of sm.metrics ?? []) {
             if (metric.name !== "claude_code.token.usage") continue;
             for (const dp of metric.sum?.dataPoints ?? []) {
@@ -57649,7 +57677,7 @@ function checkAgentsMdHub(projectRoot) {
       status: "warning",
       message: "AGENTS.md not found in project root",
       details: { path: agentsMdPath, exists: false },
-      fix: "cleo init --update-docs"
+      fix: "cleo upgrade"
     };
   }
   let content;
@@ -57672,7 +57700,7 @@ function checkAgentsMdHub(projectRoot) {
       status: "warning",
       message: "AGENTS.md exists but has no CAAMP:START marker",
       details: { path: agentsMdPath, hasCaampMarker: false },
-      fix: "cleo init --update-docs"
+      fix: "cleo upgrade"
     };
   }
   return {
@@ -58011,7 +58039,7 @@ function checkCaampMarkerIntegrity(projectRoot) {
       status: "warning",
       message: `CAAMP marker issues: ${issues.join("; ")}`,
       details: { issues },
-      fix: "cleo init --update-docs"
+      fix: "cleo upgrade"
     };
   }
   return {
@@ -58077,7 +58105,7 @@ function checkAtReferenceTargetExists(projectRoot) {
       status: "warning",
       message: `Missing @ reference targets: ${missing.join(", ")}`,
       details: { missing, totalRefs: refs.length },
-      fix: "cleo init --update-docs"
+      fix: "cleo upgrade"
     };
   }
   return {
@@ -64483,9 +64511,6 @@ async function updateDocs() {
   };
 }
 async function initProject(opts = {}) {
-  if (opts.updateDocs) {
-    return updateDocs();
-  }
   const cleoDir = getCleoDirAbsolute();
   const projRoot = getProjectRoot();
   const alreadyInitialized = existsSync100(cleoDir) && (existsSync100(join100(cleoDir, "tasks.db")) || existsSync100(join100(cleoDir, "config.json")));
@@ -64852,7 +64877,13 @@ var init_output = __esm({
 });
 
 // packages/core/src/project-info.ts
-import { existsSync as existsSync102, readFileSync as readFileSync75 } from "node:fs";
+var project_info_exports = {};
+__export(project_info_exports, {
+  getProjectInfo: () => getProjectInfo,
+  getProjectInfoSync: () => getProjectInfoSync,
+  updateProjectName: () => updateProjectName
+});
+import { existsSync as existsSync102, readFileSync as readFileSync75, writeFileSync as writeFileSync19 } from "node:fs";
 import { readFile as readFile18 } from "node:fs/promises";
 import { join as join102 } from "node:path";
 async function getProjectInfo(cwd) {
@@ -64896,6 +64927,16 @@ function getProjectInfoSync(cwd) {
     return null;
   }
 }
+function updateProjectName(cwd, name2) {
+  const cleoDir = getCleoDirAbsolute(cwd);
+  const infoPath = join102(cleoDir, "project-info.json");
+  if (!existsSync102(infoPath)) return;
+  const data = JSON.parse(readFileSync75(infoPath, "utf-8"));
+  data.projectName = name2;
+  data.lastUpdated = (/* @__PURE__ */ new Date()).toISOString();
+  writeFileSync19(infoPath, `${JSON.stringify(data, null, 2)}
+`);
+}
 var init_project_info = __esm({
   "packages/core/src/project-info.ts"() {
     "use strict";
@@ -65171,7 +65212,6 @@ var init_cleo = __esm({
 // packages/core/src/index.ts
 var init_src2 = __esm({
   "packages/core/src/index.ts"() {
-    "use strict";
     init_src();
     init_adapters();
     init_admin();
@@ -65273,6 +65313,7 @@ async function bootstrapGlobalCleo(options) {
   await injectAgentsHub(ctx);
   await installMcpToProviders(ctx);
   await installSkillsGlobally(ctx);
+  await installAgentDefinitionGlobally(ctx);
   await installProviderAdapters(ctx, options?.packageRoot);
   return ctx;
 }
@@ -65323,7 +65364,10 @@ async function injectAgentsHub(ctx) {
       await mkdir17(globalAgentsDir, { recursive: true });
       if (existsSync103(globalAgentsMd)) {
         const content = await readFile19(globalAgentsMd, "utf8");
-        const stripped = content.replace(/\n?<!-- CLEO:START -->[\s\S]*?<!-- CLEO:END -->\n?/g, "");
+        const stripped = content.replace(
+          /\n?<!-- CLEO:START[^>]*-->[\s\S]*?<!-- CLEO:END -->\n?/g,
+          ""
+        );
         if (stripped !== content) {
           await writeFile12(globalAgentsMd, stripped, "utf8");
         }
@@ -65347,7 +65391,7 @@ async function injectAgentsHub(ctx) {
           if (existsSync103(instructFilePath)) {
             const fileContent = await readFile19(instructFilePath, "utf8");
             const stripped = fileContent.replace(
-              /\n?<!-- CLEO:START -->[\s\S]*?<!-- CLEO:END -->\n?/g,
+              /\n?<!-- CLEO:START[^>]*-->[\s\S]*?<!-- CLEO:END -->\n?/g,
               ""
             );
             if (stripped !== fileContent) {
@@ -65416,6 +65460,20 @@ async function installSkillsGlobally(ctx) {
     );
   }
 }
+async function installAgentDefinitionGlobally(ctx) {
+  try {
+    if (!ctx.isDryRun) {
+      const { initAgentDefinition: initAgentDefinition2 } = await Promise.resolve().then(() => (init_init(), init_exports));
+      await initAgentDefinition2(ctx.created, ctx.warnings);
+    } else {
+      ctx.created.push("agent: cleo-subagent (would symlink)");
+    }
+  } catch (err) {
+    ctx.warnings.push(
+      `Agent definition install: ${err instanceof Error ? err.message : String(err)}`
+    );
+  }
+}
 async function installProviderAdapters(ctx, packageRootOverride) {
   try {
     const { AdapterManager: AdapterManager2 } = await Promise.resolve().then(() => (init_adapters(), adapters_exports));
@@ -72085,7 +72143,7 @@ import {
   mkdirSync as mkdirSync23,
   readdirSync as readdirSync36,
   readFileSync as readFileSync82,
-  writeFileSync as writeFileSync19
+  writeFileSync as writeFileSync20
 } from "node:fs";
 import { join as join108 } from "node:path";
 async function runUpgrade(options = {}) {
@@ -72231,7 +72289,7 @@ async function runUpgrade(options = {}) {
           if (totalImported === 0 && existsSync110(dbBackupPath)) {
             copyFileSync7(dbBackupPath, dbPath2);
             if (configBackup) {
-              writeFileSync19(configPath, configBackup);
+              writeFileSync20(configPath, configBackup);
             }
             actions.push({
               action: "storage_migration",
@@ -72252,7 +72310,7 @@ async function runUpgrade(options = {}) {
               config2.storage = {};
             }
             config2.storage.engine = "sqlite";
-            writeFileSync19(configPath, JSON.stringify(config2, null, 2));
+            writeFileSync20(configPath, JSON.stringify(config2, null, 2));
             actions.push({
               action: "storage_migration",
               status: "applied",
@@ -72274,7 +72332,7 @@ async function runUpgrade(options = {}) {
             copyFileSync7(dbBackupPath, dbPath2);
           }
           if (configBackup) {
-            writeFileSync19(configPath, configBackup);
+            writeFileSync20(configPath, configBackup);
           }
           await updateMigrationPhase2(cleoDir2, "failed");
           for (const error40 of result.errors) {
@@ -72527,7 +72585,9 @@ async function runUpgrade(options = {}) {
         }
       }
     } else {
-      const contextResult = await ensureProjectContext(projectRootForContext, { staleDays: 30 });
+      const contextResult = await ensureProjectContext(projectRootForContext, {
+        staleDays: options.forceDetect ? 0 : 30
+      });
       actions.push({
         action: "project_context_detection",
         status: contextResult.action === "skipped" ? "skipped" : "applied",
@@ -72725,6 +72785,35 @@ async function runUpgrade(options = {}) {
       }
     } catch {
     }
+    if (options.mapCodebase) {
+      try {
+        const { mapCodebase: mapCodebase3 } = await Promise.resolve().then(() => (init_codebase_map(), codebase_map_exports));
+        const mapResult = await mapCodebase3(projectRootForMaint, { storeToBrain: true });
+        actions.push({
+          action: "codebase_map",
+          status: "applied",
+          details: `Analyzed: ${mapResult.stack?.languages?.length ?? 0} languages, ${mapResult.concerns?.todos?.length ?? 0} TODOs found`
+        });
+      } catch (err) {
+        actions.push({
+          action: "codebase_map",
+          status: "error",
+          details: `Codebase mapping failed: ${err instanceof Error ? err.message : String(err)}`
+        });
+      }
+    }
+    if (options.projectName) {
+      try {
+        const { updateProjectName: updateProjectName2 } = await Promise.resolve().then(() => (init_project_info(), project_info_exports));
+        await updateProjectName2(projectRootForMaint, options.projectName);
+        actions.push({
+          action: "project_name_update",
+          status: "applied",
+          details: `Project name set to "${options.projectName}"`
+        });
+      } catch {
+      }
+    }
     try {
       const { existsSync: fsExistsSync } = await import("node:fs");
       const { join: pathJoin } = await import("node:path");