@cleocode/core 2026.3.49 → 2026.3.51

package/dist/index.js

@@ -1783,7 +1783,7 @@ var init_sql = __esm({
         return new SQL([new StringChunk(str)]);
       }
       _sql.raw = raw;
-      function join103(chunks, separator) {
+      function join104(chunks, separator) {
         const result = [];
         for (const [i, chunk] of chunks.entries()) {
           if (i > 0 && separator !== void 0) result.push(separator);
@@ -1791,7 +1791,7 @@ var init_sql = __esm({
         }
         return new SQL(result);
       }
-      _sql.join = join103;
+      _sql.join = join104;
       function identifier(value) {
         return new Name(value);
       }
@@ -6565,7 +6565,7 @@ var init_select2 = __esm({
           const baseTableName = this.tableName;
           const tableName = getTableLikeName(table);
           for (const item of extractUsedTable(table)) this.usedTables.add(item);
-          if (typeof tableName === "string" && this.config.joins?.some((join103) => join103.alias === tableName)) throw new Error(`Alias "${tableName}" is already used in this query`);
+          if (typeof tableName === "string" && this.config.joins?.some((join104) => join104.alias === tableName)) throw new Error(`Alias "${tableName}" is already used in this query`);
           if (!this.isPartialSelect) {
             if (Object.keys(this.joinsNotNullableMap).length === 1 && typeof baseTableName === "string") this.config.fields = { [baseTableName]: this.config.fields };
             if (typeof tableName === "string" && !is(table, SQL)) {
@@ -7850,7 +7850,7 @@ var init_dialect = __esm({
           if (!joins2) return;
           const withEntries = Object.entries(joins2).filter(([_, v]) => v);
           if (!withEntries.length) return;
-          return sql.join(withEntries.map(([k, join103]) => {
+          return sql.join(withEntries.map(([k, join104]) => {
             const relation = tableConfig.relations[k];
             const isSingle2 = is(relation, One3);
             const targetTable = aliasedTable(relation.targetTable, `d${currentDepth + 1}`);
@@ -7861,7 +7861,7 @@ var init_dialect = __esm({
               table: targetTable,
               mode: isSingle2 ? "first" : "many",
               schema,
-              queryConfig: join103,
+              queryConfig: join104,
               tableConfig: schema[relation.targetTableName],
               relationWhere: filter,
               isNested: true,
@@ -7875,7 +7875,7 @@ var init_dialect = __esm({
               key: k,
               selection: innerQuery.selection,
               isArray: !isSingle2,
-              isOptional: (relation.optional ?? false) || join103 !== true && !!join103.where
+              isOptional: (relation.optional ?? false) || join104 !== true && !!join104.where
             });
             const jsonColumns = sql.join(innerQuery.selection.map((s) => {
               return sql`${sql.raw(this.escapeString(s.key))}, ${s.selection ? sql`${jsonb2}(${sql.identifier(s.key)})` : sql.identifier(s.key)}`;
@@ -8274,7 +8274,7 @@ var init_update = __esm({
       createJoin(joinType) {
         return ((table, on) => {
           const tableName = getTableLikeName(table);
-          if (typeof tableName === "string" && this.config.joins.some((join103) => join103.alias === tableName)) throw new Error(`Alias "${tableName}" is already used in this query`);
+          if (typeof tableName === "string" && this.config.joins.some((join104) => join104.alias === tableName)) throw new Error(`Alias "${tableName}" is already used in this query`);
           if (typeof on === "function") {
             const from = this.config.from ? is(table, SQLiteTable) ? table[Table.Symbol.Columns] : is(table, Subquery) ? table._.selectedFields : is(table, SQLiteViewBase) ? table[ViewBaseConfig].selectedFields : void 0 : void 0;
             on = on(new Proxy(this.config.table[Table.Symbol.Columns], new SelectionProxyHandler({
@@ -20966,6 +20966,225 @@ var init_decisions2 = __esm({
   }
 });
 
+// packages/core/src/migration/agent-outputs.ts
+import {
+  copyFileSync as copyFileSync5,
+  existsSync as existsSync45,
+  mkdirSync as mkdirSync10,
+  readdirSync as readdirSync20,
+  readFileSync as readFileSync30,
+  rmSync,
+  statSync as statSync11,
+  writeFileSync as writeFileSync4
+} from "node:fs";
+import { join as join50 } from "node:path";
+function detectLegacyAgentOutputs(projectRoot, cleoDir) {
+  const hasResearchOutputs = existsSync45(join50(projectRoot, "claudedocs", "research-outputs"));
+  const hasLegacyAgentOutputs = existsSync45(join50(projectRoot, "claudedocs", "agent-outputs"));
+  const hasCanonical = existsSync45(join50(cleoDir, "agent-outputs"));
+  const legacyPaths = [];
+  if (hasResearchOutputs) legacyPaths.push("claudedocs/research-outputs/");
+  if (hasLegacyAgentOutputs) legacyPaths.push("claudedocs/agent-outputs/");
+  return {
+    hasLegacy: hasResearchOutputs || hasLegacyAgentOutputs,
+    hasResearchOutputs,
+    hasLegacyAgentOutputs,
+    hasCanonical,
+    legacyPaths
+  };
+}
+function migrateAgentOutputs(projectRoot, cleoDir) {
+  const detection = detectLegacyAgentOutputs(projectRoot, cleoDir);
+  if (!detection.hasLegacy) {
+    return {
+      migrated: false,
+      filesCopied: 0,
+      manifestEntries: 0,
+      removed: [],
+      summary: "No legacy output directories found"
+    };
+  }
+  const newDir = join50(cleoDir, "agent-outputs");
+  const hadCanonical = detection.hasCanonical;
+  mkdirSync10(newDir, { recursive: true });
+  let totalCopied = 0;
+  const mergedManifestLines = [];
+  const copiedFiles = /* @__PURE__ */ new Set();
+  const legacySources = [
+    {
+      path: join50(projectRoot, "claudedocs", "research-outputs"),
+      exists: detection.hasResearchOutputs
+    },
+    {
+      path: join50(projectRoot, "claudedocs", "agent-outputs"),
+      exists: detection.hasLegacyAgentOutputs
+    }
+  ];
+  for (const source of legacySources) {
+    if (!source.exists) continue;
+    totalCopied += copyDirContents(source.path, newDir, mergedManifestLines, copiedFiles);
+  }
+  const manifestEntries2 = mergeManifests(newDir, hadCanonical, mergedManifestLines);
+  updateConfigPaths(cleoDir);
+  const removed = removeLegacyDirs(projectRoot, detection);
+  const parts = [`Migrated ${totalCopied} files \u2192 ${CANONICAL_DIR}/`];
+  if (manifestEntries2 > 0) parts.push(`merged ${manifestEntries2} manifest entries`);
+  if (removed.length > 0) parts.push(`removed: ${removed.join(", ")}`);
+  return {
+    migrated: true,
+    filesCopied: totalCopied,
+    manifestEntries: manifestEntries2,
+    removed,
+    summary: parts.join("; ")
+  };
+}
+function copyDirContents(srcDir, dstDir, manifestLines, copiedFiles) {
+  let count2 = 0;
+  const entries = readdirSync20(srcDir);
+  for (const entry of entries) {
+    if (entry === "MANIFEST.jsonl") {
+      collectManifestLines(join50(srcDir, entry), manifestLines);
+      continue;
+    }
+    const srcPath = join50(srcDir, entry);
+    const dstPath = join50(dstDir, entry);
+    try {
+      const st = statSync11(srcPath);
+      if (st.isDirectory()) {
+        mkdirSync10(dstPath, { recursive: true });
+        for (const sf of readdirSync20(srcPath)) {
+          if (!copiedFiles.has(sf)) {
+            try {
+              copyFileSync5(join50(srcPath, sf), join50(dstPath, sf));
+              copiedFiles.add(sf);
+              count2++;
+            } catch {
+            }
+          }
+        }
+      } else if (!copiedFiles.has(entry)) {
+        copyFileSync5(srcPath, dstPath);
+        copiedFiles.add(entry);
+        count2++;
+      }
+    } catch {
+    }
+  }
+  return count2;
+}
+function collectManifestLines(manifestPath, out) {
+  try {
+    const content = readFileSync30(manifestPath, "utf-8");
+    for (const line2 of content.split("\n")) {
+      if (!line2.trim()) continue;
+      let rewritten = line2;
+      for (const [pattern, replacement] of MANIFEST_PATH_REWRITES) {
+        rewritten = rewritten.replace(pattern, replacement);
+      }
+      out.push(rewritten);
+    }
+  } catch {
+  }
+}
+function mergeManifests(newDir, hadCanonical, legacyLines) {
+  const manifestPath = join50(newDir, "MANIFEST.jsonl");
+  const existingLines = [];
+  if (hadCanonical && existsSync45(manifestPath)) {
+    try {
+      const existing = readFileSync30(manifestPath, "utf-8");
+      for (const line2 of existing.split("\n")) {
+        if (line2.trim()) existingLines.push(line2);
+      }
+    } catch {
+    }
+  }
+  const seenIds = /* @__PURE__ */ new Set();
+  const finalLines = [];
+  for (const line2 of existingLines) {
+    try {
+      const p = JSON.parse(line2);
+      if (p.id) seenIds.add(p.id);
+    } catch {
+    }
+    finalLines.push(line2);
+  }
+  for (const line2 of legacyLines) {
+    try {
+      const p = JSON.parse(line2);
+      if (p.id && seenIds.has(p.id)) continue;
+      if (p.id) seenIds.add(p.id);
+    } catch {
+    }
+    finalLines.push(line2);
+  }
+  if (finalLines.length > 0) {
+    writeFileSync4(manifestPath, finalLines.join("\n") + "\n");
+  }
+  return finalLines.length;
+}
+function updateConfigPaths(cleoDir) {
+  const configPath = join50(cleoDir, "config.json");
+  if (!existsSync45(configPath)) return;
+  try {
+    const config2 = JSON.parse(readFileSync30(configPath, "utf-8"));
+    const currentDir = config2.agentOutputs?.directory ?? config2.agentOutputs ?? config2.research?.outputDir;
+    if (currentDir && currentDir !== CANONICAL_DIR) {
+      if (typeof config2.agentOutputs === "object") {
+        config2.agentOutputs.directory = CANONICAL_DIR;
+      } else {
+        config2.agentOutputs = { directory: CANONICAL_DIR };
+      }
+      if (config2.research?.outputDir) {
+        delete config2.research.outputDir;
+        if (Object.keys(config2.research).length === 0) {
+          delete config2.research;
+        }
+      }
+      writeFileSync4(configPath, JSON.stringify(config2, null, 2));
+    }
+  } catch {
+  }
+}
+function removeLegacyDirs(projectRoot, detection) {
+  const removed = [];
+  if (detection.hasResearchOutputs) {
+    try {
+      rmSync(join50(projectRoot, "claudedocs", "research-outputs"), { recursive: true, force: true });
+      removed.push("claudedocs/research-outputs/");
+    } catch {
+    }
+  }
+  if (detection.hasLegacyAgentOutputs) {
+    try {
+      rmSync(join50(projectRoot, "claudedocs", "agent-outputs"), { recursive: true, force: true });
+      removed.push("claudedocs/agent-outputs/");
+    } catch {
+    }
+  }
+  const claudedocsDir = join50(projectRoot, "claudedocs");
+  if (existsSync45(claudedocsDir)) {
+    try {
+      if (readdirSync20(claudedocsDir).length === 0) {
+        rmSync(claudedocsDir, { recursive: true, force: true });
+        removed.push("claudedocs/ (empty)");
+      }
+    } catch {
+    }
+  }
+  return removed;
+}
+var CANONICAL_DIR, MANIFEST_PATH_REWRITES;
+var init_agent_outputs = __esm({
+  "packages/core/src/migration/agent-outputs.ts"() {
+    "use strict";
+    CANONICAL_DIR = ".cleo/agent-outputs";
+    MANIFEST_PATH_REWRITES = [
+      [/claudedocs\/research-outputs\//g, `${CANONICAL_DIR}/`],
+      [/claudedocs\/agent-outputs\//g, `${CANONICAL_DIR}/`]
+    ];
+  }
+});
+
 // packages/core/src/nexus/migrate-json-to-sqlite.ts
 var migrate_json_to_sqlite_exports = {};
 __export(migrate_json_to_sqlite_exports, {
@@ -21202,10 +21421,10 @@ async function readProjectMeta(projectPath) {
 }
 async function readProjectId(projectPath) {
   try {
-    const { readFileSync: readFileSync76, existsSync: existsSync102 } = await import("node:fs");
+    const { readFileSync: readFileSync77, existsSync: existsSync103 } = await import("node:fs");
     const infoPath = join57(projectPath, ".cleo", "project-info.json");
-    if (!existsSync102(infoPath)) return "";
-    const data = JSON.parse(readFileSync76(infoPath, "utf-8"));
+    if (!existsSync103(infoPath)) return "";
+    const data = JSON.parse(readFileSync77(infoPath, "utf-8"));
     return typeof data.projectId === "string" ? data.projectId : "";
   } catch {
     return "";
@@ -24005,6 +24224,539 @@ var init_hooks = __esm({
   }
 });
 
+// packages/core/src/init.ts
+var init_exports = {};
+__export(init_exports, {
+  ensureInitialized: () => ensureInitialized,
+  getVersion: () => getVersion2,
+  initAgentDefinition: () => initAgentDefinition,
+  initCoreSkills: () => initCoreSkills,
+  initMcpServer: () => initMcpServer,
+  initNexusRegistration: () => initNexusRegistration,
+  initProject: () => initProject,
+  installGitHubTemplates: () => installGitHubTemplates,
+  isAutoInitEnabled: () => isAutoInitEnabled,
+  updateDocs: () => updateDocs
+});
+import { existsSync as existsSync99, readdirSync as readdirSync33, readFileSync as readFileSync73 } from "node:fs";
+import { copyFile as copyFile3, lstat, mkdir as mkdir16, readFile as readFile17, symlink, unlink as unlink4, writeFile as writeFile11 } from "node:fs/promises";
+import { platform as platform4 } from "node:os";
+import { basename as basename17, dirname as dirname19, join as join100 } from "node:path";
+async function initAgentDefinition(created, warnings) {
+  let agentSourceDir = null;
+  try {
+    const { createRequire: createRequire5 } = await import("node:module");
+    const req = createRequire5(import.meta.url);
+    const agentsPkgMain = req.resolve("@cleocode/agents/package.json");
+    const agentsPkgRoot = dirname19(agentsPkgMain);
+    const candidate = join100(agentsPkgRoot, "cleo-subagent");
+    if (existsSync99(candidate)) {
+      agentSourceDir = candidate;
+    }
+  } catch {
+  }
+  if (!agentSourceDir) {
+    const packageRoot = getPackageRoot();
+    const bundled = join100(packageRoot, "agents", "cleo-subagent");
+    if (existsSync99(bundled)) {
+      agentSourceDir = bundled;
+    }
+  }
+  if (!agentSourceDir) {
+    warnings.push("agents/cleo-subagent/ not found in package, skipping agent definition install");
+    return;
+  }
+  const globalAgentsDir = join100(getAgentsHome(), "agents", "cleo-subagent");
+  await mkdir16(dirname19(globalAgentsDir), { recursive: true });
+  try {
+    try {
+      const stat2 = await lstat(globalAgentsDir);
+      if (stat2.isSymbolicLink()) {
+        const { readlink } = await import("node:fs/promises");
+        const currentTarget = await readlink(globalAgentsDir);
+        if (currentTarget === agentSourceDir) {
+          return;
+        }
+        await unlink4(globalAgentsDir);
+      } else if (stat2.isDirectory()) {
+        return;
+      }
+    } catch {
+    }
+    await symlink(agentSourceDir, globalAgentsDir, DIR_SYMLINK_TYPE2);
+    created.push("agent: cleo-subagent (symlinked)");
+  } catch (_err) {
+    try {
+      await mkdir16(globalAgentsDir, { recursive: true });
+      const files = readdirSync33(agentSourceDir);
+      for (const file2 of files) {
+        await copyFile3(join100(agentSourceDir, file2), join100(globalAgentsDir, file2));
+      }
+      created.push("agent: cleo-subagent (copied)");
+    } catch (copyErr) {
+      warnings.push(
+        `Agent definition install: ${copyErr instanceof Error ? copyErr.message : String(copyErr)}`
+      );
+    }
+  }
+}
+async function initMcpServer(projectRoot, created, warnings) {
+  try {
+    const { detectEnvMode: detectEnvMode2, generateMcpServerEntry: generateMcpServerEntry2, getMcpServerName: getMcpServerName2 } = await Promise.resolve().then(() => (init_mcp(), mcp_exports));
+    const { getInstalledProviders: getInstalledProviders3, installMcpServerToAll } = await import("@cleocode/caamp");
+    const env = detectEnvMode2();
+    const serverEntry = generateMcpServerEntry2(env);
+    const serverName = getMcpServerName2(env);
+    const providers = getInstalledProviders3();
+    if (providers.length === 0) {
+      return;
+    }
+    const results = await installMcpServerToAll(
+      providers,
+      serverName,
+      serverEntry,
+      "global",
+      projectRoot
+    );
+    const successes = results.filter((r) => r.success);
+    const failures = results.filter((r) => !r.success);
+    if (successes.length > 0) {
+      created.push(`MCP server: ${successes.map((r) => r.provider.id).join(", ")}`);
+    }
+    for (const f of failures) {
+      if (f.error) {
+        warnings.push(`MCP install to ${f.provider.id}: ${f.error}`);
+      }
+    }
+  } catch (err) {
+    warnings.push(`MCP server install: ${err instanceof Error ? err.message : String(err)}`);
+  }
+}
+async function initCoreSkills(created, warnings) {
+  try {
+    const { getInstalledProviders: getInstalledProviders3, installSkill: installSkill2, registerSkillLibraryFromPath } = await import("@cleocode/caamp");
+    const providers = getInstalledProviders3();
+    if (providers.length === 0) {
+      return;
+    }
+    const packageRoot = getPackageRoot();
+    let ctSkillsRoot = null;
+    try {
+      const { createRequire: createRequire5 } = await import("node:module");
+      const req = createRequire5(import.meta.url);
+      const skillsPkgMain = req.resolve("@cleocode/skills/package.json");
+      const skillsPkgRoot = dirname19(skillsPkgMain);
+      if (existsSync99(join100(skillsPkgRoot, "skills.json"))) {
+        ctSkillsRoot = skillsPkgRoot;
+      }
+    } catch {
+    }
+    if (!ctSkillsRoot) {
+      try {
+        const bundledPath = join100(packageRoot, "packages", "skills");
+        if (existsSync99(join100(bundledPath, "skills.json"))) {
+          ctSkillsRoot = bundledPath;
+        } else {
+          const ctSkillsPath = join100(packageRoot, "node_modules", "@cleocode", "skills");
+          if (existsSync99(join100(ctSkillsPath, "skills.json"))) {
+            ctSkillsRoot = ctSkillsPath;
+          }
+        }
+      } catch {
+      }
+    }
+    if (!ctSkillsRoot) {
+      warnings.push("skills package not found, skipping core skill installation");
+      return;
+    }
+    try {
+      registerSkillLibraryFromPath(ctSkillsRoot);
+    } catch {
+      warnings.push("Failed to register skill library with CAAMP");
+    }
+    const catalogPath = join100(ctSkillsRoot, "skills.json");
+    const catalog3 = JSON.parse(readFileSync73(catalogPath, "utf-8"));
+    const skills = catalog3.skills ?? [];
+    const coreSkills = skills.filter((s) => s.tier <= 2);
+    const installed = [];
+    for (const skill of coreSkills) {
+      const skillSourceDir = dirname19(join100(ctSkillsRoot, skill.path));
+      if (!existsSync99(skillSourceDir)) {
+        continue;
+      }
+      try {
+        const result = await installSkill2(skillSourceDir, skill.name, providers, true);
+        if (result.success) {
+          installed.push(skill.name);
+        }
+      } catch {
+      }
+    }
+    if (installed.length > 0) {
+      created.push(`skills: ${installed.length} core skills installed`);
+    }
+  } catch (err) {
+    warnings.push(`Core skill install: ${err instanceof Error ? err.message : String(err)}`);
+  }
+}
+async function initNexusRegistration(projectRoot, created, warnings) {
+  try {
+    const { nexusReconcile: nexusReconcile2 } = await Promise.resolve().then(() => (init_registry3(), registry_exports3));
+    const result = await nexusReconcile2(projectRoot);
+    if (result.status === "auto_registered") {
+      created.push("NEXUS registration (auto-registered new project)");
+    } else if (result.status === "path_updated") {
+      created.push(`NEXUS registration (path updated: ${result.oldPath} \u2192 ${result.newPath})`);
+    } else if (result.status === "ok") {
+      created.push("NEXUS registration (project verified and active)");
+    }
+  } catch (err) {
+    const errStr = String(err);
+    if (errStr.includes("NEXUS_PROJECT_EXISTS")) {
+      warnings.push("NEXUS registration: Project already registered");
+    } else if (errStr.includes("NEXUS_REGISTRY_CORRUPT")) {
+      warnings.push(
+        `NEXUS registration: Identity conflict - ${err instanceof Error ? err.message : errStr}. Run 'cleo nexus unregister' and re-register.`
+      );
+    } else {
+      warnings.push(`NEXUS registration: ${err instanceof Error ? err.message : errStr}`);
+    }
+  }
+}
+async function installGitHubTemplates(projectRoot, created, skipped) {
+  if (!existsSync99(join100(projectRoot, ".git"))) {
+    return;
+  }
+  const githubDir = join100(projectRoot, ".github");
+  const issueTemplateDir = join100(githubDir, "ISSUE_TEMPLATE");
+  const packageRoot = getPackageRoot();
+  const templateSrcDir = join100(packageRoot, "templates", "github");
+  if (!existsSync99(templateSrcDir)) {
+    return;
+  }
+  await mkdir16(issueTemplateDir, { recursive: true });
+  const issueSrcDir = join100(templateSrcDir, "ISSUE_TEMPLATE");
+  if (existsSync99(issueSrcDir)) {
+    const issueFiles = readdirSync33(issueSrcDir);
+    for (const file2 of issueFiles) {
+      const dest = join100(issueTemplateDir, file2);
+      if (existsSync99(dest)) {
+        skipped.push(`.github/ISSUE_TEMPLATE/${file2}`);
+        continue;
+      }
+      const content = readFileSync73(join100(issueSrcDir, file2), "utf-8");
+      await writeFile11(dest, content, "utf-8");
+      created.push(`.github/ISSUE_TEMPLATE/${file2}`);
+    }
+  }
+  const prTemplateSrc = join100(templateSrcDir, "pull_request_template.md");
+  const prTemplateDest = join100(githubDir, "pull_request_template.md");
+  if (existsSync99(prTemplateSrc)) {
+    if (existsSync99(prTemplateDest)) {
+      skipped.push(".github/pull_request_template.md");
+    } else {
+      const content = readFileSync73(prTemplateSrc, "utf-8");
+      await writeFile11(prTemplateDest, content, "utf-8");
+      created.push(".github/pull_request_template.md");
+    }
+  }
+}
+async function updateDocs() {
+  const cleoDir = getCleoDirAbsolute();
+  const projRoot = getProjectRoot();
+  const created = [];
+  const warnings = [];
+  try {
+    const result = await ensureInjection(projRoot);
+    if (result.action !== "skipped") {
+      created.push(`injection: ${result.details ?? result.action}`);
+    }
+  } catch (err) {
+    warnings.push(`CAAMP injection: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  return {
+    initialized: true,
+    directory: cleoDir,
+    created,
+    skipped: [],
+    warnings,
+    updateDocsOnly: true
+  };
+}
+async function initProject(opts = {}) {
+  const cleoDir = getCleoDirAbsolute();
+  const projRoot = getProjectRoot();
+  const alreadyInitialized = existsSync99(cleoDir) && (existsSync99(join100(cleoDir, "tasks.db")) || existsSync99(join100(cleoDir, "config.json")));
+  if (alreadyInitialized && !opts.force) {
+    throw new CleoError(
+      1 /* GENERAL_ERROR */,
+      "Project already initialized. DANGER ZONE: use --force to wipe and re-init.",
+      { fix: "cleo init --force" }
+    );
+  }
+  const force = !!opts.force;
+  const created = [];
+  const skipped = [];
+  const warnings = [];
+  const structureResult = await ensureCleoStructure(projRoot);
+  if (structureResult.action === "created") {
+    created.push(".cleo/ directory structure");
+  }
+  const configResult = await ensureConfig(projRoot, { force });
+  if (configResult.action === "skipped") {
+    skipped.push("config.json");
+  } else {
+    created.push("config.json");
+  }
+  try {
+    const { getDb: getDb3 } = await Promise.resolve().then(() => (init_sqlite2(), sqlite_exports));
+    await getDb3(join100(cleoDir, ".."));
+    created.push("tasks.db");
+  } catch (err) {
+    created.push(`tasks.db (deferred: ${err instanceof Error ? err.message : String(err)})`);
+  }
+  try {
+    const brainResult = await ensureBrainDb(projRoot);
+    if (brainResult.action === "created") {
+      created.push("brain.db");
+    }
+  } catch (err) {
+    created.push(`brain.db (deferred: ${err instanceof Error ? err.message : String(err)})`);
+  }
+  if (force) {
+    const gitignoreResult = await ensureGitignore(projRoot);
+    if (gitignoreResult.action === "skipped") {
+      skipped.push(".gitignore");
+    } else {
+      created.push(".gitignore");
+    }
+  } else {
+    const gitignorePath = join100(cleoDir, ".gitignore");
+    if (existsSync99(gitignorePath)) {
+      skipped.push(".gitignore");
+    } else {
+      const gitignoreResult = await ensureGitignore(projRoot);
+      if (gitignoreResult.action !== "skipped") {
+        created.push(".gitignore");
+      } else {
+        skipped.push(".gitignore");
+      }
+    }
+  }
+  const legacySequencePath = join100(cleoDir, ".sequence");
+  try {
+    await unlink4(legacySequencePath);
+  } catch {
+  }
+  const legacySequenceJsonPath = join100(cleoDir, ".sequence.json");
+  try {
+    await unlink4(legacySequenceJsonPath);
+  } catch {
+  }
+  try {
+    const gitRepoResult = await ensureCleoGitRepo(projRoot);
+    if (gitRepoResult.action === "created") {
+      created.push(".cleo/.git (isolated checkpoint repository)");
+    }
+  } catch (err) {
+    warnings.push(
+      `Could not initialize .cleo/.git: ${err instanceof Error ? err.message : String(err)}`
+    );
+  }
+  try {
+    const migrationResult = migrateAgentOutputs(projRoot, cleoDir);
+    if (migrationResult.migrated) {
+      created.push(`agent-outputs migration: ${migrationResult.summary}`);
+    }
+  } catch {
+    warnings.push("Agent-outputs migration failed (best-effort, run cleo upgrade to retry)");
+  }
+  try {
+    const schemaResult = ensureGlobalSchemas({ force });
+    const total = schemaResult.installed + schemaResult.updated;
+    if (total > 0) {
+      created.push(`schemas/ (${total} files)`);
+    }
+  } catch (err) {
+    warnings.push(`Schema installation: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  try {
+    const hooksResult = await ensureGitHooks(projRoot, { force });
+    if (hooksResult.action === "created") {
+      created.push(hooksResult.details ?? "git hooks installed");
+    } else if (hooksResult.action === "skipped" && hooksResult.details?.includes("No .git/")) {
+      warnings.push(hooksResult.details);
+    } else if (hooksResult.action === "skipped" && hooksResult.details?.includes("not found in package root")) {
+      warnings.push(hooksResult.details);
+    } else if (hooksResult.action === "repaired" && hooksResult.details?.includes("error")) {
+      const match = hooksResult.details.match(/Installed (\d+)/);
+      if (match && parseInt(match[1], 10) > 0) {
+        created.push(`git hooks (${match[1]} installed)`);
+      }
+      warnings.push(hooksResult.details);
+    }
+  } catch (err) {
+    warnings.push(`Git hook installation: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  const projectInfoResult = await ensureProjectInfo(projRoot, { force });
+  if (projectInfoResult.action === "skipped") {
+    skipped.push("project-info.json");
+  } else {
+    created.push("project-info.json");
+  }
+  try {
+    const detectResult = await ensureProjectContext(projRoot, { force: !!opts.detect });
+    if (detectResult.action !== "skipped") {
+      created.push("project-context.json");
+    }
+  } catch (err) {
+    warnings.push(`Project detection failed: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  if (opts.mapCodebase) {
+    try {
+      const { mapCodebase: mapCodebase2 } = await Promise.resolve().then(() => (init_codebase_map(), codebase_map_exports));
+      const mapResult = await mapCodebase2(projRoot, { storeToBrain: true });
+      created.push(
+        `codebase-map: ${mapResult.stack.languages.length} languages, ${mapResult.architecture.layers.length} layers analyzed`
+      );
+    } catch (err) {
+      warnings.push(`Codebase mapping: ${err instanceof Error ? err.message : String(err)}`);
+    }
+  }
+  try {
+    const bridgeResult = await writeMemoryBridge(projRoot);
+    if (bridgeResult.written) {
+      created.push("memory-bridge.md");
+    }
+  } catch (err) {
+    warnings.push(`Memory bridge: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  try {
+    const injectionResult = await ensureInjection(projRoot);
+    if (injectionResult.action !== "skipped") {
+      if (injectionResult.details) {
+        created.push(`injection: ${injectionResult.details}`);
+      }
+    } else if (injectionResult.details) {
+      warnings.push(injectionResult.details);
+    }
+  } catch (err) {
+    warnings.push(`CAAMP injection: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  try {
+    const { ensureContributorMcp: ensureContributorMcp2 } = await Promise.resolve().then(() => (init_scaffold(), scaffold_exports));
+    const mcpResult = await ensureContributorMcp2(projRoot);
+    if (mcpResult.action !== "skipped") {
+      created.push(`contributor MCP: ${mcpResult.details ?? mcpResult.action}`);
+    }
+  } catch (err) {
+    warnings.push(`Contributor MCP setup: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  await initAgentDefinition(created, warnings);
+  await initNexusRegistration(projRoot, created, warnings);
+  try {
+    const { AdapterManager: AdapterManager2 } = await Promise.resolve().then(() => (init_adapters(), adapters_exports));
+    const mgr = AdapterManager2.getInstance(projRoot);
+    const manifests = mgr.discover();
+    if (manifests.length > 0) {
+      created.push(`adapters: ${manifests.length} adapter(s) discovered`);
+      const detected = mgr.detectActive();
+      if (detected.length > 0) {
+        created.push(`adapters: active provider detected (${detected.join(", ")})`);
+        for (const adapterId of detected) {
+          try {
+            const adapter = await mgr.activate(adapterId);
+            const installResult = await adapter.install.install({
+              projectDir: projRoot
+            });
+            if (installResult.success) {
+              created.push(`adapter install (${adapterId}): installed`);
+            } else {
+              warnings.push(`adapter install (${adapterId}): failed`);
+            }
+          } catch (err) {
+            warnings.push(
+              `adapter activate/install (${adapterId}): ${err instanceof Error ? err.message : String(err)}`
+            );
+          }
+        }
+      }
+    }
+  } catch (err) {
+    warnings.push(`Adapter discovery: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  try {
+    await installGitHubTemplates(projRoot, created, skipped);
+  } catch (err) {
+    warnings.push(`GitHub templates: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  const rootGitignoreResult = await removeCleoFromRootGitignore(projRoot);
+  if (rootGitignoreResult.removed) {
+    warnings.push(
+      ".cleo/ was found in root .gitignore and has been removed. CLEO uses .cleo/.gitignore for selective tracking."
+    );
+  }
+  return {
+    initialized: true,
+    directory: cleoDir,
+    created,
+    skipped,
+    warnings
+  };
+}
+function isAutoInitEnabled() {
+  return process.env.CLEO_AUTO_INIT === "true";
+}
+async function ensureInitialized(projectRoot) {
+  const root = projectRoot ?? getProjectRoot();
+  const cleoDir = join100(root, ".cleo");
+  const isInit = existsSync99(cleoDir) && (existsSync99(join100(cleoDir, "tasks.db")) || existsSync99(join100(cleoDir, "config.json")));
+  if (isInit) {
+    return { initialized: true };
+  }
+  if (isAutoInitEnabled()) {
+    await initProject({ name: basename17(root) });
+    return { initialized: true };
+  }
+  throw new Error("CLEO project not initialized. Run system.init or set CLEO_AUTO_INIT=true");
+}
+async function getVersion2(projectRoot) {
+  const root = projectRoot ?? getProjectRoot();
+  const versionPaths = [join100(root, "VERSION"), join100(root, "..", "VERSION")];
+  for (const versionPath of versionPaths) {
+    try {
+      const content = await readFile17(versionPath, "utf-8");
+      const version2 = content.trim();
+      if (version2) {
+        return { version: version2 };
+      }
+    } catch {
+    }
+  }
+  const pkg = await readJson(join100(root, "package.json"));
+  if (pkg?.version) {
+    return { version: pkg.version };
+  }
+  return { version: "0.0.0" };
+}
+var DIR_SYMLINK_TYPE2;
+var init_init = __esm({
+  "packages/core/src/init.ts"() {
+    "use strict";
+    init_src();
+    init_errors3();
+    init_hooks();
+    init_injection();
+    init_memory_bridge();
+    init_agent_outputs();
+    init_paths();
+    init_scaffold();
+    init_schema_management();
+    init_json2();
+    DIR_SYMLINK_TYPE2 = platform4() === "win32" ? "junction" : "dir";
+  }
+});
+
 // packages/core/src/index.ts
 init_src();
 init_adapters();
@@ -42540,219 +43292,7 @@ __export(migration_exports, {
   verifyBackup: () => verifyBackup,
   verifySourceIntegrity: () => verifySourceIntegrity
 });
-
-// packages/core/src/migration/agent-outputs.ts
-import {
-  copyFileSync as copyFileSync5,
-  existsSync as existsSync45,
-  mkdirSync as mkdirSync10,
-  readdirSync as readdirSync20,
-  readFileSync as readFileSync30,
-  rmSync,
-  statSync as statSync11,
-  writeFileSync as writeFileSync4
-} from "node:fs";
-import { join as join50 } from "node:path";
-var CANONICAL_DIR = ".cleo/agent-outputs";
-var MANIFEST_PATH_REWRITES = [
-  [/claudedocs\/research-outputs\//g, `${CANONICAL_DIR}/`],
-  [/claudedocs\/agent-outputs\//g, `${CANONICAL_DIR}/`]
-];
-function detectLegacyAgentOutputs(projectRoot, cleoDir) {
-  const hasResearchOutputs = existsSync45(join50(projectRoot, "claudedocs", "research-outputs"));
-  const hasLegacyAgentOutputs = existsSync45(join50(projectRoot, "claudedocs", "agent-outputs"));
-  const hasCanonical = existsSync45(join50(cleoDir, "agent-outputs"));
-  const legacyPaths = [];
-  if (hasResearchOutputs) legacyPaths.push("claudedocs/research-outputs/");
-  if (hasLegacyAgentOutputs) legacyPaths.push("claudedocs/agent-outputs/");
-  return {
-    hasLegacy: hasResearchOutputs || hasLegacyAgentOutputs,
-    hasResearchOutputs,
-    hasLegacyAgentOutputs,
-    hasCanonical,
-    legacyPaths
-  };
-}
-function migrateAgentOutputs(projectRoot, cleoDir) {
-  const detection = detectLegacyAgentOutputs(projectRoot, cleoDir);
-  if (!detection.hasLegacy) {
-    return {
-      migrated: false,
-      filesCopied: 0,
-      manifestEntries: 0,
-      removed: [],
-      summary: "No legacy output directories found"
-    };
-  }
-  const newDir = join50(cleoDir, "agent-outputs");
-  const hadCanonical = detection.hasCanonical;
-  mkdirSync10(newDir, { recursive: true });
-  let totalCopied = 0;
-  const mergedManifestLines = [];
-  const copiedFiles = /* @__PURE__ */ new Set();
-  const legacySources = [
-    {
-      path: join50(projectRoot, "claudedocs", "research-outputs"),
-      exists: detection.hasResearchOutputs
-    },
-    {
-      path: join50(projectRoot, "claudedocs", "agent-outputs"),
-      exists: detection.hasLegacyAgentOutputs
-    }
-  ];
-  for (const source of legacySources) {
-    if (!source.exists) continue;
-    totalCopied += copyDirContents(source.path, newDir, mergedManifestLines, copiedFiles);
-  }
-  const manifestEntries2 = mergeManifests(newDir, hadCanonical, mergedManifestLines);
-  updateConfigPaths(cleoDir);
-  const removed = removeLegacyDirs(projectRoot, detection);
-  const parts = [`Migrated ${totalCopied} files \u2192 ${CANONICAL_DIR}/`];
-  if (manifestEntries2 > 0) parts.push(`merged ${manifestEntries2} manifest entries`);
-  if (removed.length > 0) parts.push(`removed: ${removed.join(", ")}`);
-  return {
-    migrated: true,
-    filesCopied: totalCopied,
-    manifestEntries: manifestEntries2,
-    removed,
-    summary: parts.join("; ")
-  };
-}
-function copyDirContents(srcDir, dstDir, manifestLines, copiedFiles) {
-  let count2 = 0;
-  const entries = readdirSync20(srcDir);
-  for (const entry of entries) {
-    if (entry === "MANIFEST.jsonl") {
-      collectManifestLines(join50(srcDir, entry), manifestLines);
-      continue;
-    }
-    const srcPath = join50(srcDir, entry);
-    const dstPath = join50(dstDir, entry);
-    try {
-      const st = statSync11(srcPath);
-      if (st.isDirectory()) {
-        mkdirSync10(dstPath, { recursive: true });
-        for (const sf of readdirSync20(srcPath)) {
-          if (!copiedFiles.has(sf)) {
-            try {
-              copyFileSync5(join50(srcPath, sf), join50(dstPath, sf));
-              copiedFiles.add(sf);
-              count2++;
-            } catch {
-            }
-          }
-        }
-      } else if (!copiedFiles.has(entry)) {
-        copyFileSync5(srcPath, dstPath);
-        copiedFiles.add(entry);
-        count2++;
-      }
-    } catch {
-    }
-  }
-  return count2;
-}
-function collectManifestLines(manifestPath, out) {
-  try {
-    const content = readFileSync30(manifestPath, "utf-8");
-    for (const line2 of content.split("\n")) {
-      if (!line2.trim()) continue;
-      let rewritten = line2;
-      for (const [pattern, replacement] of MANIFEST_PATH_REWRITES) {
-        rewritten = rewritten.replace(pattern, replacement);
-      }
-      out.push(rewritten);
-    }
-  } catch {
-  }
-}
-function mergeManifests(newDir, hadCanonical, legacyLines) {
-  const manifestPath = join50(newDir, "MANIFEST.jsonl");
-  const existingLines = [];
-  if (hadCanonical && existsSync45(manifestPath)) {
-    try {
-      const existing = readFileSync30(manifestPath, "utf-8");
-      for (const line2 of existing.split("\n")) {
-        if (line2.trim()) existingLines.push(line2);
-      }
-    } catch {
-    }
-  }
-  const seenIds = /* @__PURE__ */ new Set();
-  const finalLines = [];
-  for (const line2 of existingLines) {
-    try {
-      const p = JSON.parse(line2);
-      if (p.id) seenIds.add(p.id);
-    } catch {
-    }
-    finalLines.push(line2);
-  }
-  for (const line2 of legacyLines) {
-    try {
-      const p = JSON.parse(line2);
-      if (p.id && seenIds.has(p.id)) continue;
-      if (p.id) seenIds.add(p.id);
-    } catch {
-    }
-    finalLines.push(line2);
-  }
-  if (finalLines.length > 0) {
-    writeFileSync4(manifestPath, finalLines.join("\n") + "\n");
-  }
-  return finalLines.length;
-}
-function updateConfigPaths(cleoDir) {
-  const configPath = join50(cleoDir, "config.json");
-  if (!existsSync45(configPath)) return;
-  try {
-    const config2 = JSON.parse(readFileSync30(configPath, "utf-8"));
-    const currentDir = config2.agentOutputs?.directory ?? config2.agentOutputs ?? config2.research?.outputDir;
-    if (currentDir && currentDir !== CANONICAL_DIR) {
-      if (typeof config2.agentOutputs === "object") {
-        config2.agentOutputs.directory = CANONICAL_DIR;
-      } else {
-        config2.agentOutputs = { directory: CANONICAL_DIR };
-      }
-      if (config2.research?.outputDir) {
-        delete config2.research.outputDir;
-        if (Object.keys(config2.research).length === 0) {
-          delete config2.research;
-        }
-      }
-      writeFileSync4(configPath, JSON.stringify(config2, null, 2));
-    }
-  } catch {
-  }
-}
-function removeLegacyDirs(projectRoot, detection) {
-  const removed = [];
-  if (detection.hasResearchOutputs) {
-    try {
-      rmSync(join50(projectRoot, "claudedocs", "research-outputs"), { recursive: true, force: true });
-      removed.push("claudedocs/research-outputs/");
-    } catch {
-    }
-  }
-  if (detection.hasLegacyAgentOutputs) {
-    try {
-      rmSync(join50(projectRoot, "claudedocs", "agent-outputs"), { recursive: true, force: true });
-      removed.push("claudedocs/agent-outputs/");
-    } catch {
-    }
-  }
-  const claudedocsDir = join50(projectRoot, "claudedocs");
-  if (existsSync45(claudedocsDir)) {
-    try {
-      if (readdirSync20(claudedocsDir).length === 0) {
-        rmSync(claudedocsDir, { recursive: true, force: true });
-        removed.push("claudedocs/ (empty)");
-      }
-    } catch {
-    }
-  }
-  return removed;
-}
+init_agent_outputs();
 
 // packages/core/src/migration/checksum.ts
 import { createHash as createHash5 } from "node:crypto";
@@ -54215,8 +54755,8 @@ async function initializeSpawnAdapters(manifests) {
     if (!manifest.capabilities?.supportsSpawn) continue;
     if (spawnRegistry.hasAdapterForProvider(manifest.provider)) continue;
     try {
-      const { join: join103 } = await import("node:path");
-      const modulePath = join103(manifest.packagePath, manifest.entryPoint);
+      const { join: join104 } = await import("node:path");
+      const modulePath = join104(manifest.packagePath, manifest.entryPoint);
       const adapterModule = await import(modulePath);
       let SpawnProviderClass;
       for (const [exportName, exportValue] of Object.entries(adapterModule)) {
@@ -55804,6 +56344,7 @@ var CORE_PROTECTED_FILES = [
 ];
 
 // packages/core/src/validation/doctor/checks.ts
+init_agent_outputs();
 init_paths();
 init_scaffold();
 init_schema_management();
@@ -61813,400 +62354,7 @@ function isCleoRegisteredCode(lafsCode) {
 
 // packages/core/src/index.ts
 init_errors3();
-
-// packages/core/src/init.ts
-init_src();
-init_errors3();
-init_hooks();
-init_injection();
-init_memory_bridge();
-import { existsSync as existsSync99, readdirSync as readdirSync33, readFileSync as readFileSync73 } from "node:fs";
-import { copyFile as copyFile3, lstat, mkdir as mkdir16, readFile as readFile17, symlink, unlink as unlink4, writeFile as writeFile11 } from "node:fs/promises";
-import { platform as platform4 } from "node:os";
-import { basename as basename17, dirname as dirname19, join as join100 } from "node:path";
-init_paths();
-init_scaffold();
-init_schema_management();
-init_json2();
-var DIR_SYMLINK_TYPE2 = platform4() === "win32" ? "junction" : "dir";
-async function initAgentDefinition(created, warnings) {
-  let agentSourceDir = null;
-  try {
-    const { createRequire: createRequire5 } = await import("node:module");
-    const req = createRequire5(import.meta.url);
-    const agentsPkgMain = req.resolve("@cleocode/agents/package.json");
-    const agentsPkgRoot = dirname19(agentsPkgMain);
-    const candidate = join100(agentsPkgRoot, "cleo-subagent");
-    if (existsSync99(candidate)) {
-      agentSourceDir = candidate;
-    }
-  } catch {
-  }
-  if (!agentSourceDir) {
-    const packageRoot = getPackageRoot();
-    const bundled = join100(packageRoot, "agents", "cleo-subagent");
-    if (existsSync99(bundled)) {
-      agentSourceDir = bundled;
-    }
-  }
-  if (!agentSourceDir) {
-    warnings.push("agents/cleo-subagent/ not found in package, skipping agent definition install");
-    return;
-  }
-  const globalAgentsDir = join100(getAgentsHome(), "agents", "cleo-subagent");
-  await mkdir16(dirname19(globalAgentsDir), { recursive: true });
-  try {
-    try {
-      const stat2 = await lstat(globalAgentsDir);
-      if (stat2.isSymbolicLink()) {
-        const { readlink } = await import("node:fs/promises");
-        const currentTarget = await readlink(globalAgentsDir);
-        if (currentTarget === agentSourceDir) {
-          return;
-        }
-        await unlink4(globalAgentsDir);
-      } else if (stat2.isDirectory()) {
-        return;
-      }
-    } catch {
-    }
-    await symlink(agentSourceDir, globalAgentsDir, DIR_SYMLINK_TYPE2);
-    created.push("agent: cleo-subagent (symlinked)");
-  } catch (_err) {
-    try {
-      await mkdir16(globalAgentsDir, { recursive: true });
-      const files = readdirSync33(agentSourceDir);
-      for (const file2 of files) {
-        await copyFile3(join100(agentSourceDir, file2), join100(globalAgentsDir, file2));
-      }
-      created.push("agent: cleo-subagent (copied)");
-    } catch (copyErr) {
-      warnings.push(
-        `Agent definition install: ${copyErr instanceof Error ? copyErr.message : String(copyErr)}`
-      );
-    }
-  }
-}
-async function initNexusRegistration(projectRoot, created, warnings) {
-  try {
-    const { nexusReconcile: nexusReconcile2 } = await Promise.resolve().then(() => (init_registry3(), registry_exports3));
-    const result = await nexusReconcile2(projectRoot);
-    if (result.status === "auto_registered") {
-      created.push("NEXUS registration (auto-registered new project)");
-    } else if (result.status === "path_updated") {
-      created.push(`NEXUS registration (path updated: ${result.oldPath} \u2192 ${result.newPath})`);
-    } else if (result.status === "ok") {
-      created.push("NEXUS registration (project verified and active)");
-    }
-  } catch (err) {
-    const errStr = String(err);
-    if (errStr.includes("NEXUS_PROJECT_EXISTS")) {
-      warnings.push("NEXUS registration: Project already registered");
-    } else if (errStr.includes("NEXUS_REGISTRY_CORRUPT")) {
-      warnings.push(
-        `NEXUS registration: Identity conflict - ${err instanceof Error ? err.message : errStr}. Run 'cleo nexus unregister' and re-register.`
-      );
-    } else {
-      warnings.push(`NEXUS registration: ${err instanceof Error ? err.message : errStr}`);
-    }
-  }
-}
-async function installGitHubTemplates(projectRoot, created, skipped) {
-  if (!existsSync99(join100(projectRoot, ".git"))) {
-    return;
-  }
-  const githubDir = join100(projectRoot, ".github");
-  const issueTemplateDir = join100(githubDir, "ISSUE_TEMPLATE");
-  const packageRoot = getPackageRoot();
-  const templateSrcDir = join100(packageRoot, "templates", "github");
-  if (!existsSync99(templateSrcDir)) {
-    return;
-  }
-  await mkdir16(issueTemplateDir, { recursive: true });
-  const issueSrcDir = join100(templateSrcDir, "ISSUE_TEMPLATE");
-  if (existsSync99(issueSrcDir)) {
-    const issueFiles = readdirSync33(issueSrcDir);
-    for (const file2 of issueFiles) {
-      const dest = join100(issueTemplateDir, file2);
-      if (existsSync99(dest)) {
-        skipped.push(`.github/ISSUE_TEMPLATE/${file2}`);
-        continue;
-      }
-      const content = readFileSync73(join100(issueSrcDir, file2), "utf-8");
-      await writeFile11(dest, content, "utf-8");
-      created.push(`.github/ISSUE_TEMPLATE/${file2}`);
-    }
-  }
-  const prTemplateSrc = join100(templateSrcDir, "pull_request_template.md");
-  const prTemplateDest = join100(githubDir, "pull_request_template.md");
-  if (existsSync99(prTemplateSrc)) {
-    if (existsSync99(prTemplateDest)) {
-      skipped.push(".github/pull_request_template.md");
-    } else {
-      const content = readFileSync73(prTemplateSrc, "utf-8");
-      await writeFile11(prTemplateDest, content, "utf-8");
-      created.push(".github/pull_request_template.md");
-    }
-  }
-}
-async function initProject(opts = {}) {
-  const cleoDir = getCleoDirAbsolute();
-  const projRoot = getProjectRoot();
-  const alreadyInitialized = existsSync99(cleoDir) && (existsSync99(join100(cleoDir, "tasks.db")) || existsSync99(join100(cleoDir, "config.json")));
-  if (alreadyInitialized && !opts.force) {
-    throw new CleoError(
-      1 /* GENERAL_ERROR */,
-      "Project already initialized. DANGER ZONE: use --force to wipe and re-init.",
-      { fix: "cleo init --force" }
-    );
-  }
-  const force = !!opts.force;
-  const created = [];
-  const skipped = [];
-  const warnings = [];
-  const structureResult = await ensureCleoStructure(projRoot);
-  if (structureResult.action === "created") {
-    created.push(".cleo/ directory structure");
-  }
-  const configResult = await ensureConfig(projRoot, { force });
-  if (configResult.action === "skipped") {
-    skipped.push("config.json");
-  } else {
-    created.push("config.json");
-  }
-  try {
-    const { getDb: getDb3 } = await Promise.resolve().then(() => (init_sqlite2(), sqlite_exports));
-    await getDb3(join100(cleoDir, ".."));
-    created.push("tasks.db");
-  } catch (err) {
-    created.push(`tasks.db (deferred: ${err instanceof Error ? err.message : String(err)})`);
-  }
-  try {
-    const brainResult = await ensureBrainDb(projRoot);
-    if (brainResult.action === "created") {
-      created.push("brain.db");
-    }
-  } catch (err) {
-    created.push(`brain.db (deferred: ${err instanceof Error ? err.message : String(err)})`);
-  }
-  if (force) {
-    const gitignoreResult = await ensureGitignore(projRoot);
-    if (gitignoreResult.action === "skipped") {
-      skipped.push(".gitignore");
-    } else {
-      created.push(".gitignore");
-    }
-  } else {
-    const gitignorePath = join100(cleoDir, ".gitignore");
-    if (existsSync99(gitignorePath)) {
-      skipped.push(".gitignore");
-    } else {
-      const gitignoreResult = await ensureGitignore(projRoot);
-      if (gitignoreResult.action !== "skipped") {
-        created.push(".gitignore");
-      } else {
-        skipped.push(".gitignore");
-      }
-    }
-  }
-  const legacySequencePath = join100(cleoDir, ".sequence");
-  try {
-    await unlink4(legacySequencePath);
-  } catch {
-  }
-  const legacySequenceJsonPath = join100(cleoDir, ".sequence.json");
-  try {
-    await unlink4(legacySequenceJsonPath);
-  } catch {
-  }
-  try {
-    const gitRepoResult = await ensureCleoGitRepo(projRoot);
-    if (gitRepoResult.action === "created") {
-      created.push(".cleo/.git (isolated checkpoint repository)");
-    }
-  } catch (err) {
-    warnings.push(
-      `Could not initialize .cleo/.git: ${err instanceof Error ? err.message : String(err)}`
-    );
-  }
-  try {
-    const migrationResult = migrateAgentOutputs(projRoot, cleoDir);
-    if (migrationResult.migrated) {
-      created.push(`agent-outputs migration: ${migrationResult.summary}`);
-    }
-  } catch {
-    warnings.push("Agent-outputs migration failed (best-effort, run cleo upgrade to retry)");
-  }
-  try {
-    const schemaResult = ensureGlobalSchemas({ force });
-    const total = schemaResult.installed + schemaResult.updated;
-    if (total > 0) {
-      created.push(`schemas/ (${total} files)`);
-    }
-  } catch (err) {
-    warnings.push(`Schema installation: ${err instanceof Error ? err.message : String(err)}`);
-  }
-  try {
-    const hooksResult = await ensureGitHooks(projRoot, { force });
-    if (hooksResult.action === "created") {
-      created.push(hooksResult.details ?? "git hooks installed");
-    } else if (hooksResult.action === "skipped" && hooksResult.details?.includes("No .git/")) {
-      warnings.push(hooksResult.details);
-    } else if (hooksResult.action === "skipped" && hooksResult.details?.includes("not found in package root")) {
-      warnings.push(hooksResult.details);
-    } else if (hooksResult.action === "repaired" && hooksResult.details?.includes("error")) {
-      const match = hooksResult.details.match(/Installed (\d+)/);
-      if (match && parseInt(match[1], 10) > 0) {
-        created.push(`git hooks (${match[1]} installed)`);
-      }
-      warnings.push(hooksResult.details);
-    }
-  } catch (err) {
-    warnings.push(`Git hook installation: ${err instanceof Error ? err.message : String(err)}`);
-  }
-  const projectInfoResult = await ensureProjectInfo(projRoot, { force });
-  if (projectInfoResult.action === "skipped") {
-    skipped.push("project-info.json");
-  } else {
-    created.push("project-info.json");
-  }
-  try {
-    const detectResult = await ensureProjectContext(projRoot, { force: !!opts.detect });
-    if (detectResult.action !== "skipped") {
-      created.push("project-context.json");
-    }
-  } catch (err) {
-    warnings.push(`Project detection failed: ${err instanceof Error ? err.message : String(err)}`);
-  }
-  if (opts.mapCodebase) {
-    try {
-      const { mapCodebase: mapCodebase2 } = await Promise.resolve().then(() => (init_codebase_map(), codebase_map_exports));
-      const mapResult = await mapCodebase2(projRoot, { storeToBrain: true });
-      created.push(
-        `codebase-map: ${mapResult.stack.languages.length} languages, ${mapResult.architecture.layers.length} layers analyzed`
-      );
-    } catch (err) {
-      warnings.push(`Codebase mapping: ${err instanceof Error ? err.message : String(err)}`);
-    }
-  }
-  try {
-    const bridgeResult = await writeMemoryBridge(projRoot);
-    if (bridgeResult.written) {
-      created.push("memory-bridge.md");
-    }
-  } catch (err) {
-    warnings.push(`Memory bridge: ${err instanceof Error ? err.message : String(err)}`);
-  }
-  try {
-    const injectionResult = await ensureInjection(projRoot);
-    if (injectionResult.action !== "skipped") {
-      if (injectionResult.details) {
-        created.push(`injection: ${injectionResult.details}`);
-      }
-    } else if (injectionResult.details) {
-      warnings.push(injectionResult.details);
-    }
-  } catch (err) {
-    warnings.push(`CAAMP injection: ${err instanceof Error ? err.message : String(err)}`);
-  }
-  try {
-    const { ensureContributorMcp: ensureContributorMcp2 } = await Promise.resolve().then(() => (init_scaffold(), scaffold_exports));
-    const mcpResult = await ensureContributorMcp2(projRoot);
-    if (mcpResult.action !== "skipped") {
-      created.push(`contributor MCP: ${mcpResult.details ?? mcpResult.action}`);
-    }
-  } catch (err) {
-    warnings.push(`Contributor MCP setup: ${err instanceof Error ? err.message : String(err)}`);
-  }
-  await initAgentDefinition(created, warnings);
-  await initNexusRegistration(projRoot, created, warnings);
-  try {
-    const { AdapterManager: AdapterManager2 } = await Promise.resolve().then(() => (init_adapters(), adapters_exports));
-    const mgr = AdapterManager2.getInstance(projRoot);
-    const manifests = mgr.discover();
-    if (manifests.length > 0) {
-      created.push(`adapters: ${manifests.length} adapter(s) discovered`);
-      const detected = mgr.detectActive();
-      if (detected.length > 0) {
-        created.push(`adapters: active provider detected (${detected.join(", ")})`);
-        for (const adapterId of detected) {
-          try {
-            const adapter = await mgr.activate(adapterId);
-            const installResult = await adapter.install.install({
-              projectDir: projRoot
-            });
-            if (installResult.success) {
-              created.push(`adapter install (${adapterId}): installed`);
-            } else {
-              warnings.push(`adapter install (${adapterId}): failed`);
-            }
-          } catch (err) {
-            warnings.push(
-              `adapter activate/install (${adapterId}): ${err instanceof Error ? err.message : String(err)}`
-            );
-          }
-        }
-      }
-    }
-  } catch (err) {
-    warnings.push(`Adapter discovery: ${err instanceof Error ? err.message : String(err)}`);
-  }
-  try {
-    await installGitHubTemplates(projRoot, created, skipped);
-  } catch (err) {
-    warnings.push(`GitHub templates: ${err instanceof Error ? err.message : String(err)}`);
-  }
-  const rootGitignoreResult = await removeCleoFromRootGitignore(projRoot);
-  if (rootGitignoreResult.removed) {
-    warnings.push(
-      ".cleo/ was found in root .gitignore and has been removed. CLEO uses .cleo/.gitignore for selective tracking."
-    );
-  }
-  return {
-    initialized: true,
-    directory: cleoDir,
-    created,
-    skipped,
-    warnings
-  };
-}
-function isAutoInitEnabled() {
-  return process.env.CLEO_AUTO_INIT === "true";
-}
-async function ensureInitialized(projectRoot) {
-  const root = projectRoot ?? getProjectRoot();
-  const cleoDir = join100(root, ".cleo");
-  const isInit = existsSync99(cleoDir) && (existsSync99(join100(cleoDir, "tasks.db")) || existsSync99(join100(cleoDir, "config.json")));
-  if (isInit) {
-    return { initialized: true };
-  }
-  if (isAutoInitEnabled()) {
-    await initProject({ name: basename17(root) });
-    return { initialized: true };
-  }
-  throw new Error("CLEO project not initialized. Run system.init or set CLEO_AUTO_INIT=true");
-}
-async function getVersion2(projectRoot) {
-  const root = projectRoot ?? getProjectRoot();
-  const versionPaths = [join100(root, "VERSION"), join100(root, "..", "VERSION")];
-  for (const versionPath of versionPaths) {
-    try {
-      const content = await readFile17(versionPath, "utf-8");
-      const version2 = content.trim();
-      if (version2) {
-        return { version: version2 };
-      }
-    } catch {
-    }
-  }
-  const pkg = await readJson(join100(root, "package.json"));
-  if (pkg?.version) {
-    return { version: pkg.version };
-  }
-  return { version: "0.0.0" };
-}
-
-// packages/core/src/index.ts
+init_init();
 init_json_schema_validator();
 init_logger();
 
@@ -62346,6 +62494,219 @@ function getProjectInfoSync(cwd) {
 init_scaffold();
 init_adapters();
 
+// packages/core/src/bootstrap.ts
+init_paths();
+init_scaffold();
+import { existsSync as existsSync102, readFileSync as readFileSync76 } from "node:fs";
+import { mkdir as mkdir17, readFile as readFile19, writeFile as writeFile12 } from "node:fs/promises";
+import { homedir as homedir6 } from "node:os";
+import { join as join103 } from "node:path";
+async function bootstrapGlobalCleo(options) {
+  const ctx = {
+    created: [],
+    warnings: [],
+    isDryRun: options?.dryRun ?? false
+  };
+  try {
+    await ensureGlobalHome();
+  } catch {
+  }
+  await ensureGlobalTemplatesBootstrap(ctx, options?.packageRoot);
+  await injectAgentsHub(ctx);
+  await installMcpToProviders(ctx);
+  await installSkillsGlobally(ctx);
+  await installAgentDefinitionGlobally(ctx);
+  await installProviderAdapters(ctx, options?.packageRoot);
+  return ctx;
+}
+async function ensureGlobalTemplatesBootstrap(ctx, packageRootOverride) {
+  const globalTemplatesDir = getCleoTemplatesDir();
+  if (!ctx.isDryRun) {
+    await mkdir17(globalTemplatesDir, { recursive: true });
+  }
+  try {
+    const pkgRoot = packageRootOverride ?? getPackageRoot();
+    const templatePath = join103(pkgRoot, "templates", "CLEO-INJECTION.md");
+    if (existsSync102(templatePath)) {
+      const content = readFileSync76(templatePath, "utf-8");
+      const destPath = join103(globalTemplatesDir, "CLEO-INJECTION.md");
+      if (!ctx.isDryRun) {
+        await writeFile12(destPath, content);
+      }
+      ctx.created.push(
+        `~/.cleo/templates/CLEO-INJECTION.md (${ctx.isDryRun ? "would refresh" : "refreshed"})`
+      );
+    } else {
+      try {
+        const { getInjectionTemplateContent: getInjectionTemplateContent2 } = await Promise.resolve().then(() => (init_injection(), injection_exports));
+        const content = getInjectionTemplateContent2();
+        if (content) {
+          const destPath = join103(globalTemplatesDir, "CLEO-INJECTION.md");
+          if (!ctx.isDryRun) {
+            await writeFile12(destPath, content);
+          }
+          ctx.created.push(
+            `~/.cleo/templates/CLEO-INJECTION.md (${ctx.isDryRun ? "would refresh" : "refreshed"} from embedded)`
+          );
+        }
+      } catch {
+        ctx.warnings.push("Could not refresh CLEO-INJECTION.md template");
+      }
+    }
+  } catch {
+    ctx.warnings.push("Could not refresh CLEO-INJECTION.md template");
+  }
+}
+async function injectAgentsHub(ctx) {
+  const globalAgentsDir = getAgentsHome();
+  const globalAgentsMd = join103(globalAgentsDir, "AGENTS.md");
+  try {
+    const { inject: inject2, getInstalledProviders: getInstalledProviders3, injectAll: injectAll2, buildInjectionContent } = await import("@cleocode/caamp");
+    if (!ctx.isDryRun) {
+      await mkdir17(globalAgentsDir, { recursive: true });
+      if (existsSync102(globalAgentsMd)) {
+        const content = await readFile19(globalAgentsMd, "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 ? `${stripped}
+` : "", "utf8");
+      }
+      const expectedContent = "@~/.cleo/templates/CLEO-INJECTION.md";
+      const action = await inject2(globalAgentsMd, expectedContent);
+      ctx.created.push(`~/.agents/AGENTS.md (${action})`);
+    } else {
+      ctx.created.push("~/.agents/AGENTS.md (would create/update CAAMP block)");
+    }
+    const providers = getInstalledProviders3();
+    if (providers.length === 0) {
+      ctx.warnings.push("No AI provider installations detected");
+    } else {
+      const injectionContent = buildInjectionContent({
+        references: ["@~/.agents/AGENTS.md"]
+      });
+      if (!ctx.isDryRun) {
+        for (const provider of providers) {
+          const instructFilePath = join103(provider.pathGlobal, provider.instructFile);
+          if (existsSync102(instructFilePath)) {
+            const fileContent = await readFile19(instructFilePath, "utf8");
+            const stripped = fileContent.replace(
+              /\n?<!-- CLEO:START[^>]*-->[\s\S]*?<!-- CLEO:END -->\n?/g,
+              ""
+            );
+            if (stripped !== fileContent) {
+              await writeFile12(instructFilePath, stripped, "utf8");
+            }
+          }
+        }
+        const results = await injectAll2(providers, homedir6(), "global", injectionContent);
+        for (const [filePath, action] of results) {
+          const displayPath = filePath.replace(homedir6(), "~");
+          ctx.created.push(`${displayPath} (${action})`);
+        }
+      } else {
+        for (const p of providers) {
+          const displayPath = join103(p.pathGlobal, p.instructFile).replace(homedir6(), "~");
+          ctx.created.push(`${displayPath} (would update CAAMP block)`);
+        }
+      }
+    }
+  } catch (err) {
+    ctx.warnings.push(`CAAMP injection: ${err instanceof Error ? err.message : String(err)}`);
+  }
+}
+async function installMcpToProviders(ctx) {
+  try {
+    const { detectEnvMode: detectEnvMode2, generateMcpServerEntry: generateMcpServerEntry2, getMcpServerName: getMcpServerName2 } = await Promise.resolve().then(() => (init_mcp(), mcp_exports));
+    const { getInstalledProviders: getInstalledProviders3, installMcpServerToAll } = await import("@cleocode/caamp");
+    const env = detectEnvMode2();
+    const serverEntry = generateMcpServerEntry2(env);
+    const serverName = getMcpServerName2(env);
+    const providers = getInstalledProviders3();
+    if (providers.length > 0) {
+      if (!ctx.isDryRun) {
+        const results = await installMcpServerToAll(
+          providers,
+          serverName,
+          serverEntry,
+          "global",
+          homedir6()
+        );
+        const successes = results.filter((r) => r.success);
+        if (successes.length > 0) {
+          ctx.created.push(
+            `MCP configs: ${successes.map((r) => r.provider.id).join(", ")}`
+          );
+        }
+      } else {
+        ctx.created.push("MCP configs (would update)");
+      }
+    }
+  } catch {
+    ctx.warnings.push("MCP config update skipped (non-critical)");
+  }
+}
+async function installSkillsGlobally(ctx) {
+  try {
+    if (!ctx.isDryRun) {
+      const { initCoreSkills: initCoreSkills2 } = await Promise.resolve().then(() => (init_init(), init_exports));
+      await initCoreSkills2(ctx.created, ctx.warnings);
+    } else {
+      ctx.created.push("core skills (would install/update)");
+    }
+  } catch (err) {
+    ctx.warnings.push(
+      `Core skills installation failed: ${err instanceof Error ? err.message : String(err)}`
+    );
+  }
+}
+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: ${err instanceof Error ? err.message : String(err)}`
+    );
+  }
+}
+async function installProviderAdapters(ctx, packageRootOverride) {
+  try {
+    const { AdapterManager: AdapterManager2 } = await Promise.resolve().then(() => (init_adapters(), adapters_exports));
+    const pkgRoot = packageRootOverride ?? getPackageRoot();
+    const manager = AdapterManager2.getInstance(pkgRoot);
+    manager.discover();
+    const detected = manager.detectActive();
+    for (const adapterId of detected) {
+      try {
+        const adapter = await manager.activate(adapterId);
+        if (adapter.install) {
+          if (!ctx.isDryRun) {
+            const installResult = await adapter.install.install({
+              projectDir: process.cwd()
+            });
+            if (installResult.success) {
+              ctx.created.push(`${adapterId} adapter (installed)`);
+            }
+          } else {
+            ctx.created.push(`${adapterId} adapter (would install)`);
+          }
+        }
+      } catch (activateErr) {
+        ctx.warnings.push(
+          `Adapter ${adapterId} skipped: ${activateErr instanceof Error ? activateErr.message : String(activateErr)}`
+        );
+      }
+    }
+  } catch (err) {
+    ctx.warnings.push(
+      `Adapter install skipped: ${err instanceof Error ? err.message : String(err)}`
+    );
+  }
+}
+
 // packages/core/src/cleo.ts
 import path from "node:path";
 init_brain_retrieval();
@@ -62632,6 +62993,7 @@ export {
   agentTypeSchema,
   agents_exports as agents,
   archiveTasks,
+  bootstrapGlobalCleo,
   brainConfidenceLevelSchema,
   brainDecisionTypeSchema,
   brainEdgeTypeSchema,