@cleocode/core 2026.4.52 → 2026.4.54

package/dist/index.js

@@ -11117,44 +11117,6 @@ var init_platform_paths = __esm({
 });
 
 // packages/core/src/paths.ts
-var paths_exports = {};
-__export(paths_exports, {
-  getAgentOutputsAbsolute: () => getAgentOutputsAbsolute,
-  getAgentOutputsDir: () => getAgentOutputsDir,
-  getAgentsHome: () => getAgentsHome,
-  getArchivePath: () => getArchivePath,
-  getBackupDir: () => getBackupDir,
-  getClaudeAgentsDir: () => getClaudeAgentsDir,
-  getClaudeMemDbPath: () => getClaudeMemDbPath,
-  getCleoCacheDir: () => getCleoCacheDir,
-  getCleoCantWorkflowsDir: () => getCleoCantWorkflowsDir,
-  getCleoConfigDir: () => getCleoConfigDir,
-  getCleoDir: () => getCleoDir,
-  getCleoDirAbsolute: () => getCleoDirAbsolute,
-  getCleoDocsDir: () => getCleoDocsDir,
-  getCleoGlobalAgentsDir: () => getCleoGlobalAgentsDir,
-  getCleoGlobalJustfilePath: () => getCleoGlobalJustfilePath,
-  getCleoGlobalRecipesDir: () => getCleoGlobalRecipesDir,
-  getCleoHome: () => getCleoHome,
-  getCleoLogDir: () => getCleoLogDir,
-  getCleoPiExtensionsDir: () => getCleoPiExtensionsDir,
-  getCleoSchemasDir: () => getCleoSchemasDir,
-  getCleoTempDir: () => getCleoTempDir,
-  getCleoTemplatesDir: () => getCleoTemplatesDir,
-  getCleoTemplatesTildePath: () => getCleoTemplatesTildePath,
-  getConfigPath: () => getConfigPath,
-  getGlobalConfigPath: () => getGlobalConfigPath,
-  getLogPath: () => getLogPath,
-  getManifestArchivePath: () => getManifestArchivePath,
-  getManifestPath: () => getManifestPath,
-  getProjectRoot: () => getProjectRoot,
-  getSessionsPath: () => getSessionsPath,
-  getTaskPath: () => getTaskPath,
-  isAbsolutePath: () => isAbsolutePath,
-  isProjectInitialized: () => isProjectInitialized,
-  resolveProjectPath: () => resolveProjectPath,
-  worktreeScope: () => worktreeScope
-});
 import { AsyncLocalStorage } from "node:async_hooks";
 import { existsSync as existsSync3, readFileSync as readFileSync2 } from "node:fs";
 import { homedir } from "node:os";
@@ -11173,9 +11135,6 @@ function getCleoTemplatesDir() {
 function getCleoSchemasDir() {
   return join4(getCleoHome(), "schemas");
 }
-function getCleoDocsDir() {
-  return join4(getCleoHome(), "docs");
-}
 function getCleoDir(cwd) {
   if (cwd) {
     return getCleoDirAbsolute(cwd);
@@ -11247,15 +11206,6 @@ function getTaskPath(cwd) {
 function getConfigPath(cwd) {
   return join4(getCleoDirAbsolute(cwd), "config.json");
 }
-function getSessionsPath(cwd) {
-  return join4(getCleoDirAbsolute(cwd), "sessions.json");
-}
-function getArchivePath(cwd) {
-  return join4(getCleoDirAbsolute(cwd), "tasks-archive.json");
-}
-function getLogPath(cwd) {
-  return join4(getCleoDirAbsolute(cwd), "logs", "cleo.log");
-}
 function getBackupDir(cwd) {
   return join4(getCleoDirAbsolute(cwd), "backups", "operational");
 }
@@ -11363,9 +11313,6 @@ function getClaudeAgentsDir() {
   const claudeDir = process.env["CLAUDE_HOME"] ?? join4(homedir(), ".claude");
   return join4(claudeDir, "agents");
 }
-function getClaudeMemDbPath() {
-  return process.env["CLAUDE_MEM_DB"] ?? join4(homedir(), ".claude-mem", "claude-mem.db");
-}
 var worktreeScope, DEFAULT_AGENT_OUTPUTS_DIR;
 var init_paths = __esm({
   "packages/core/src/paths.ts"() {
@@ -11459,6 +11406,54 @@ function insertJournalEntry(nativeDb, hash2, createdAt, name2) {
     `INSERT OR IGNORE INTO "__drizzle_migrations" ("hash", "created_at", "name") VALUES ('${hash2}', ${createdAt}, '${name2}')`
   );
 }
+function probeAndMarkApplied(nativeDb, migration, logSubsystem) {
+  const sqlStatements = Array.isArray(migration.sql) ? migration.sql : [migration.sql ?? ""];
+  const fullSql = sqlStatements.join("\n");
+  const alterColumnRegex = /ALTER\s+TABLE\s+[`"]?(\w+)[`"]?\s+ADD\s+COLUMN\s+[`"]?(\w+)[`"]?/gi;
+  const createTableRegex = /CREATE\s+TABLE\s+(?:IF\s+NOT\s+EXISTS\s+)?[`"]?(\w+)[`"]?/gi;
+  const createIndexRegex = /CREATE\s+(?:UNIQUE\s+)?INDEX\s+(?:IF\s+NOT\s+EXISTS\s+)?[`"]?(\w+)[`"]?/gi;
+  const alterTargets = [];
+  for (const m of fullSql.matchAll(alterColumnRegex)) {
+    alterTargets.push({ table: m[1], column: m[2] });
+  }
+  const tableTargets = [];
+  for (const m of fullSql.matchAll(createTableRegex)) {
+    tableTargets.push(m[1]);
+  }
+  const indexTargets = [];
+  for (const m of fullSql.matchAll(createIndexRegex)) {
+    indexTargets.push(m[1]);
+  }
+  const totalTargets = alterTargets.length + tableTargets.length + indexTargets.length;
+  if (totalTargets === 0) {
+    return false;
+  }
+  const allAltersPresent = alterTargets.every(({ table, column }) => {
+    if (!tableExists(nativeDb, table)) return false;
+    const cols = nativeDb.prepare(`PRAGMA table_info(${table})`).all();
+    return cols.some((c) => c.name === column);
+  });
+  const allTablesPresent = tableTargets.every((t) => tableExists(nativeDb, t));
+  const allIndexesPresent = indexTargets.every((idx) => {
+    const rows = nativeDb.prepare(`SELECT name FROM sqlite_master WHERE type='index' AND name=?`).all(idx);
+    return rows.length > 0;
+  });
+  if (allAltersPresent && allTablesPresent && allIndexesPresent) {
+    insertJournalEntry(nativeDb, migration.hash, migration.folderMillis, migration.name ?? "");
+    const log11 = getLogger(logSubsystem);
+    log11.debug(
+      {
+        migration: migration.name,
+        alters: alterTargets.length,
+        tables: tableTargets.length,
+        indexes: indexTargets.length
+      },
+      `Migration ${migration.name} DDL already present in schema \u2014 marked applied.`
+    );
+    return true;
+  }
+  return false;
+}
 function reconcileJournal(nativeDb, migrationsFolder, existenceTable, logSubsystem) {
   if (tableExists(nativeDb, existenceTable) && !tableExists(nativeDb, "__drizzle_migrations")) {
     const migrations = readMigrationFiles({ migrationsFolder });
@@ -11495,11 +11490,11 @@ function reconcileJournal(nativeDb, migrationsFolder, existenceTable, logSubsyst
         const log11 = getLogger(logSubsystem);
         log11.warn(
           { orphaned: orphanedEntries.length },
-          `Detected stale migration journal entries from a previous CLEO version. Reconciling.`
+          `Detected stale migration journal entries from a previous CLEO version. Reconciling via DDL probe.`
         );
         nativeDb.exec('DELETE FROM "__drizzle_migrations"');
         for (const m of localMigrations) {
-          insertJournalEntry(nativeDb, m.hash, m.folderMillis, m.name ?? "");
+          probeAndMarkApplied(nativeDb, m, logSubsystem);
         }
       }
     }
@@ -14481,7 +14476,6 @@ function runBrainMigrations(nativeDb, db) {
       "brain"
     );
   }
-  ensureColumns(nativeDb, "brain_observations", [{ name: "agent", ddl: "text" }], "brain");
   if (tableExists(nativeDb, "brain_page_edges")) {
     nativeDb.prepare(
       `UPDATE brain_page_edges
@@ -49750,6 +49744,7 @@ __export(scaffold_exports, {
   checkConfig: () => checkConfig,
   checkGitignore: () => checkGitignore,
   checkGlobalHome: () => checkGlobalHome,
+  checkGlobalIdentity: () => checkGlobalIdentity,
   checkGlobalTemplates: () => checkGlobalTemplates,
   checkLogDir: () => checkLogDir,
   checkMemoryBridge: () => checkMemoryBridge,
@@ -49766,6 +49761,7 @@ __export(scaffold_exports, {
   ensureContributorMcp: () => ensureContributorMcp,
   ensureGitignore: () => ensureGitignore,
   ensureGlobalHome: () => ensureGlobalHome,
+  ensureGlobalIdentity: () => ensureGlobalIdentity,
   ensureGlobalScaffold: () => ensureGlobalScaffold,
   ensureGlobalTemplates: () => ensureGlobalTemplates,
   ensureProjectContext: () => ensureProjectContext,
@@ -49783,6 +49779,7 @@ import { execFile as execFile3 } from "node:child_process";
 import { randomUUID as randomUUID2 } from "node:crypto";
 import { existsSync as existsSync38, constants as fsConstants3, readFileSync as readFileSync23, statSync as statSync8 } from "node:fs";
 import { access as access3, copyFile as copyFile2, mkdir as mkdir6, readdir as readdir2, readFile as readFile7, rm as rm2, writeFile as writeFile6 } from "node:fs/promises";
+import { createRequire as createRequire6 } from "node:module";
 import { homedir as getHomedir } from "node:os";
 import { dirname as dirname10, join as join40, resolve as resolve5 } from "node:path";
 import { fileURLToPath as fileURLToPath4 } from "node:url";
@@ -50638,6 +50635,102 @@ async function ensureCleoOsHub() {
     details: `pi-extensions: ${piResult.copied} created/${piResult.kept} kept, global-recipes: ${recipesResult.copied} created/${recipesResult.kept} kept`
   };
 }
+function resolveIdentitySourcePath() {
+  const monorepoPath = join40(
+    process.cwd(),
+    "packages",
+    "cleo-os",
+    "starter-bundle",
+    "CLEOOS-IDENTITY.md"
+  );
+  if (existsSync38(monorepoPath)) return monorepoPath;
+  try {
+    const require2 = createRequire6(import.meta.url);
+    const pkgJson = require2.resolve("@cleocode/cleo-os/package.json");
+    const pkgDir = pkgJson.replace(/\/package\.json$/, "");
+    const installedPath = join40(pkgDir, "starter-bundle", "CLEOOS-IDENTITY.md");
+    if (existsSync38(installedPath)) return installedPath;
+  } catch {
+  }
+  return null;
+}
+async function ensureGlobalIdentity(forceRefresh = false) {
+  const sourcePath = resolveIdentitySourcePath();
+  if (!sourcePath) {
+    return {
+      action: "skipped",
+      path: "",
+      details: "CLEOOS-IDENTITY.md source not found in monorepo or installed package"
+    };
+  }
+  const cleoHome = getCleoHome();
+  const dst = join40(cleoHome, "CLEOOS-IDENTITY.md");
+  try {
+    await mkdir6(cleoHome, { recursive: true });
+  } catch (err) {
+    return {
+      action: "skipped",
+      path: dst,
+      details: `Failed to create global cleo home: ${err instanceof Error ? err.message : String(err)}`
+    };
+  }
+  if (existsSync38(dst) && !forceRefresh) {
+    return { action: "skipped", path: dst, details: "identity already present" };
+  }
+  const existedBefore = existsSync38(dst);
+  try {
+    const content = readFileSync23(sourcePath, "utf-8");
+    await writeFile6(dst, content);
+    return {
+      action: existedBefore ? "repaired" : "created",
+      path: dst,
+      details: `from ${sourcePath}`
+    };
+  } catch (err) {
+    return {
+      action: "skipped",
+      path: dst,
+      details: `Failed to write identity: ${err instanceof Error ? err.message : String(err)}`
+    };
+  }
+}
+function checkGlobalIdentity() {
+  const cleoHome = getCleoHome();
+  const identityPath = join40(cleoHome, "CLEOOS-IDENTITY.md");
+  if (!existsSync38(identityPath)) {
+    return {
+      id: "global_identity",
+      category: "global",
+      status: "failed",
+      message: "Global CLEOOS-IDENTITY.md not found \u2014 orchestrator persona missing",
+      details: { path: identityPath, exists: false },
+      fix: "cleo upgrade (auto-deploys identity)"
+    };
+  }
+  let size = 0;
+  try {
+    size = statSync8(identityPath).size;
+  } catch {
+  }
+  if (size === 0) {
+    return {
+      id: "global_identity",
+      category: "global",
+      status: "failed",
+      message: "Global CLEOOS-IDENTITY.md exists but is empty",
+      details: { path: identityPath, exists: true, size: 0 },
+      fix: "cleo upgrade --refresh-identity"
+    };
+  }
+  return {
+    id: "global_identity",
+    category: "global",
+    status: "passed",
+    message: "Global CLEOOS-IDENTITY.md present",
+    details: { path: identityPath, exists: true, size },
+    fix: ""
+  };
+}
 function checkGlobalHome() {
   const cleoHome = getCleoHome();
   if (!existsSync38(cleoHome)) {
@@ -54045,7 +54138,7 @@ __export(parser_exports, {
   parseFile: () => parseFile2
 });
 import { readFileSync as readFileSync64 } from "node:fs";
-import { createRequire as createRequire7 } from "node:module";
+import { createRequire as createRequire8 } from "node:module";
 import { relative as relative7 } from "node:path";
 function tryRequire(id) {
   try {
@@ -54246,7 +54339,7 @@ var init_parser3 = __esm({
   "packages/core/src/code/parser.ts"() {
     "use strict";
     init_tree_sitter_languages();
-    _require7 = createRequire7(import.meta.url);
+    _require7 = createRequire8(import.meta.url);
     _ParserClass = null;
     _QueryClass = null;
     _parserInstance = null;
@@ -54346,7 +54439,7 @@ var init_parser3 = __esm({
 
 // packages/core/src/system/dependencies.ts
 import { execFileSync as execFileSync10 } from "node:child_process";
-import { createRequire as createRequire8 } from "node:module";
+import { createRequire as createRequire9 } from "node:module";
 import { dirname as dirname19 } from "node:path";
 import { fileURLToPath as fileURLToPath5 } from "node:url";
 function tryExec(cmd, args, timeoutMs = 3e3) {
@@ -54616,7 +54709,7 @@ var init_dependencies = __esm({
   "packages/core/src/system/dependencies.ts"() {
     "use strict";
     init_platform();
-    _require8 = createRequire8(import.meta.url);
+    _require8 = createRequire9(import.meta.url);
     _dirname = dirname19(fileURLToPath5(import.meta.url));
     DEPENDENCY_SPECS = [
       // ── Required ────────────────────────────────────────────────────────────
@@ -54818,8 +54911,8 @@ import { platform as platform4 } from "node:os";
 import { basename as basename17, dirname as dirname23, join as join106 } from "node:path";
 async function resolveSeedAgentsDir() {
   try {
-    const { createRequire: createRequire10 } = await import("node:module");
-    const req = createRequire10(import.meta.url);
+    const { createRequire: createRequire11 } = await import("node:module");
+    const req = createRequire11(import.meta.url);
     const agentsPkgMain = req.resolve("@cleocode/agents/package.json");
     const agentsPkgRoot = dirname23(agentsPkgMain);
     const candidate = join106(agentsPkgRoot, "seed-agents");
@@ -54846,8 +54939,8 @@ async function resolveSeedAgentsDir() {
 async function initAgentDefinition(created, warnings) {
   let agentSourceDir = null;
   try {
-    const { createRequire: createRequire10 } = await import("node:module");
-    const req = createRequire10(import.meta.url);
+    const { createRequire: createRequire11 } = await import("node:module");
+    const req = createRequire11(import.meta.url);
     const agentsPkgMain = req.resolve("@cleocode/agents/package.json");
     const agentsPkgRoot = dirname23(agentsPkgMain);
     const candidate = join106(agentsPkgRoot, "cleo-subagent");
@@ -54913,8 +55006,8 @@ async function initCoreSkills(created, warnings) {
     const packageRoot = getPackageRoot();
     let ctSkillsRoot = null;
     try {
-      const { createRequire: createRequire10 } = await import("node:module");
-      const req = createRequire10(import.meta.url);
+      const { createRequire: createRequire11 } = await import("node:module");
+      const req = createRequire11(import.meta.url);
       const skillsPkgMain = req.resolve("@cleocode/skills/package.json");
       const skillsPkgRoot = dirname23(skillsPkgMain);
       if (existsSync106(join106(skillsPkgRoot, "skills.json"))) {
@@ -55422,8 +55515,8 @@ async function deployStarterBundle(cleoDir, created, warnings) {
   if (hasCantFiles) return;
   let starterBundleSrc = null;
   try {
-    const { createRequire: createRequire10 } = await import("node:module");
-    const req = createRequire10(import.meta.url);
+    const { createRequire: createRequire11 } = await import("node:module");
+    const req = createRequire11(import.meta.url);
     const cleoOsPkgMain = req.resolve("@cleocode/cleo-os/package.json");
     const cleoOsPkgRoot = dirname23(cleoOsPkgMain);
     const candidate = join106(cleoOsPkgRoot, "starter-bundle");
@@ -55463,20 +55556,20 @@ async function deployStarterBundle(cleoDir, created, warnings) {
       }
     }
   }
-  const identitySrc = join106(starterBundleSrc, "CLEOOS-IDENTITY.md");
-  const identityDst = join106(cleoDir, "CLEOOS-IDENTITY.md");
-  if (existsSync106(identitySrc) && !existsSync106(identityDst)) {
-    await copyFile4(identitySrc, identityDst);
-  }
   try {
-    const { getCleoHome: getCleoHome2 } = await Promise.resolve().then(() => (init_paths(), paths_exports));
-    const globalIdentityDst = join106(getCleoHome2(), "CLEOOS-IDENTITY.md");
-    if (existsSync106(identitySrc) && !existsSync106(globalIdentityDst)) {
-      await copyFile4(identitySrc, globalIdentityDst);
+    const { ensureGlobalIdentity: ensureGlobalIdentity2 } = await Promise.resolve().then(() => (init_scaffold(), scaffold_exports));
+    const identityResult = await ensureGlobalIdentity2();
+    if (identityResult.action === "created") {
+      created.push(`identity: ${identityResult.path}`);
+    } else if (identityResult.action === "skipped" && identityResult.details) {
+      warnings.push(`identity skipped: ${identityResult.details}`);
     }
-  } catch {
+  } catch (err) {
+    warnings.push(`identity deploy failed: ${err instanceof Error ? err.message : String(err)}`);
   }
-  created.push("starter-bundle: team + agent .cant files + identity deployed to .cleo/");
+  created.push(
+    "starter-bundle: team + agent .cant files deployed to .cleo/ (identity at global XDG)"
+  );
 }
 var DIR_SYMLINK_TYPE2;
 var init_init = __esm({
@@ -64390,8 +64483,8 @@ init_agent_outputs();
 // packages/core/src/migration/checksum.ts
 import { createHash as createHash7 } from "node:crypto";
 import { readFileSync as readFileSync34 } from "node:fs";
-import { createRequire as createRequire6 } from "node:module";
-var _require6 = createRequire6(import.meta.url);
+import { createRequire as createRequire7 } from "node:module";
+var _require6 = createRequire7(import.meta.url);
 var { DatabaseSync: DatabaseSync4 } = _require6("node:sqlite");
 async function computeChecksum(filePath) {
   const content = readFileSync34(filePath);
@@ -77277,7 +77370,7 @@ init_schema_management();
 init_data_accessor();
 import { execFileSync as execFileSync11 } from "node:child_process";
 import { existsSync as existsSync90, readFileSync as readFileSync65, statSync as statSync19 } from "node:fs";
-import { createRequire as createRequire9 } from "node:module";
+import { createRequire as createRequire10 } from "node:module";
 import { join as join92 } from "node:path";
 
 // packages/core/src/validation/doctor/checks.ts
@@ -78091,7 +78184,7 @@ function calculateHealthStatus(checks) {
 
 // packages/core/src/system/health.ts
 init_dependencies();
-var _require9 = createRequire9(import.meta.url);
+var _require9 = createRequire10(import.meta.url);
 var databaseSyncCtor = (() => {
   try {
     return _require9("node:sqlite").DatabaseSync;
@@ -78639,6 +78732,7 @@ async function coreDoctorReport(projectRoot) {
   });
   checks.push(mapCheckResult(checkGlobalHome()));
   checks.push(mapCheckResult(checkGlobalTemplates()));
+  checks.push(mapCheckResult(checkGlobalIdentity()));
   checks.push(mapSchemaCheckResult(checkGlobalSchemas()));
   checks.push(mapCheckResult(checkLogDir(projectRoot)));
   const hookResults = await checkGitHooks(projectRoot);