@codebyplan/cli 2.0.1 → 2.1.0

package/README.md

@@ -71,6 +71,17 @@ claude mcp add codebyplan -e CODEBYPLAN_API_KEY=your_key_here -- npx -y @codebyp
 |------|-------------|
 | `health_check` | Check server version, API connectivity, and latency |
 
+### Settings File Model
+
+The `sync_claude_files` tool writes a `settings.json` file to the project's `.claude/` directory. This file contains shared settings (hooks, statusLine, attribution, permissions.deny/ask/additionalDirectories) merged from global and repo-specific scopes in the database.
+
+A separate `settings.local.json` file (not managed by sync) holds local-only configuration: `permissions.allow` and MCP server definitions. Claude Code merges both files at runtime, with `settings.local.json` taking precedence.
+
+| File | Managed By | Contains |
+|------|------------|----------|
+| `settings.json` | `sync_claude_files` (synced from DB) | Shared settings: hooks, statusLine, attribution, permissions.deny/ask/additionalDirectories |
+| `settings.local.json` | User (local-only) | Machine-specific: permissions.allow, MCP server config |
+
 ## Environment Variables
 
 | Variable | Required | Description |

package/dist/cli.js

@@ -37,7 +37,7 @@ var VERSION, PACKAGE_NAME;
 var init_version = __esm({
   "src/lib/version.ts"() {
     "use strict";
-    VERSION = "2.0.1";
+    VERSION = "2.1.0";
     PACKAGE_NAME = "@codebyplan/cli";
   }
 });
@@ -49,7 +49,52 @@ __export(setup_exports, {
 });
 import { createInterface } from "node:readline/promises";
 import { stdin, stdout } from "node:process";
-import { execFile } from "node:child_process";
+import { readFile, writeFile } from "node:fs/promises";
+import { homedir } from "node:os";
+import { join } from "node:path";
+function getConfigPath(scope) {
+  return scope === "user" ? join(homedir(), ".claude.json") : join(process.cwd(), ".mcp.json");
+}
+async function readConfig(path) {
+  try {
+    const raw = await readFile(path, "utf-8");
+    const parsed = JSON.parse(raw);
+    if (typeof parsed === "object" && parsed !== null && !Array.isArray(parsed)) {
+      return parsed;
+    }
+    return {};
+  } catch {
+    return {};
+  }
+}
+function buildMcpEntry(apiKey) {
+  return {
+    command: "npx",
+    args: ["-y", PACKAGE_NAME],
+    env: { CODEBYPLAN_API_KEY: apiKey }
+  };
+}
+async function writeMcpConfig(scope, apiKey) {
+  const configPath = getConfigPath(scope);
+  const config2 = await readConfig(configPath);
+  if (typeof config2.mcpServers !== "object" || config2.mcpServers === null || Array.isArray(config2.mcpServers)) {
+    config2.mcpServers = {};
+  }
+  config2.mcpServers.codebyplan = buildMcpEntry(apiKey);
+  await writeFile(configPath, JSON.stringify(config2, null, 2) + "\n", "utf-8");
+  return configPath;
+}
+async function verifyMcpConfig(scope, apiKey) {
+  try {
+    const config2 = await readConfig(getConfigPath(scope));
+    const servers = config2.mcpServers;
+    if (!servers) return false;
+    const entry = servers.codebyplan;
+    return entry?.env?.CODEBYPLAN_API_KEY === apiKey;
+  } catch {
+    return false;
+  }
+}
 async function runSetup() {
   const rl = createInterface({ input: stdin, output: stdout });
   console.log("\n  CodeByPlan MCP Server Setup\n");
@@ -76,53 +121,38 @@ async function runSetup() {
       console.log(`  Warning: API returned status ${res.status}, but continuing.
 `);
     } else {
-      console.log("  API key is valid!\n");
-    }
-    const addCmd = `claude mcp add --scope user codebyplan -e CODEBYPLAN_API_KEY=${apiKey} -- npx -y ${PACKAGE_NAME}`;
-    console.log("  Run this command to add the MCP server to Claude Code:\n");
-    console.log(`  ${addCmd}
-`);
-    const autoAdd = (await rl.question("  Run it now? (Y/n): ")).trim().toLowerCase();
-    if (autoAdd === "" || autoAdd === "y" || autoAdd === "yes") {
-      console.log("\n  Adding MCP server to Claude Code...\n");
-      await new Promise((resolve2) => {
-        execFile("claude", ["mcp", "remove", "--scope", "user", "codebyplan"], () => resolve2());
-      });
-      await new Promise((resolve2) => {
-        execFile(
-          "claude",
-          [
-            "mcp",
-            "add",
-            "--scope",
-            "user",
-            "codebyplan",
-            "-e",
-            `CODEBYPLAN_API_KEY=${apiKey}`,
-            "--",
-            "npx",
-            "-y",
-            PACKAGE_NAME
-          ],
-          (err, _stdout, stderr) => {
-            if (err) {
-              console.log(`  Could not run 'claude mcp add' automatically.`);
-              console.log(`  Error: ${stderr || err.message}`);
-              console.log(`
-  Run it manually:
-  ${addCmd}
+      try {
+        const body = await res.json();
+        if (Array.isArray(body.data) && body.data.length === 0) {
+          console.log("  API key is valid but no repositories found.");
+          console.log("  Create one at https://codebyplan.com after setup.\n");
+        } else {
+          console.log("  API key is valid!\n");
+        }
+      } catch {
+        console.log("  API key is valid!\n");
+      }
+    }
+    console.log("  Where should the MCP server be configured?\n");
+    console.log("    1. Global \u2014 available in all projects (~/.claude.json)");
+    console.log("    2. Project \u2014 only this project (.mcp.json)\n");
+    const scopeInput = (await rl.question("  Select (1/2, default: 1): ")).trim();
+    const scope = scopeInput === "2" ? "project" : "user";
+    console.log("\n  Configuring MCP server...");
+    const configPath = await writeMcpConfig(scope, apiKey);
+    const verified = await verifyMcpConfig(scope, apiKey);
+    if (verified) {
+      console.log(`  Done! Config written to ${configPath}
 `);
-              resolve2();
-            } else {
-              console.log("  Done! CodeByPlan MCP server is now configured.\n");
-              console.log("  Start a new Claude Code session to begin using it.\n");
-              resolve2();
-            }
-          }
-        );
-      });
+      if (scope === "project") {
+        console.log("  Note: .mcp.json contains your API key \u2014 add it to .gitignore.\n");
+      }
+      console.log("  Start a new Claude Code session to begin using it.\n");
     } else {
-      console.log("\n  Run the command above when you're ready.\n");
+      console.log("  Warning: Could not verify the saved configuration.\n");
+      console.log("  You can configure manually by adding to your Claude config:\n");
+      console.log(`  claude mcp add codebyplan -e CODEBYPLAN_API_KEY=${apiKey} -- npx -y ${PACKAGE_NAME}
+`);
     }
   } finally {
     rl.close();
@@ -136,8 +166,8 @@ var init_setup = __esm({
 });
 
 // src/cli/config.ts
-import { readFile } from "node:fs/promises";
-import { join } from "node:path";
+import { readFile as readFile2 } from "node:fs/promises";
+import { join as join2 } from "node:path";
 function parseFlags(startIndex) {
   const flags = {};
   const args = process.argv.slice(startIndex);
@@ -159,8 +189,8 @@ async function resolveConfig(flags) {
   let worktreeId = flags["worktree-id"] ?? process.env.CODEBYPLAN_WORKTREE_ID;
   if (!repoId || !worktreeId) {
     try {
-      const configPath = join(projectPath, ".codebyplan.json");
-      const raw = await readFile(configPath, "utf-8");
+      const configPath = join2(projectPath, ".codebyplan.json");
+      const raw = await readFile2(configPath, "utf-8");
       const config2 = JSON.parse(raw);
       if (!repoId) repoId = config2.repo_id;
       if (!worktreeId) worktreeId = config2.worktree_id;
@@ -354,7 +384,36 @@ function mergeSettings(template, local) {
   }
   return merged;
 }
-var TEMPLATE_MANAGED_KEYS, TEMPLATE_MANAGED_PERMISSION_KEYS;
+function mergeGlobalAndRepoSettings(global, repo) {
+  const merged = { ...global, ...repo };
+  const globalPerms = global.permissions && typeof global.permissions === "object" ? global.permissions : {};
+  const repoPerms = repo.permissions && typeof repo.permissions === "object" ? repo.permissions : {};
+  if (Object.keys(globalPerms).length > 0 || Object.keys(repoPerms).length > 0) {
+    const mergedPerms = { ...globalPerms, ...repoPerms };
+    for (const key of ARRAY_PERMISSION_KEYS) {
+      const globalArr = Array.isArray(globalPerms[key]) ? globalPerms[key] : [];
+      const repoArr = Array.isArray(repoPerms[key]) ? repoPerms[key] : [];
+      if (globalArr.length > 0 || repoArr.length > 0) {
+        mergedPerms[key] = [.../* @__PURE__ */ new Set([...globalArr, ...repoArr])];
+      }
+    }
+    merged.permissions = mergedPerms;
+  }
+  return merged;
+}
+function stripPermissionsAllow(settings) {
+  if (!settings.permissions || typeof settings.permissions !== "object") {
+    return settings;
+  }
+  const perms = { ...settings.permissions };
+  delete perms.allow;
+  if (Object.keys(perms).length === 0) {
+    const { permissions: _, ...rest } = settings;
+    return rest;
+  }
+  return { ...settings, permissions: perms };
+}
+var TEMPLATE_MANAGED_KEYS, TEMPLATE_MANAGED_PERMISSION_KEYS, ARRAY_PERMISSION_KEYS;
 var init_settings_merge = __esm({
   "src/lib/settings-merge.ts"() {
     "use strict";
@@ -368,12 +427,13 @@ var init_settings_merge = __esm({
       "ask",
       "additionalDirectories"
     ];
+    ARRAY_PERMISSION_KEYS = ["deny", "ask"];
   }
 });
 
 // src/lib/hook-registry.ts
-import { readdir, readFile as readFile2 } from "node:fs/promises";
-import { join as join2 } from "node:path";
+import { readdir, readFile as readFile3 } from "node:fs/promises";
+import { join as join3 } from "node:path";
 function parseHookMeta(content) {
   const match = content.match(/^#\s*@hook:\s*(\S+)(?:\s+(.+))?$/m);
   if (!match) return null;
@@ -392,7 +452,7 @@ async function discoverHooks(hooksDir) {
     return discovered;
   }
   for (const filename of filenames) {
-    const content = await readFile2(join2(hooksDir, filename), "utf-8");
+    const content = await readFile3(join3(hooksDir, filename), "utf-8");
     const meta = parseHookMeta(content);
     if (meta) {
       discovered.set(filename.replace(/\.sh$/, ""), meta);
@@ -430,6 +490,25 @@ function mergeDiscoveredHooks(existing, discovered, hooksRelPath = ".claude/hook
   }
   return merged;
 }
+function stripDiscoveredHooks(config2, hooksRelPath = ".claude/hooks") {
+  const prefix = `bash ${hooksRelPath}/`;
+  const stripped = {};
+  for (const [event, matchers] of Object.entries(config2)) {
+    const filteredMatchers = [];
+    for (const matcher of matchers) {
+      const filteredHooks = matcher.hooks.filter(
+        (h) => !(h.command && h.command.startsWith(prefix) && h.command.endsWith(".sh"))
+      );
+      if (filteredHooks.length > 0) {
+        filteredMatchers.push({ matcher: matcher.matcher, hooks: filteredHooks });
+      }
+    }
+    if (filteredMatchers.length > 0) {
+      stripped[event] = filteredMatchers;
+    }
+  }
+  return stripped;
+}
 var init_hook_registry = __esm({
   "src/lib/hook-registry.ts"() {
     "use strict";
@@ -478,38 +557,38 @@ var init_variables = __esm({
 });
 
 // src/lib/sync-engine.ts
-import { readdir as readdir2, readFile as readFile3, writeFile, unlink, mkdir, rmdir, chmod, stat } from "node:fs/promises";
-import { join as join3, dirname } from "node:path";
+import { readdir as readdir2, readFile as readFile4, writeFile as writeFile2, unlink, mkdir, rmdir, chmod, stat } from "node:fs/promises";
+import { join as join4, dirname } from "node:path";
 function getTypeDir(claudeDir, dir) {
-  if (dir === "commands") return join3(claudeDir, dir, "cbp");
-  return join3(claudeDir, dir);
+  if (dir === "commands") return join4(claudeDir, dir, "cbp");
+  return join4(claudeDir, dir);
 }
 function getFilePath(claudeDir, typeName, file) {
   const cfg = typeConfig[typeName];
   const typeDir = getTypeDir(claudeDir, cfg.dir);
   if (cfg.subfolder) {
-    return join3(typeDir, file.name, `${cfg.subfolder}${cfg.ext}`);
+    return join4(typeDir, file.name, `${cfg.subfolder}${cfg.ext}`);
   }
   if (typeName === "command" && file.category) {
-    return join3(typeDir, file.category, `${file.name}${cfg.ext}`);
+    return join4(typeDir, file.category, `${file.name}${cfg.ext}`);
   }
   if (typeName === "template") {
-    return join3(typeDir, file.name);
+    return join4(typeDir, file.name);
   }
-  return join3(typeDir, `${file.name}${cfg.ext}`);
+  return join4(typeDir, `${file.name}${cfg.ext}`);
 }
 async function readDirRecursive(dir, base = dir) {
   const result = /* @__PURE__ */ new Map();
   try {
     const entries = await readdir2(dir, { withFileTypes: true });
     for (const entry of entries) {
-      const fullPath = join3(dir, entry.name);
+      const fullPath = join4(dir, entry.name);
       if (entry.isDirectory()) {
         const sub = await readDirRecursive(fullPath, base);
         for (const [k, v] of sub) result.set(k, v);
       } else {
         const relPath = fullPath.slice(base.length + 1);
-        const fileContent = await readFile3(fullPath, "utf-8");
+        const fileContent = await readFile4(fullPath, "utf-8");
         result.set(relPath, fileContent);
       }
     }
@@ -519,7 +598,7 @@ async function readDirRecursive(dir, base = dir) {
 }
 async function isGitWorktree(projectPath) {
   try {
-    const gitPath = join3(projectPath, ".git");
+    const gitPath = join4(projectPath, ".git");
     const info = await stat(gitPath);
     return info.isFile();
   } catch {
@@ -546,7 +625,7 @@ async function executeSyncToLocal(options) {
   const syncData = syncRes.data;
   const repoData = repoRes.data;
   syncData.claude_md = [];
-  const claudeDir = join3(projectPath, ".claude");
+  const claudeDir = join4(projectPath, ".claude");
   const worktree = await isGitWorktree(projectPath);
   const byType = {};
   const totals = { created: 0, updated: 0, deleted: 0, unchanged: 0 };
@@ -571,19 +650,19 @@ async function executeSyncToLocal(options) {
       remotePathMap.set(relPath, { content: substituted, name: remote.name });
     }
     for (const [relPath, { content, name }] of remotePathMap) {
-      const fullPath = join3(targetDir, relPath);
+      const fullPath = join4(targetDir, relPath);
       const localContent = localFiles.get(relPath);
       if (localContent === void 0) {
         if (!dryRun) {
           await mkdir(dirname(fullPath), { recursive: true });
-          await writeFile(fullPath, content, "utf-8");
+          await writeFile2(fullPath, content, "utf-8");
           if (typeName === "hook") await chmod(fullPath, 493);
         }
         result.created.push(name);
         totals.created++;
       } else if (localContent !== content) {
         if (!dryRun) {
-          await writeFile(fullPath, content, "utf-8");
+          await writeFile2(fullPath, content, "utf-8");
           if (typeName === "hook") await chmod(fullPath, 493);
         }
         result.updated.push(name);
@@ -595,7 +674,7 @@ async function executeSyncToLocal(options) {
     }
     for (const [relPath] of localFiles) {
       if (!remotePathMap.has(relPath)) {
-        const fullPath = join3(targetDir, relPath);
+        const fullPath = join4(targetDir, relPath);
         if (!dryRun) {
           await unlink(fullPath);
           await removeEmptyParents(fullPath, targetDir);
@@ -607,9 +686,65 @@ async function executeSyncToLocal(options) {
     }
     byType[`${typeName}s`] = result;
   }
+  {
+    const typeName = "docs_stack";
+    const syncKey = "docs_stack";
+    const targetDir = join4(projectPath, "docs", "stack");
+    const remoteFiles = syncData[syncKey] ?? [];
+    const result = { created: [], updated: [], deleted: [], unchanged: [] };
+    if (remoteFiles.length > 0 && !dryRun) {
+      await mkdir(targetDir, { recursive: true });
+    }
+    const localFiles = await readDirRecursive(targetDir);
+    const remotePathMap = /* @__PURE__ */ new Map();
+    for (const remote of remoteFiles) {
+      const relPath = remote.category ? join4(remote.category, remote.name) : remote.name;
+      const substituted = substituteVariables(remote.content, repoData);
+      remotePathMap.set(relPath, { content: substituted, name: `${remote.category ?? ""}/${remote.name}` });
+    }
+    for (const [relPath, { content, name }] of remotePathMap) {
+      const fullPath = join4(targetDir, relPath);
+      const localContent = localFiles.get(relPath);
+      if (localContent === void 0) {
+        if (!dryRun) {
+          await mkdir(dirname(fullPath), { recursive: true });
+          await writeFile2(fullPath, content, "utf-8");
+        }
+        result.created.push(name);
+        totals.created++;
+      } else if (localContent !== content) {
+        if (!dryRun) {
+          await writeFile2(fullPath, content, "utf-8");
+        }
+        result.updated.push(name);
+        totals.updated++;
+      } else {
+        result.unchanged.push(name);
+        totals.unchanged++;
+      }
+    }
+    for (const [relPath] of localFiles) {
+      if (!remotePathMap.has(relPath)) {
+        const fullPath = join4(targetDir, relPath);
+        if (!dryRun) {
+          await unlink(fullPath);
+          await removeEmptyParents(fullPath, targetDir);
+        }
+        result.deleted.push(relPath);
+        totals.deleted++;
+      }
+    }
+    byType[typeName] = result;
+  }
+  const globalSettingsFiles = syncData.global_settings ?? [];
+  let globalSettings = {};
+  for (const gf of globalSettingsFiles) {
+    const parsed = JSON.parse(substituteVariables(gf.content, repoData));
+    globalSettings = { ...globalSettings, ...parsed };
+  }
   const specialTypes = {
-    claude_md: () => join3(projectPath, "CLAUDE.md"),
-    settings: () => join3(projectPath, ".claude", "settings.local.json")
+    claude_md: () => join4(projectPath, "CLAUDE.md"),
+    settings: () => join4(projectPath, ".claude", "settings.json")
   };
   for (const [typeName, getPath] of Object.entries(specialTypes)) {
     const remoteFiles = syncData[typeName] ?? [];
@@ -619,29 +754,32 @@ async function executeSyncToLocal(options) {
       const remoteContent = substituteVariables(remote.content, repoData);
       let localContent;
       try {
-        localContent = await readFile3(targetPath, "utf-8");
+        localContent = await readFile4(targetPath, "utf-8");
       } catch {
       }
       if (typeName === "settings") {
-        const templateSettings = JSON.parse(remoteContent);
-        const hooksDir = join3(projectPath, ".claude", "hooks");
+        const repoSettings = JSON.parse(remoteContent);
+        const combinedTemplate = mergeGlobalAndRepoSettings(globalSettings, repoSettings);
+        const hooksDir = join4(projectPath, ".claude", "hooks");
         const discovered = await discoverHooks(hooksDir);
         if (localContent === void 0) {
+          let finalSettings = stripPermissionsAllow(combinedTemplate);
           if (discovered.size > 0) {
-            templateSettings.hooks = mergeDiscoveredHooks(
-              templateSettings.hooks ?? {},
+            finalSettings.hooks = mergeDiscoveredHooks(
+              finalSettings.hooks ?? {},
               discovered
             );
           }
           if (!dryRun) {
             await mkdir(dirname(targetPath), { recursive: true });
-            await writeFile(targetPath, JSON.stringify(templateSettings, null, 2) + "\n", "utf-8");
+            await writeFile2(targetPath, JSON.stringify(finalSettings, null, 2) + "\n", "utf-8");
           }
           result.created.push(remote.name);
           totals.created++;
         } else {
           const localSettings = JSON.parse(localContent);
-          const merged = mergeSettings(templateSettings, localSettings);
+          let merged = mergeSettings(combinedTemplate, localSettings);
+          merged = stripPermissionsAllow(merged);
           if (discovered.size > 0) {
             merged.hooks = mergeDiscoveredHooks(
               merged.hooks ?? {},
@@ -651,7 +789,7 @@ async function executeSyncToLocal(options) {
           const mergedContent = JSON.stringify(merged, null, 2) + "\n";
           if (localContent !== mergedContent) {
             if (!dryRun) {
-              await writeFile(targetPath, mergedContent, "utf-8");
+              await writeFile2(targetPath, mergedContent, "utf-8");
             }
             result.updated.push(remote.name);
             totals.updated++;
@@ -664,13 +802,13 @@ async function executeSyncToLocal(options) {
         if (localContent === void 0) {
           if (!dryRun) {
             await mkdir(dirname(targetPath), { recursive: true });
-            await writeFile(targetPath, remoteContent, "utf-8");
+            await writeFile2(targetPath, remoteContent, "utf-8");
           }
           result.created.push(remote.name);
           totals.created++;
         } else if (localContent !== remoteContent) {
           if (!dryRun) {
-            await writeFile(targetPath, remoteContent, "utf-8");
+            await writeFile2(targetPath, remoteContent, "utf-8");
           }
           result.updated.push(remote.name);
           totals.updated++;
@@ -734,8 +872,8 @@ var init_confirm = __esm({
 });
 
 // src/lib/tech-detect.ts
-import { readFile as readFile4, access } from "node:fs/promises";
-import { join as join4 } from "node:path";
+import { readFile as readFile5, access } from "node:fs/promises";
+import { join as join5 } from "node:path";
 async function fileExists(filePath) {
   try {
     await access(filePath);
@@ -747,7 +885,7 @@ async function fileExists(filePath) {
 async function detectTechStack(projectPath) {
   const seen = /* @__PURE__ */ new Map();
   try {
-    const raw = await readFile4(join4(projectPath, "package.json"), "utf-8");
+    const raw = await readFile5(join5(projectPath, "package.json"), "utf-8");
     const pkg = JSON.parse(raw);
     const allDeps = {
       ...pkg.dependencies,
@@ -766,7 +904,7 @@ async function detectTechStack(projectPath) {
   }
   for (const { file, rule } of CONFIG_FILE_MAP) {
     const key = rule.name.toLowerCase();
-    if (!seen.has(key) && await fileExists(join4(projectPath, file))) {
+    if (!seen.has(key) && await fileExists(join5(projectPath, file))) {
       seen.set(key, { name: rule.name, category: rule.category });
     }
   }
@@ -1022,19 +1160,20 @@ var init_pull = __esm({
 });
 
 // src/cli/fileMapper.ts
-import { readdir as readdir3, readFile as readFile5 } from "node:fs/promises";
-import { join as join5, extname } from "node:path";
+import { readdir as readdir3, readFile as readFile6 } from "node:fs/promises";
+import { join as join6, extname } from "node:path";
 function compositeKey(type, name, category) {
   return category ? `${type}:${category}/${name}` : `${type}:${name}`;
 }
-async function scanLocalFiles(claudeDir) {
+async function scanLocalFiles(claudeDir, projectPath) {
   const result = /* @__PURE__ */ new Map();
-  await scanCommands(join5(claudeDir, "commands", "cbp"), result);
-  await scanSubfolderType(join5(claudeDir, "agents"), "agent", "AGENT.md", result);
-  await scanSubfolderType(join5(claudeDir, "skills"), "skill", "SKILL.md", result);
-  await scanFlatType(join5(claudeDir, "rules"), "rule", ".md", result);
-  await scanFlatType(join5(claudeDir, "hooks"), "hook", ".sh", result);
-  await scanTemplates(join5(claudeDir, "templates"), result);
+  await scanCommands(join6(claudeDir, "commands", "cbp"), result);
+  await scanSubfolderType(join6(claudeDir, "agents"), "agent", "AGENT.md", result);
+  await scanSubfolderType(join6(claudeDir, "skills"), "skill", "SKILL.md", result);
+  await scanFlatType(join6(claudeDir, "rules"), "rule", ".md", result);
+  await scanFlatType(join6(claudeDir, "hooks"), "hook", ".sh", result);
+  await scanTemplates(join6(claudeDir, "templates"), result);
+  await scanSettings(claudeDir, projectPath, result);
   return result;
 }
 async function scanCommands(dir, result) {
@@ -1049,10 +1188,10 @@ async function scanCommandsRecursive(baseDir, currentDir, result) {
   }
   for (const entry of entries) {
     if (entry.isDirectory()) {
-      await scanCommandsRecursive(baseDir, join5(currentDir, entry.name), result);
+      await scanCommandsRecursive(baseDir, join6(currentDir, entry.name), result);
     } else if (entry.isFile() && entry.name.endsWith(".md")) {
       const name = entry.name.slice(0, -3);
-      const content = await readFile5(join5(currentDir, entry.name), "utf-8");
+      const content = await readFile6(join6(currentDir, entry.name), "utf-8");
       const relDir = currentDir.slice(baseDir.length + 1);
       const category = relDir || null;
       const key = compositeKey("command", name, category);
@@ -1069,9 +1208,9 @@ async function scanSubfolderType(dir, type, fileName, result) {
   }
   for (const entry of entries) {
     if (entry.isDirectory()) {
-      const filePath = join5(dir, entry.name, fileName);
+      const filePath = join6(dir, entry.name, fileName);
       try {
-        const content = await readFile5(filePath, "utf-8");
+        const content = await readFile6(filePath, "utf-8");
         const key = compositeKey(type, entry.name, null);
         result.set(key, { type, name: entry.name, category: null, content });
       } catch {
@@ -1089,7 +1228,7 @@ async function scanFlatType(dir, type, ext, result) {
   for (const entry of entries) {
     if (entry.isFile() && entry.name.endsWith(ext)) {
       const name = entry.name.slice(0, -ext.length);
-      const content = await readFile5(join5(dir, entry.name), "utf-8");
+      const content = await readFile6(join6(dir, entry.name), "utf-8");
       const key = compositeKey(type, name, null);
       result.set(key, { type, name, category: null, content });
     }
@@ -1104,15 +1243,49 @@ async function scanTemplates(dir, result) {
   }
   for (const entry of entries) {
     if (entry.isFile() && extname(entry.name)) {
-      const content = await readFile5(join5(dir, entry.name), "utf-8");
+      const content = await readFile6(join6(dir, entry.name), "utf-8");
       const key = compositeKey("template", entry.name, null);
       result.set(key, { type: "template", name: entry.name, category: null, content });
     }
   }
 }
+async function scanSettings(claudeDir, projectPath, result) {
+  const settingsPath = join6(claudeDir, "settings.json");
+  let raw;
+  try {
+    raw = await readFile6(settingsPath, "utf-8");
+  } catch {
+    return;
+  }
+  let parsed;
+  try {
+    parsed = JSON.parse(raw);
+  } catch {
+    return;
+  }
+  parsed = stripPermissionsAllow(parsed);
+  if (parsed.hooks && typeof parsed.hooks === "object") {
+    const hooksDir = projectPath ? join6(projectPath, ".claude", "hooks") : join6(claudeDir, "hooks");
+    const discovered = await discoverHooks(hooksDir);
+    if (discovered.size > 0) {
+      parsed.hooks = stripDiscoveredHooks(
+        parsed.hooks,
+        ".claude/hooks"
+      );
+      if (Object.keys(parsed.hooks).length === 0) {
+        delete parsed.hooks;
+      }
+    }
+  }
+  const content = JSON.stringify(parsed, null, 2) + "\n";
+  const key = compositeKey("settings", "settings", null);
+  result.set(key, { type: "settings", name: "settings", category: null, content });
+}
 var init_fileMapper = __esm({
   "src/cli/fileMapper.ts"() {
     "use strict";
+    init_settings_merge();
+    init_hook_registry();
   }
 });
 
@@ -1190,11 +1363,12 @@ __export(push_exports, {
   runPush: () => runPush
 });
 import { stat as stat2 } from "node:fs/promises";
-import { join as join6 } from "node:path";
+import { join as join7 } from "node:path";
 async function runPush() {
   const flags = parseFlags(3);
   const dryRun = hasFlag("dry-run", 3);
   const force = hasFlag("force", 3);
+  const isGlobal = hasFlag("global", 3);
   validateApiKey();
   const config2 = await resolveConfig(flags);
   const { repoId, projectPath } = config2;
@@ -1205,7 +1379,7 @@ async function runPush() {
   if (dryRun) console.log(`  Mode: dry-run (no changes will be made)`);
   if (force) console.log(`  Mode: force (no conflict prompts)`);
   console.log();
-  const claudeDir = join6(projectPath, ".claude");
+  const claudeDir = join7(projectPath, ".claude");
   try {
     await stat2(claudeDir);
   } catch {
@@ -1213,7 +1387,7 @@ async function runPush() {
     return;
   }
   console.log("  Scanning local files...");
-  const localFiles = await scanLocalFiles(claudeDir);
+  const localFiles = await scanLocalFiles(claudeDir, projectPath);
   console.log(`  Found ${localFiles.size} local files.`);
   console.log("  Fetching remote state...");
   const [syncRes, repoRes] = await Promise.all([
@@ -1302,7 +1476,8 @@ async function runPush() {
       type: f.type,
       name: f.name,
       category: f.category,
-      content: f.content
+      content: f.content,
+      ...f.type === "settings" ? { scope: isGlobal ? "global" : "repo" } : {}
     })),
     delete_keys: toDelete
   });
@@ -1336,7 +1511,8 @@ function flattenSyncData(data) {
     skills: "skill",
     rules: "rule",
     hooks: "hook",
-    templates: "template"
+    templates: "template",
+    settings: "settings"
   };
   for (const [syncKey, typeName] of Object.entries(typeMap)) {
     const files = data[syncKey] ?? [];
@@ -1377,8 +1553,8 @@ __export(init_exports, {
 });
 import { createInterface as createInterface4 } from "node:readline/promises";
 import { stdin as stdin4, stdout as stdout4 } from "node:process";
-import { writeFile as writeFile2, mkdir as mkdir2, chmod as chmod2 } from "node:fs/promises";
-import { join as join7, dirname as dirname2 } from "node:path";
+import { writeFile as writeFile3, mkdir as mkdir2, chmod as chmod2 } from "node:fs/promises";
+import { join as join8, dirname as dirname2 } from "node:path";
 async function runInit() {
   const flags = parseFlags(3);
   const projectPath = flags["path"] ?? process.cwd();
@@ -1417,27 +1593,27 @@ async function runInit() {
       if (match) worktreeId = match.id;
     } catch {
     }
-    const configPath = join7(projectPath, ".codebyplan.json");
+    const configPath = join8(projectPath, ".codebyplan.json");
     const configData = { repo_id: repoId };
     if (worktreeId) configData.worktree_id = worktreeId;
     const configContent = JSON.stringify(configData, null, 2) + "\n";
-    await writeFile2(configPath, configContent, "utf-8");
+    await writeFile3(configPath, configContent, "utf-8");
     console.log(`  Created ${configPath}`);
     const seedAnswer = (await rl.question("\n  Seed with CodeByPlan defaults? (Y/n): ")).trim().toLowerCase();
     if (seedAnswer === "" || seedAnswer === "y" || seedAnswer === "yes") {
       let getFilePath3 = function(typeName, file) {
         const cfg = typeConfig2[typeName];
-        const typeDir = typeName === "command" ? join7(claudeDir, cfg.dir, "cbp") : join7(claudeDir, cfg.dir);
+        const typeDir = typeName === "command" ? join8(claudeDir, cfg.dir, "cbp") : join8(claudeDir, cfg.dir);
         if (cfg.subfolder) {
-          return join7(typeDir, file.name, `${cfg.subfolder}${cfg.ext}`);
+          return join8(typeDir, file.name, `${cfg.subfolder}${cfg.ext}`);
         }
         if (typeName === "command" && file.category) {
-          return join7(typeDir, file.category, `${file.name}${cfg.ext}`);
+          return join8(typeDir, file.category, `${file.name}${cfg.ext}`);
         }
         if (typeName === "template") {
-          return join7(typeDir, file.name);
+          return join8(typeDir, file.name);
         }
-        return join7(typeDir, `${file.name}${cfg.ext}`);
+        return join8(typeDir, `${file.name}${cfg.ext}`);
       };
       var getFilePath2 = getFilePath3;
       console.log("\n  Fetching default files...");
@@ -1452,7 +1628,7 @@ async function runInit() {
         printNextSteps(projectPath);
         return;
       }
-      const claudeDir = join7(projectPath, ".claude");
+      const claudeDir = join8(projectPath, ".claude");
       let written = 0;
       const typeConfig2 = {
         command: { dir: "commands", ext: ".md" },
@@ -1475,7 +1651,7 @@ async function runInit() {
         for (const file of files) {
           const filePath = getFilePath3(typeName, file);
           await mkdir2(dirname2(filePath), { recursive: true });
-          await writeFile2(filePath, file.content, "utf-8");
+          await writeFile3(filePath, file.content, "utf-8");
           if (typeName === "hook") await chmod2(filePath, 493);
           written++;
         }
@@ -1484,16 +1660,16 @@ async function runInit() {
         ...defaultsData.claude_md ?? []
       ];
       for (const file of specialFiles) {
-        const targetPath = join7(projectPath, "CLAUDE.md");
+        const targetPath = join8(projectPath, "CLAUDE.md");
         await mkdir2(dirname2(targetPath), { recursive: true });
-        await writeFile2(targetPath, file.content, "utf-8");
+        await writeFile3(targetPath, file.content, "utf-8");
         written++;
       }
       const settingsFiles = defaultsData.settings ?? [];
       for (const file of settingsFiles) {
-        const targetPath = join7(claudeDir, "settings.json");
+        const targetPath = join8(claudeDir, "settings.json");
         await mkdir2(dirname2(targetPath), { recursive: true });
-        await writeFile2(targetPath, file.content, "utf-8");
+        await writeFile3(targetPath, file.content, "utf-8");
         written++;
       }
       console.log(`  Wrote ${written} files to .claude/
@@ -1516,7 +1692,7 @@ async function runInit() {
           allFiles.push({ type: "claude_md", name: file.name, content: file.content });
         }
         for (const file of settingsFiles) {
-          allFiles.push({ type: "settings", name: file.name, content: file.content });
+          allFiles.push({ type: "settings", name: file.name, content: file.content, scope: file.scope ?? "repo" });
         }
         if (allFiles.length > 0) {
           await apiPost("/sync/files", {
@@ -23300,21 +23476,6 @@ function registerReadTools(server) {
       return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
     }
   });
-  server.registerTool("get_handoff", {
-    description: "Get handoff state for a repo (status, summary, resume command/context).",
-    inputSchema: {
-      repo_id: external_exports.string().uuid().describe("The repo UUID")
-    }
-  }, async ({ repo_id }) => {
-    try {
-      const res = await apiGet(`/repos/${repo_id}`);
-      const { id, name, handoff_status, handoff_summary, handoff_resume_command, handoff_resume_context, handoff_updated_at } = res.data;
-      const data = { id, name, handoff_status, handoff_summary, handoff_resume_command, handoff_resume_context, handoff_updated_at };
-      return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }] };
-    } catch (err) {
-      return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
-    }
-  });
   server.registerTool("get_sync_status", {
     description: "Get cross-repo sync status. Shows which repos need a claude files sync based on latest updates.",
     inputSchema: {}
@@ -23326,6 +23487,22 @@ function registerReadTools(server) {
       return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
     }
   });
+  server.registerTool("get_next_action", {
+    description: "Compute the next action for a repo based on current workflow state. Returns command, instructions, state, and context.",
+    inputSchema: {
+      repo_id: external_exports.string().uuid().describe("The repo UUID"),
+      worktree_id: external_exports.string().uuid().optional().describe("Optional worktree UUID to filter by assignment")
+    }
+  }, async ({ repo_id, worktree_id }) => {
+    try {
+      const params = {};
+      if (worktree_id) params.worktree_id = worktree_id;
+      const res = await apiGet(`/repos/${repo_id}/next-action`, params);
+      return { content: [{ type: "text", text: JSON.stringify(res.data, null, 2) }] };
+    } catch (err) {
+      return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
+    }
+  });
   server.registerTool("get_worktrees", {
     description: "List worktrees for a repo. Optionally filter by status.",
     inputSchema: {
@@ -23434,24 +23611,37 @@ function registerWriteTools(server) {
     description: "Create a new checkpoint for a repo. Optionally connect it to a launch via launch_id.",
     inputSchema: {
       repo_id: external_exports.string().uuid().describe("The repo UUID"),
-      title: external_exports.string().describe("Checkpoint title"),
+      title: external_exports.string().optional().describe("Checkpoint title (optional \u2014 Claude can generate if missing)"),
       number: external_exports.number().int().describe("Checkpoint number (e.g. 1 for CHK-001)"),
-      goal: external_exports.string().optional().describe("Checkpoint goal description"),
+      goal: external_exports.string().optional().describe("Checkpoint goal description (max 300 chars, brief overview)"),
       deadline: external_exports.string().optional().describe("Deadline date (ISO format)"),
       status: external_exports.string().optional().describe("Initial status (default: pending). Use 'draft' for checkpoints not ready for development."),
-      launch_id: external_exports.string().uuid().optional().describe("Optional launch UUID to connect this checkpoint to")
-    }
-  }, async ({ repo_id, title, number: number3, goal, deadline, status, launch_id }) => {
+      launch_id: external_exports.string().uuid().optional().describe("Optional launch UUID to connect this checkpoint to"),
+      ideas: external_exports.array(external_exports.object({
+        description: external_exports.string().describe("Idea description"),
+        requirements: external_exports.array(external_exports.string()).optional().describe("List of requirements for this idea"),
+        images: external_exports.array(external_exports.string()).optional().describe("Image URLs for this idea")
+      })).optional().describe("Ideas array \u2014 each idea has description, requirements[], images[]"),
+      context: external_exports.any().optional().describe("Context JSONB (decisions, discoveries, dependencies, constraints, qa_answers)"),
+      research: external_exports.any().optional().describe("Research JSONB (topics with findings and sources)"),
+      qa: external_exports.any().optional().describe("QA JSONB (checklist items with type, check, status)")
+    }
+  }, async ({ repo_id, title, number: number3, goal, deadline, status, launch_id, ideas, context, research, qa }) => {
     try {
-      const res = await apiPost("/checkpoints", {
+      const body = {
         repo_id,
-        title,
+        title: title ?? null,
         number: number3,
         goal: goal ?? null,
         deadline: deadline ?? null,
         status: status ?? "pending",
         launch_id: launch_id ?? null
-      });
+      };
+      if (ideas !== void 0) body.ideas = ideas;
+      if (context !== void 0) body.context = context;
+      if (research !== void 0) body.research = research;
+      if (qa !== void 0) body.qa = qa;
+      const res = await apiPost("/checkpoints", body);
       return { content: [{ type: "text", text: JSON.stringify(res.data, null, 2) }] };
     } catch (err) {
       return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
@@ -23461,16 +23651,24 @@ function registerWriteTools(server) {
     description: "Update an existing checkpoint. Can connect or disconnect a launch via launch_id.",
     inputSchema: {
       checkpoint_id: external_exports.string().uuid().describe("The checkpoint UUID"),
-      title: external_exports.string().optional().describe("New title"),
-      goal: external_exports.string().optional().describe("New goal"),
+      title: external_exports.string().nullable().optional().describe("New title (or null to clear)"),
+      goal: external_exports.string().optional().describe("New goal (max 300 chars, brief overview)"),
       status: external_exports.string().optional().describe("New status (draft, pending, active, completed)"),
       deadline: external_exports.string().optional().describe("New deadline (ISO format)"),
       completed_at: external_exports.string().optional().describe("Completion timestamp (ISO format)"),
       launch_id: external_exports.string().uuid().nullable().optional().describe("Launch UUID to connect (or null to disconnect)"),
       worktree_id: external_exports.string().uuid().nullable().optional().describe("Worktree UUID to assign (or null to unassign)"),
-      assigned_to: external_exports.string().nullable().optional().describe("Who/what claimed this checkpoint")
-    }
-  }, async ({ checkpoint_id, title, goal, status, deadline, completed_at, launch_id, worktree_id, assigned_to }) => {
+      assigned_to: external_exports.string().nullable().optional().describe("Who/what claimed this checkpoint"),
+      ideas: external_exports.array(external_exports.object({
+        description: external_exports.string().describe("Idea description"),
+        requirements: external_exports.array(external_exports.string()).optional().describe("List of requirements for this idea"),
+        images: external_exports.array(external_exports.string()).optional().describe("Image URLs for this idea")
+      })).optional().describe("Ideas array \u2014 each idea has description, requirements[], images[]"),
+      context: external_exports.any().optional().describe("Context JSONB (decisions, discoveries, dependencies, constraints, qa_answers)"),
+      research: external_exports.any().optional().describe("Research JSONB (topics with findings and sources)"),
+      qa: external_exports.any().optional().describe("QA JSONB (checklist items with type, check, status)")
+    }
+  }, async ({ checkpoint_id, title, goal, status, deadline, completed_at, launch_id, worktree_id, assigned_to, ideas, context, research, qa }) => {
     const update = {};
     if (title !== void 0) update.title = title;
     if (goal !== void 0) update.goal = goal;
@@ -23480,6 +23678,10 @@ function registerWriteTools(server) {
     if (launch_id !== void 0) update.launch_id = launch_id;
     if (worktree_id !== void 0) update.worktree_id = worktree_id;
     if (assigned_to !== void 0) update.assigned_to = assigned_to;
+    if (ideas !== void 0) update.ideas = ideas;
+    if (context !== void 0) update.context = context;
+    if (research !== void 0) update.research = research;
+    if (qa !== void 0) update.qa = qa;
     if (Object.keys(update).length === 0) {
       return { content: [{ type: "text", text: "Error: No fields to update" }], isError: true };
     }
@@ -23515,17 +23717,24 @@ function registerWriteTools(server) {
       title: external_exports.string().describe("Task title"),
       number: external_exports.number().int().describe("Task number (e.g. 1 for TASK-1)"),
       requirements: external_exports.string().optional().describe("Task requirements text"),
-      status: external_exports.string().optional().describe("Initial status (default: pending)")
+      status: external_exports.string().optional().describe("Initial status (default: pending)"),
+      context: external_exports.any().optional().describe("Context JSONB (decisions, discoveries, dependencies, constraints)"),
+      qa: external_exports.any().optional().describe("QA JSONB (checklist items with type, check, status)"),
+      research: external_exports.any().optional().describe("Research JSONB (topics with findings and sources)")
     }
-  }, async ({ checkpoint_id, title, number: number3, requirements, status }) => {
+  }, async ({ checkpoint_id, title, number: number3, requirements, status, context, qa, research }) => {
     try {
-      const res = await apiPost("/tasks", {
+      const body = {
         checkpoint_id,
         title,
         number: number3,
         requirements: requirements ?? null,
         status: status ?? "pending"
-      });
+      };
+      if (context !== void 0) body.context = context;
+      if (qa !== void 0) body.qa = qa;
+      if (research !== void 0) body.research = research;
+      const res = await apiPost("/tasks", body);
       return { content: [{ type: "text", text: JSON.stringify(res.data, null, 2) }] };
     } catch (err) {
       return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
@@ -23541,17 +23750,25 @@ function registerWriteTools(server) {
       files_changed: external_exports.array(external_exports.object({
         path: external_exports.string().describe("File path relative to repo root"),
         action: external_exports.string().describe("File action (new, modified, deleted)"),
-        status: external_exports.string().describe("Approval status (approved, not_approved)")
+        status: external_exports.string().describe("Approval status (approved, not_approved)"),
+        claude_approved: external_exports.boolean().optional().describe("Whether Claude's automated checks passed for this file"),
+        user_approved: external_exports.boolean().optional().describe("Whether the user has approved this file (via git add or web UI)")
       })).optional().describe("Files changed across all rounds"),
-      claim_worktree_id: external_exports.string().uuid().optional().describe("Worktree UUID to auto-claim the parent checkpoint when setting status to in_progress")
+      claim_worktree_id: external_exports.string().uuid().optional().describe("Worktree UUID to auto-claim the parent checkpoint when setting status to in_progress"),
+      context: external_exports.any().optional().describe("Context JSONB (decisions, discoveries, dependencies, constraints)"),
+      qa: external_exports.any().optional().describe("QA JSONB (checklist items with type, check, status)"),
+      research: external_exports.any().optional().describe("Research JSONB (topics with findings and sources)")
     }
-  }, async ({ task_id, title, requirements, status, files_changed, claim_worktree_id }) => {
+  }, async ({ task_id, title, requirements, status, files_changed, claim_worktree_id, context, qa, research }) => {
     const update = {};
     if (title !== void 0) update.title = title;
     if (requirements !== void 0) update.requirements = requirements;
     if (status !== void 0) update.status = status;
     if (files_changed !== void 0) update.files_changed = files_changed;
     if (claim_worktree_id !== void 0) update.claim_worktree_id = claim_worktree_id;
+    if (context !== void 0) update.context = context;
+    if (qa !== void 0) update.qa = qa;
+    if (research !== void 0) update.research = research;
     if (Object.keys(update).length === 0) {
       return { content: [{ type: "text", text: "Error: No fields to update" }], isError: true };
     }
@@ -23585,17 +23802,22 @@ function registerWriteTools(server) {
       number: external_exports.number().int().describe("Round number"),
       requirements: external_exports.string().optional().describe("Round requirements text"),
       status: external_exports.string().optional().describe("Initial status (default: pending)"),
-      started_at: external_exports.string().optional().describe("Start timestamp (ISO format)")
+      started_at: external_exports.string().optional().describe("Start timestamp (ISO format)"),
+      context: external_exports.any().optional().describe("Context JSONB"),
+      qa: external_exports.any().optional().describe("QA JSONB (checklist items with type, check, status)")
     }
-  }, async ({ task_id, number: number3, requirements, status, started_at }) => {
+  }, async ({ task_id, number: number3, requirements, status, started_at, context, qa }) => {
     try {
-      const res = await apiPost("/rounds", {
+      const body = {
         task_id,
         number: number3,
         requirements: requirements ?? null,
         status: status ?? "pending",
         started_at: started_at ?? null
-      });
+      };
+      if (context !== void 0) body.context = context;
+      if (qa !== void 0) body.qa = qa;
+      const res = await apiPost("/rounds", body);
       return { content: [{ type: "text", text: JSON.stringify(res.data, null, 2) }] };
     } catch (err) {
       return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
@@ -23613,10 +23835,14 @@ function registerWriteTools(server) {
       files_changed: external_exports.array(external_exports.object({
         path: external_exports.string().describe("File path relative to repo root"),
         action: external_exports.string().describe("File action (new, modified, deleted)"),
-        status: external_exports.string().describe("Approval status (approved, not_approved)")
-      })).optional().describe("Files changed in this round with approval status")
-    }
-  }, async ({ round_id, requirements, status, started_at, completed_at, duration_minutes, files_changed }) => {
+        status: external_exports.string().describe("Approval status (approved, not_approved)"),
+        claude_approved: external_exports.boolean().optional().describe("Whether Claude's automated checks passed for this file"),
+        user_approved: external_exports.boolean().optional().describe("Whether the user has approved this file (via git add or web UI)")
+      })).optional().describe("Files changed in this round with approval status"),
+      context: external_exports.any().optional().describe("Context JSONB"),
+      qa: external_exports.any().optional().describe("QA JSONB (checklist items with type, check, status)")
+    }
+  }, async ({ round_id, requirements, status, started_at, completed_at, duration_minutes, files_changed, context, qa }) => {
     const update = {};
     if (requirements !== void 0) update.requirements = requirements;
     if (status !== void 0) update.status = status;
@@ -23624,6 +23850,8 @@ function registerWriteTools(server) {
     if (completed_at !== void 0) update.completed_at = completed_at;
     if (duration_minutes !== void 0) update.duration_minutes = duration_minutes;
     if (files_changed !== void 0) update.files_changed = files_changed;
+    if (context !== void 0) update.context = context;
+    if (qa !== void 0) update.qa = qa;
     if (Object.keys(update).length === 0) {
       return { content: [{ type: "text", text: "Error: No fields to update" }], isError: true };
     }
@@ -23783,7 +24011,7 @@ function registerWriteTools(server) {
     }
   });
   server.registerTool("sync_claude_files", {
-    description: "Sync .claude infrastructure from CodeByPlan DB to local project. Uses aggregated defaults (latest version across all repos) for shared files (commands, agents, skills, rules, hooks, templates). Repo-specific files (CLAUDE.md, settings) are not overwritten.",
+    description: "Sync .claude infrastructure from CodeByPlan DB to local project. Uses aggregated defaults (latest version across all repos) for shared files (commands, agents, skills, rules, hooks, templates, stack docs). Repo-specific files (CLAUDE.md, settings) are not overwritten.",
     inputSchema: {
       repo_id: external_exports.string().uuid().describe("Repository ID to sync files for"),
       project_path: external_exports.string().describe("Absolute path to the project root directory")
@@ -23839,31 +24067,6 @@ function registerWriteTools(server) {
       return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
     }
   });
-  server.registerTool("update_handoff", {
-    description: "Update handoff state for a repo (status, summary, resume command/context). Automatically sets handoff_updated_at.",
-    inputSchema: {
-      repo_id: external_exports.string().uuid().describe("The repo UUID"),
-      status: external_exports.string().optional().describe("Handoff status"),
-      summary: external_exports.string().optional().describe("Handoff summary"),
-      resume_command: external_exports.string().optional().describe("Resume command"),
-      resume_context: external_exports.string().optional().describe("Resume context")
-    }
-  }, async ({ repo_id, status, summary, resume_command, resume_context }) => {
-    const body = {};
-    if (status !== void 0) body.status = status;
-    if (summary !== void 0) body.summary = summary;
-    if (resume_command !== void 0) body.resume_command = resume_command;
-    if (resume_context !== void 0) body.resume_context = resume_context;
-    if (Object.keys(body).length === 0) {
-      return { content: [{ type: "text", text: "Error: No fields to update" }], isError: true };
-    }
-    try {
-      const res = await apiPatch(`/repos/${repo_id}/handoff`, body);
-      return { content: [{ type: "text", text: JSON.stringify(res.data, null, 2) }] };
-    } catch (err) {
-      return { content: [{ type: "text", text: `Error: ${err instanceof Error ? err.message : String(err)}` }], isError: true };
-    }
-  });
   server.registerTool("create_worktree", {
     description: "Create a new worktree for a repo.",
     inputSchema: {
@@ -24048,6 +24251,11 @@ if (!process.env.CODEBYPLAN_API_KEY) {
   } catch {
   }
 }
+if (process.env.CODEBYPLAN_API_KEY?.startsWith("CODEBYPLAN_API_KEY=")) {
+  process.env.CODEBYPLAN_API_KEY = process.env.CODEBYPLAN_API_KEY.slice(
+    "CODEBYPLAN_API_KEY=".length
+  );
+}
 var arg = process.argv[2];
 if (arg === "--version" || arg === "-v") {
   console.log(VERSION);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@codebyplan/cli",
-  "version": "2.0.1",
+  "version": "2.1.0",
   "description": "MCP server for CodeByPlan — AI-powered development planning and tracking",
   "type": "module",
   "bin": {