@cleocode/cleo 2026.3.47 → 2026.3.49

package/dist/cli/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 {
@@ -57677,7 +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;
@@ -57700,7 +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 {
@@ -58039,7 +58039,7 @@ function checkCaampMarkerIntegrity(projectRoot) {
       status: "warning",
       message: `CAAMP marker issues: ${issues.join("; ")}`,
       details: { issues },
-      fix: "cleo init --update-docs"
+      fix: "cleo upgrade"
     };
   }
   return {
@@ -58105,7 +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 {
@@ -64333,7 +64333,14 @@ async function initAgentDefinition(created, warnings) {
   try {
     try {
       const stat3 = await lstat(globalAgentsDir);
-      if (stat3.isSymbolicLink() || stat3.isDirectory()) {
+      if (stat3.isSymbolicLink()) {
+        const { readlink } = await import("node:fs/promises");
+        const currentTarget = await readlink(globalAgentsDir);
+        if (currentTarget === agentSourceDir) {
+          return;
+        }
+        await unlink4(globalAgentsDir);
+      } else if (stat3.isDirectory()) {
         return;
       }
     } catch {
@@ -64539,9 +64546,6 @@ 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")));
@@ -64908,7 +64912,13 @@ 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) {
@@ -64952,6 +64962,16 @@ 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, `${JSON.stringify(data, null, 2)}
+`);
+}
 var init_project_info = __esm({
   "packages/core/src/project-info.ts"() {
     "use strict";
@@ -65547,6 +65567,11 @@ async function bootstrapGlobalCleo(options) {
     warnings: [],
     isDryRun: options?.dryRun ?? false
   };
+  try {
+    const { ensureGlobalHome: ensureGlobalHome2 } = await Promise.resolve().then(() => (init_scaffold(), scaffold_exports));
+    await ensureGlobalHome2();
+  } catch {
+  }
   await ensureGlobalTemplatesBootstrap(ctx, options?.packageRoot);
   await injectAgentsHub(ctx);
   await installMcpToProviders(ctx);
@@ -65602,13 +65627,9 @@ async function injectAgentsHub(ctx) {
       await mkdir17(globalAgentsDir, { recursive: true });
       if (existsSync103(globalAgentsMd)) {
         const content = await readFile19(globalAgentsMd, "utf8");
-        const stripped = content.replace(
-          /\n?<!-- CLEO:START[^>]*-->[\s\S]*?<!-- CLEO:END -->\n?/g,
-          ""
-        );
-        if (stripped !== content) {
-          await writeFile12(globalAgentsMd, stripped, "utf8");
-        }
+        const stripped = content.replace(/\n?<!-- CLEO:START[^>]*-->[\s\S]*?<!-- CLEO:END -->\n?/g, "").replace(/\n?<!-- CAAMP:START -->[\s\S]*?<!-- CAAMP:END -->\n?/g, "").trim();
+        await writeFile12(globalAgentsMd, stripped ? `${stripped}
+` : "", "utf8");
       }
       const expectedContent = "@~/.cleo/templates/CLEO-INJECTION.md";
       const action = await inject2(globalAgentsMd, expectedContent);
@@ -72381,7 +72402,7 @@ 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 = {}) {
@@ -72527,7 +72548,7 @@ 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",
@@ -72548,7 +72569,7 @@ 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",
@@ -72570,7 +72591,7 @@ 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) {
@@ -72823,7 +72844,9 @@ 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",
@@ -73021,6 +73044,35 @@ 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");
@@ -91598,6 +91650,24 @@ function registerTreeCommand(program) {
   });
 }
 
+// packages/cleo/src/cli/commands/detect.ts
+init_internal();
+init_renderers();
+function registerDetectCommand(program) {
+  program.command("detect").description("Re-detect project type and update project-context.json").action(async () => {
+    const projectRoot = getProjectRoot();
+    const result = await ensureProjectContext(projectRoot, { staleDays: 0 });
+    cliOutput(
+      {
+        action: result.action,
+        path: result.path,
+        details: result.details
+      },
+      { command: "detect" }
+    );
+  });
+}
+
 // packages/cleo/src/cli/commands/detect-drift.ts
 init_src();
 init_renderers();
@@ -92402,7 +92472,7 @@ init_src();
 init_src2();
 init_renderers();
 import { execFileSync as execFileSync14 } from "node:child_process";
-import { existsSync as existsSync121, mkdirSync as mkdirSync25, readFileSync as readFileSync95, writeFileSync as writeFileSync20 } from "node:fs";
+import { existsSync as existsSync121, mkdirSync as mkdirSync25, readFileSync as readFileSync95, writeFileSync as writeFileSync21 } from "node:fs";
 import { dirname as dirname23, join as join115 } from "node:path";
 function getChangelogSource(cwd) {
   const configPath = getConfigPath(cwd);
@@ -92556,7 +92626,7 @@ function registerGenerateChangelogCommand(program) {
         if (!dryRun) {
           const fullPath = join115(getProjectRoot(), outputPath);
           mkdirSync25(dirname23(fullPath), { recursive: true });
-          writeFileSync20(fullPath, content, "utf-8");
+          writeFileSync21(fullPath, content, "utf-8");
         }
         results.push({ platform: targetPlatform, path: outputPath, written: !dryRun });
       } else {
@@ -92577,7 +92647,7 @@ function registerGenerateChangelogCommand(program) {
           if (!dryRun) {
             const fullPath = join115(getProjectRoot(), platformConfig.path);
             mkdirSync25(dirname23(fullPath), { recursive: true });
-            writeFileSync20(fullPath, content, "utf-8");
+            writeFileSync21(fullPath, content, "utf-8");
           }
           results.push({
             platform: platformConfig.platform,
@@ -92718,14 +92788,12 @@ function registerImportTasksCommand(program) {
 init_src2();
 init_renderers();
 function registerInitCommand(program) {
-  program.command("init").description("Initialize CLEO in a project directory").option("--name <name>", "Project name").option("--force", "Overwrite existing files").option("--detect", "Auto-detect project configuration").option("--refresh", "Force re-detection of project type (alias for --detect)").option("--update-docs", "Update agent documentation injections").option("--map-codebase", "Run codebase analysis and store findings to brain.db").argument("[projectName]", "Project name (alternative to --name)").action(async (projectName, opts) => {
+  program.command("init").description("Initialize CLEO in a project directory").option("--name <name>", "Project name").option("--force", "Overwrite existing files").option("--detect", "Auto-detect project configuration").option("--map-codebase", "Run codebase analysis and store findings to brain.db").argument("[projectName]", "Project name (alternative to --name)").action(async (projectName, opts) => {
     try {
-      if (opts["refresh"]) opts["detect"] = true;
       const initOpts = {
         name: opts["name"] || projectName || void 0,
         force: !!opts["force"],
         detect: !!opts["detect"],
-        updateDocs: !!opts["updateDocs"],
         mapCodebase: !!opts["mapCodebase"]
       };
       const result = await initProject(initOpts);
@@ -95640,7 +95708,9 @@ function registerUpdateCommand(program) {
 init_internal();
 init_renderers();
 function registerUpgradeCommand(program) {
-  program.command("upgrade").description("Unified project maintenance (storage migration, schema repair, structural fixes)").option("--status", "Show what needs updating without making changes").option("--dry-run", "Preview changes without applying").option("--include-global", "Also check global ~/.cleo data").option("--no-auto-migrate", "Skip automatic JSON\u2192SQLite migration").action(async (_opts, command) => {
+  program.command("upgrade").description(
+    "Unified project maintenance (storage migration, schema repair, structural fixes, doc refresh)"
+  ).option("--status", "Show what needs updating without making changes").option("--dry-run", "Preview changes without applying").option("--include-global", "Also check global ~/.cleo data").option("--no-auto-migrate", "Skip automatic JSON\u2192SQLite migration").option("--detect", "Force re-detection of project type (ignores staleness)").option("--map-codebase", "Run full codebase analysis and store findings to brain.db").option("--name <name>", "Update project name in project-info and nexus registry").action(async (_opts, command) => {
     const opts = command.optsWithGlobals ? command.optsWithGlobals() : command.opts();
     const isHuman = opts["human"] === true || !!process.stdout.isTTY && opts["json"] !== true;
     const progress = createUpgradeProgress(isHuman);
@@ -95648,6 +95718,9 @@ function registerUpgradeCommand(program) {
       const isDryRun = !!opts["dryRun"] || !!opts["status"];
       const includeGlobal = !!opts["includeGlobal"];
       const autoMigrate = opts["autoMigrate"] !== false;
+      const forceDetect = !!opts["detect"];
+      const mapCodebase3 = !!opts["mapCodebase"];
+      const projectName = opts["name"];
       progress.start();
       progress.step(0, "Analyzing current state");
       if (includeGlobal) {
@@ -95660,7 +95733,10 @@ function registerUpgradeCommand(program) {
       const result = await runUpgrade({
         dryRun: isDryRun,
         includeGlobal,
-        autoMigrate
+        autoMigrate,
+        forceDetect,
+        mapCodebase: mapCodebase3,
+        projectName
       });
       progress.step(4, "Verifying results");
       cliOutput(
@@ -96017,6 +96093,7 @@ registerStatsCommand(rootShim);
 registerUpgradeCommand(rootShim);
 registerValidateCommand(rootShim);
 registerVerifyCommand(rootShim);
+registerDetectCommand(rootShim);
 registerDetectDriftCommand(rootShim);
 registerOpsCommand(rootShim);
 registerSnapshotCommand(rootShim);