@cleocode/cleo 2026.5.50 → 2026.5.53

package/dist/cli/index.js

@@ -30320,7 +30320,7 @@ function capitalizeFirst(str3) {
   if (str3.length === 0) return str3;
   return str3.charAt(0).toUpperCase() + str3.slice(1);
 }
-var registerCommand, signinCommand, startCommand, stopCommand, statusCommand, assignCommand, wakeCommand, spawnCommand, reassignCommand, stopAllCommand, workCommand, listCommand3, getCommand, attachCommand, detachCommand, removeCommand, rotateKeyCommand, claimCodeCommand, watchCommand, pollCommand, sendCommand, healthCommand3, installCommand, packCommand, createCommand, mintCommand, doctorCommand, agentCommand;
+var registerCommand, signinCommand, startCommand, stopCommand, statusCommand, assignCommand, wakeCommand, spawnCommand, reassignCommand, stopAllCommand, workCommand, listCommand3, getCommand, attachCommand, detachCommand, removeCommand, rotateKeyCommand, claimCodeCommand, watchCommand, pollCommand, sendCommand, healthCommand3, installCommand, packCommand, createCommand, mintCommand, pruneOrphansCommand, doctorCommand, agentCommand;
 var init_agent = __esm({
   "packages/cleo/src/cli/commands/agent.ts"() {
     "use strict";
@@ -32646,6 +32646,67 @@ Task ${args.taskId} reassigned to you by ${active.agentId}. Run: cleo show ${arg
         }
       }
     });
+    pruneOrphansCommand = defineCommand({
+      meta: {
+        name: "prune-orphans",
+        description: "Delete orphan registry rows whose .cant path no longer exists (cross-project safe)"
+      },
+      args: {
+        json: { type: "boolean", description: "Emit raw JSON" },
+        "dry-run": { type: "boolean", description: "Report without making changes" }
+      },
+      async run({ args }) {
+        try {
+          const {
+            buildDoctorReport,
+            reconcileDoctor,
+            ensureGlobalSignaldockDb: ensureGlobalSignaldockDb2,
+            getGlobalSignaldockDbPath: getGlobalSignaldockDbPath2
+          } = await import("@cleocode/core/internal");
+          const { createRequire: createRequire2 } = await import("node:module");
+          const { DatabaseSync: DatabaseSync2 } = createRequire2(import.meta.url)(
+            "node:sqlite"
+          );
+          await ensureGlobalSignaldockDb2();
+          const db = new DatabaseSync2(getGlobalSignaldockDbPath2());
+          db.exec("PRAGMA foreign_keys = ON");
+          try {
+            const report = await buildDoctorReport(db, {});
+            const d002 = report.findings.filter((f) => f.code === "D-002");
+            const dryRun = args["dry-run"] === true;
+            let repaired = [], skipped = [];
+            if (!dryRun && d002.length > 0) {
+              const r = await reconcileDoctor(db, d002, {});
+              repaired = r.repaired;
+              skipped = r.skipped;
+            }
+            const msg = d002.length === 0 ? "No orphan rows found." : `Found ${d002.length} orphan(s)${dryRun ? " (dry-run)" : ": pruned=" + repaired.length}`;
+            cliOutput(
+              {
+                success: true,
+                data: {
+                  message: msg,
+                  found: d002.length,
+                  repaired: dryRun ? 0 : repaired.length,
+                  skipped: dryRun ? 0 : skipped.length,
+                  dryRun
+                }
+              },
+              { command: "agent prune-orphans" }
+            );
+            if (!dryRun && skipped.length > 0) process.exitCode = 1;
+          } finally {
+            db.close();
+          }
+        } catch (err) {
+          cliOutput(
+            { success: false, error: { code: "E_PRUNE_ORPHANS", message: String(err) } },
+            { command: "agent prune-orphans" }
+          );
+          process.exitCode = 1;
+        }
+      }
+    });
     doctorCommand = defineCommand({
       meta: {
         name: "doctor",
@@ -32758,6 +32819,7 @@ Task ${args.taskId} reassigned to you by ${active.agentId}. Run: cleo show ${arg
       meta: { name: "agent", description: "Agent lifecycle, credentials, and messaging" },
       subCommands: {
         doctor: doctorCommand,
+        "prune-orphans": pruneOrphansCommand,
         register: registerCommand,
         signin: signinCommand,
         start: startCommand,
@@ -56545,55 +56607,57 @@ async function runStartupMaintenance() {
   const {
     detectAndRemoveLegacyGlobalFiles,
     detectAndRemoveStrayProjectNexus,
-    ensureConduitDb,
-    ensureGlobalSignaldockDb: ensureGlobalSignaldockDb2,
     getGlobalSalt,
     getLogger: getLogger17,
     getProjectRoot: getProjectRoot33,
+    isCleanupMarkerSet,
     migrateSignaldockToConduit,
     needsSignaldockToConduitMigration,
+    setCleanupMarker,
     validateGlobalSalt
   } = await import("@cleocode/core/internal");
+  let projectRootForCleanup = "";
   try {
-    detectAndRemoveLegacyGlobalFiles();
+    projectRootForCleanup = getProjectRoot33();
   } catch {
   }
-  try {
-    detectAndRemoveStrayProjectNexus(getProjectRoot33());
-  } catch {
+  if (!isCleanupMarkerSet(CLI_VERSION, projectRootForCleanup)) {
+    try {
+      detectAndRemoveLegacyGlobalFiles();
+    } catch {
+    }
+    try {
+      if (projectRootForCleanup) {
+        detectAndRemoveStrayProjectNexus(projectRootForCleanup);
+      }
+    } catch {
+    }
+    setCleanupMarker(CLI_VERSION, projectRootForCleanup);
   }
   const _startupLog = getLogger17("cli-startup");
-  try {
-    const _projectRootForMigration = getProjectRoot33();
-    if (needsSignaldockToConduitMigration(_projectRootForMigration)) {
-      const migrationResult = migrateSignaldockToConduit(_projectRootForMigration);
-      if (migrationResult.status === "failed") {
-        _startupLog.error(
-          { errors: migrationResult.errors, projectRoot: _projectRootForMigration },
-          "T310 migration: signaldock \u2192 conduit failed \u2014 CLI continues, run `cleo doctor` to diagnose"
+  const isInitInvocation = process.argv.slice(2).some((a) => a === "init");
+  if (!isInitInvocation) {
+    try {
+      const _projectRootForMigration = getProjectRoot33();
+      if (needsSignaldockToConduitMigration(_projectRootForMigration)) {
+        const migrationResult = migrateSignaldockToConduit(_projectRootForMigration);
+        if (migrationResult.status === "failed") {
+          _startupLog.error(
+            { errors: migrationResult.errors, projectRoot: _projectRootForMigration },
+            "T310 migration: signaldock \u2192 conduit failed \u2014 CLI continues, run `cleo doctor` to diagnose"
+          );
+        }
+      }
+    } catch (err) {
+      const msg = err instanceof Error ? err.message : String(err);
+      if (msg.includes("E_NO_PROJECT") || msg.startsWith("Run cleo init")) {
+      } else {
+        _startupLog.warn(
+          { error: msg },
+          "T310 migration startup check threw unexpectedly \u2014 CLI continues"
         );
       }
     }
-  } catch (err) {
-    if (err instanceof Error && err.message.includes("E_NO_PROJECT")) {
-    } else {
-      _startupLog.warn(
-        { error: err instanceof Error ? err.message : String(err) },
-        "T310 migration startup check threw unexpectedly \u2014 CLI continues"
-      );
-    }
-  }
-  try {
-    ensureConduitDb(getProjectRoot33());
-  } catch {
-  }
-  try {
-    await ensureGlobalSignaldockDb2();
-  } catch (err) {
-    _startupLog.warn(
-      { error: err instanceof Error ? err.message : String(err) },
-      "T310 startup: ensureGlobalSignaldockDb failed \u2014 CLI continues"
-    );
   }
   try {
     validateGlobalSalt();