claudekit-cli 3.42.2-dev.11 → 3.42.2-dev.12

package/cli-manifest.json

@@ -1,6 +1,6 @@
 {
-	"version": "3.42.2-dev.11",
-	"generatedAt": "2026-05-05T16:35:17.350Z",
+	"version": "3.42.2-dev.12",
+	"generatedAt": "2026-05-05T17:01:50.472Z",
 	"commands": {
 		"agents": {
 			"name": "agents",

package/dist/index.js

@@ -62349,7 +62349,7 @@ var package_default;
 var init_package = __esm(() => {
   package_default = {
     name: "claudekit-cli",
-    version: "3.42.2-dev.11",
+    version: "3.42.2-dev.12",
     description: "CLI tool for bootstrapping and updating ClaudeKit projects",
     type: "module",
     repository: {
@@ -73505,7 +73505,7 @@ __export(exports_worktree_manager, {
   cleanupAllWorktrees: () => cleanupAllWorktrees
 });
 import { existsSync as existsSync68 } from "node:fs";
-import { readFile as readFile64, writeFile as writeFile37 } from "node:fs/promises";
+import { readFile as readFile63, writeFile as writeFile37 } from "node:fs/promises";
 import { join as join149 } from "node:path";
 async function createWorktree(projectDir, issueNumber, baseBranch) {
   const worktreePath = join149(projectDir, WORKTREE_DIR, `issue-${issueNumber}`);
@@ -73570,7 +73570,7 @@ async function cleanupAllWorktrees(projectDir) {
 async function ensureGitignore(projectDir) {
   const gitignorePath = join149(projectDir, ".gitignore");
   try {
-    const content = existsSync68(gitignorePath) ? await readFile64(gitignorePath, "utf-8") : "";
+    const content = existsSync68(gitignorePath) ? await readFile63(gitignorePath, "utf-8") : "";
     if (!content.includes(".worktrees")) {
       const newContent = content.endsWith(`
 `) ? `${content}.worktrees/
@@ -75492,12 +75492,12 @@ var init_types6 = __esm(() => {
 });
 
 // src/commands/content/phases/state-manager.ts
-import { readFile as readFile66, rename as rename15, writeFile as writeFile40 } from "node:fs/promises";
+import { readFile as readFile65, rename as rename15, writeFile as writeFile40 } from "node:fs/promises";
 import { join as join162 } from "node:path";
 async function loadContentConfig(projectDir) {
   const configPath = join162(projectDir, CK_CONFIG_FILE2);
   try {
-    const raw2 = await readFile66(configPath, "utf-8");
+    const raw2 = await readFile65(configPath, "utf-8");
     const json = JSON.parse(raw2);
     return ContentConfigSchema.parse(json.content ?? {});
   } catch {
@@ -75513,7 +75513,7 @@ async function saveContentConfig(projectDir, config) {
 async function loadContentState(projectDir) {
   const configPath = join162(projectDir, CK_CONFIG_FILE2);
   try {
-    const raw2 = await readFile66(configPath, "utf-8");
+    const raw2 = await readFile65(configPath, "utf-8");
     const json = JSON.parse(raw2);
     const contentBlock = json.content ?? {};
     return ContentStateSchema.parse(contentBlock.state ?? {});
@@ -75540,7 +75540,7 @@ async function saveContentState(projectDir, state) {
 }
 async function readJsonSafe(filePath) {
   try {
-    const raw2 = await readFile66(filePath, "utf-8");
+    const raw2 = await readFile65(filePath, "utf-8");
     return JSON.parse(raw2);
   } catch {
     return {};
@@ -104640,6 +104640,7 @@ import { basename as basename23, dirname as dirname36, join as join130, resolve
 init_logger();
 init_safe_spinner();
 var import_fs_extra34 = __toESM(require_lib(), 1);
+var KIT_MANIFEST_FILE = "metadata.json";
 var CLAUDEKIT_SUBDIRECTORIES = ["commands", "agents", "skills", "rules", "hooks"];
 async function analyzeFreshInstallation(claudeDir3) {
   const metadata = await readManifest(claudeDir3);
@@ -104648,7 +104649,8 @@ async function analyzeFreshInstallation(claudeDir3) {
       ckFiles: [],
       ckModifiedFiles: [],
       userFiles: [],
-      hasMetadata: false
+      hasMetadata: false,
+      metadata: null
     };
   }
   const allFiles = getAllTrackedFiles(metadata);
@@ -104657,7 +104659,8 @@ async function analyzeFreshInstallation(claudeDir3) {
       ckFiles: [],
       ckModifiedFiles: [],
       userFiles: [],
-      hasMetadata: false
+      hasMetadata: false,
+      metadata: null
     };
   }
   const ckFiles = [];
@@ -104680,7 +104683,8 @@ async function analyzeFreshInstallation(claudeDir3) {
     ckFiles,
     ckModifiedFiles,
     userFiles,
-    hasMetadata: true
+    hasMetadata: true,
+    metadata
   };
 }
 function cleanupEmptyDirectories2(filePath, claudeDir3) {
@@ -104706,8 +104710,13 @@ function cleanupEmptyDirectories2(filePath, claudeDir3) {
 async function removeFilesByOwnership(claudeDir3, analysis, includeModified) {
   const removedFiles = [];
   const preservedFiles = [];
-  const filesToRemove = includeModified ? [...analysis.ckFiles, ...analysis.ckModifiedFiles] : analysis.ckFiles;
+  const allFilesToRemove = includeModified ? [...analysis.ckFiles, ...analysis.ckModifiedFiles] : analysis.ckFiles;
   const filesToPreserve = includeModified ? analysis.userFiles : [...analysis.ckModifiedFiles, ...analysis.userFiles];
+  const filesToRemove = allFilesToRemove.filter((f3) => f3.path !== KIT_MANIFEST_FILE);
+  const selfTrackedManifest = allFilesToRemove.some((f3) => f3.path === KIT_MANIFEST_FILE);
+  if (selfTrackedManifest) {
+    logger.debug(`${KIT_MANIFEST_FILE} was self-tracked; skipping from delete loop — will be rewritten by updateMetadataAfterFresh`);
+  }
   for (const file of filesToRemove) {
     const fullPath = join130(claudeDir3, file.path);
     if (!existsSync62(fullPath)) {
@@ -104725,8 +104734,8 @@ async function removeFilesByOwnership(claudeDir3, analysis, includeModified) {
   for (const file of filesToPreserve) {
     preservedFiles.push(file.path);
   }
-  if (removedFiles.length > 0) {
-    await updateMetadataAfterFresh(claudeDir3, removedFiles);
+  if (analysis.metadata) {
+    await updateMetadataAfterFresh(claudeDir3, removedFiles, analysis.metadata);
   }
   return {
     success: true,
@@ -104736,23 +104745,8 @@ async function removeFilesByOwnership(claudeDir3, analysis, includeModified) {
     preservedFiles
   };
 }
-async function updateMetadataAfterFresh(claudeDir3, removedFiles) {
-  const metadataPath = join130(claudeDir3, "metadata.json");
-  if (!await import_fs_extra34.pathExists(metadataPath)) {
-    throw new Error("metadata.json is missing during fresh install cleanup");
-  }
-  let content;
-  try {
-    content = await import_fs_extra34.readFile(metadataPath, "utf-8");
-  } catch (readError) {
-    throw new Error(`Failed to read metadata.json: ${readError instanceof Error ? readError.message : String(readError)}`);
-  }
-  let metadata;
-  try {
-    metadata = JSON.parse(content);
-  } catch (parseError) {
-    throw new Error(`Failed to parse metadata.json: ${parseError instanceof Error ? parseError.message : String(parseError)}`);
-  }
+async function updateMetadataAfterFresh(claudeDir3, removedFiles, metadata) {
+  const metadataPath = join130(claudeDir3, KIT_MANIFEST_FILE);
   const removedSet = new Set(removedFiles);
   if (metadata.kits) {
     for (const kitName of Object.keys(metadata.kits)) {
@@ -104765,11 +104759,14 @@ async function updateMetadataAfterFresh(claudeDir3, removedFiles) {
   if (metadata.files) {
     metadata.files = metadata.files.filter((f3) => !removedSet.has(f3.path));
   }
+  if (!await import_fs_extra34.pathExists(metadataPath)) {
+    logger.warning(`${KIT_MANIFEST_FILE} was absent at write time (self-tracked or race condition) — recreating from in-memory snapshot`);
+  }
   try {
     await import_fs_extra34.writeFile(metadataPath, JSON.stringify(metadata, null, 2));
-    logger.debug(`Updated metadata.json, removed ${removedFiles.length} file entries`);
+    logger.debug(`Updated ${KIT_MANIFEST_FILE}, removed ${removedFiles.length} file entries`);
   } catch (writeError) {
-    throw new Error(`Failed to write metadata.json: ${writeError instanceof Error ? writeError.message : String(writeError)}`);
+    throw new Error(`Failed to write ${KIT_MANIFEST_FILE}: ${writeError instanceof Error ? writeError.message : String(writeError)}`);
   }
 }
 function getFreshBackupTargets(claudeDir3, analysis, includeModified) {
@@ -105245,7 +105242,7 @@ async function handleSelection(ctx) {
   };
 }
 // src/commands/init/phases/sync-handler.ts
-import { copyFile as copyFile8, mkdir as mkdir35, open as open5, readFile as readFile56, rename as rename10, stat as stat22, unlink as unlink12, writeFile as writeFile32 } from "node:fs/promises";
+import { copyFile as copyFile8, mkdir as mkdir35, open as open5, readFile as readFile55, rename as rename10, stat as stat22, unlink as unlink12, writeFile as writeFile32 } from "node:fs/promises";
 import { dirname as dirname37, join as join132, resolve as resolve39 } from "node:path";
 init_logger();
 init_path_resolver();
@@ -105413,7 +105410,7 @@ async function executeSyncMerge(ctx) {
     try {
       const sourceMetadataPath = join132(upstreamDir, "metadata.json");
       if (await import_fs_extra36.pathExists(sourceMetadataPath)) {
-        const content = await readFile56(sourceMetadataPath, "utf-8");
+        const content = await readFile55(sourceMetadataPath, "utf-8");
         const sourceMetadata = JSON.parse(content);
         deletions = sourceMetadata.deletions || [];
       }
@@ -105711,7 +105708,7 @@ async function renameFolders(dirsToRename, extractDir, options2) {
 // src/services/transformers/folder-transform/path-replacer.ts
 init_logger();
 init_types3();
-import { readFile as readFile57, readdir as readdir40, writeFile as writeFile33 } from "node:fs/promises";
+import { readFile as readFile56, readdir as readdir40, writeFile as writeFile33 } from "node:fs/promises";
 import { join as join134, relative as relative26 } from "node:path";
 var TRANSFORMABLE_FILE_PATTERNS = [
   ".md",
@@ -105778,7 +105775,7 @@ async function transformFileContents(dir, compiledReplacements, options2) {
       if (!shouldTransform)
         continue;
       try {
-        const content = await readFile57(fullPath, "utf-8");
+        const content = await readFile56(fullPath, "utf-8");
         let newContent = content;
         let changeCount = 0;
         for (const { regex: regex2, replacement } of compiledReplacements) {
@@ -105900,7 +105897,7 @@ async function transformFolderPaths(extractDir, folders, options2 = {}) {
 
 // src/services/transformers/global-path-transformer.ts
 init_logger();
-import { readFile as readFile58, readdir as readdir41, writeFile as writeFile34 } from "node:fs/promises";
+import { readFile as readFile57, readdir as readdir41, writeFile as writeFile34 } from "node:fs/promises";
 import { homedir as homedir46, platform as platform15 } from "node:os";
 import { extname as extname6, join as join135 } from "node:path";
 var IS_WINDOWS3 = platform15() === "win32";
@@ -106051,7 +106048,7 @@ async function transformPathsForGlobalInstall(directory, options2 = {}) {
         await processDirectory2(fullPath);
       } else if (entry.isFile() && shouldTransformFile3(entry.name)) {
         try {
-          const content = await readFile58(fullPath, "utf-8");
+          const content = await readFile57(fullPath, "utf-8");
           const { transformed, changes } = transformContent(content, {
             targetClaudeDir: options2.targetClaudeDir
           });
@@ -106312,7 +106309,7 @@ async function initCommand(options2) {
 init_dist2();
 var import_picocolors30 = __toESM(require_picocolors(), 1);
 import { existsSync as existsSync63 } from "node:fs";
-import { readFile as readFile62, rm as rm16, unlink as unlink13 } from "node:fs/promises";
+import { readFile as readFile61, rm as rm16, unlink as unlink13 } from "node:fs/promises";
 import { homedir as homedir51 } from "node:os";
 import { basename as basename25, join as join140, resolve as resolve41 } from "node:path";
 init_logger();
@@ -106786,13 +106783,13 @@ init_model_taxonomy();
 init_logger();
 init_dist2();
 init_model_taxonomy();
-import { mkdir as mkdir37, readFile as readFile61, writeFile as writeFile36 } from "node:fs/promises";
+import { mkdir as mkdir37, readFile as readFile60, writeFile as writeFile36 } from "node:fs/promises";
 import { homedir as homedir50 } from "node:os";
 import { dirname as dirname38, join as join139 } from "node:path";
 
 // src/commands/portable/models-dev-cache.ts
 init_logger();
-import { mkdir as mkdir36, readFile as readFile59, rename as rename12, writeFile as writeFile35 } from "node:fs/promises";
+import { mkdir as mkdir36, readFile as readFile58, rename as rename12, writeFile as writeFile35 } from "node:fs/promises";
 import { homedir as homedir48 } from "node:os";
 import { join as join137 } from "node:path";
 
@@ -106817,7 +106814,7 @@ function tmpFilePath(cacheDir) {
 async function readCacheEntry(cacheDir) {
   const filePath = cacheFilePath(cacheDir);
   try {
-    const raw2 = await readFile59(filePath, "utf-8");
+    const raw2 = await readFile58(filePath, "utf-8");
     const parsed = JSON.parse(raw2);
     if (parsed !== null && typeof parsed === "object" && !Array.isArray(parsed) && "fetchedAt" in parsed && typeof parsed.fetchedAt === "string" && "payload" in parsed && typeof parsed.payload === "object" && parsed.payload !== null) {
       return parsed;
@@ -106885,7 +106882,7 @@ async function getModelsDevCatalog(opts = {}) {
 
 // src/commands/portable/opencode-model-discovery.ts
 init_logger();
-import { readFile as readFile60 } from "node:fs/promises";
+import { readFile as readFile59 } from "node:fs/promises";
 import { homedir as homedir49, platform as platform17 } from "node:os";
 import { join as join138 } from "node:path";
 function resolveOpenCodeAuthPath(homeDir) {
@@ -106899,7 +106896,7 @@ function resolveOpenCodeAuthPath(homeDir) {
 async function readAuthedProviders(homeDir) {
   const authPath = resolveOpenCodeAuthPath(homeDir);
   try {
-    const raw2 = await readFile60(authPath, "utf-8");
+    const raw2 = await readFile59(authPath, "utf-8");
     const parsed = JSON.parse(raw2);
     if (parsed !== null && typeof parsed === "object" && !Array.isArray(parsed)) {
       return Object.keys(parsed);
@@ -107101,7 +107098,7 @@ async function ensureOpenCodeModel(options2) {
   const configPath = getOpenCodeConfigPath(options2);
   let existing = null;
   try {
-    const raw2 = await readFile61(configPath, "utf-8");
+    const raw2 = await readFile60(configPath, "utf-8");
     const parsed = JSON.parse(raw2);
     if (parsed !== null && typeof parsed === "object" && !Array.isArray(parsed)) {
       existing = parsed;
@@ -107961,7 +107958,7 @@ async function processMetadataDeletions(skillSourcePath, installGlobally) {
     return;
   let sourceMetadata;
   try {
-    const content = await readFile62(sourceMetadataPath, "utf-8");
+    const content = await readFile61(sourceMetadataPath, "utf-8");
     sourceMetadata = JSON.parse(content);
   } catch (error) {
     logger.debug(`[migrate] Failed to parse source metadata.json: ${error}`);
@@ -108255,7 +108252,7 @@ async function migrateCommand(options2) {
       for (const action of conflictActions) {
         if (!action.diff && action.targetPath && existsSync63(action.targetPath)) {
           try {
-            const targetContent = await readFile62(action.targetPath, "utf-8");
+            const targetContent = await readFile61(action.targetPath, "utf-8");
             const sourceItem = effectiveAgents.find((a3) => a3.name === action.item) || effectiveCommands.find((c2) => c2.name === action.item) || (effectiveConfigItem?.name === action.item ? effectiveConfigItem : null) || effectiveRuleItems.find((r2) => r2.name === action.item) || effectiveHookItems.find((h2) => h2.name === action.item);
             if (sourceItem) {
               const providerConfig = providers[action.provider];
@@ -110233,7 +110230,7 @@ init_skills_registry();
 init_skills_uninstaller();
 var import_gray_matter11 = __toESM(require_gray_matter(), 1);
 var import_picocolors37 = __toESM(require_picocolors(), 1);
-import { readFile as readFile63 } from "node:fs/promises";
+import { readFile as readFile62 } from "node:fs/promises";
 import { join as join146 } from "node:path";
 
 // src/commands/skills/types.ts
@@ -110358,7 +110355,7 @@ async function handleValidate2(sourcePath) {
   for (const skill of skills) {
     const skillMdPath = join146(skill.path, "SKILL.md");
     try {
-      const content = await readFile63(skillMdPath, "utf-8");
+      const content = await readFile62(skillMdPath, "utf-8");
       const { data } = import_gray_matter11.default(content, {
         engines: { javascript: { parse: () => ({}) } }
       });
@@ -112796,7 +112793,7 @@ init_ck_config_manager();
 init_file_io();
 init_logger();
 import { existsSync as existsSync69 } from "node:fs";
-import { mkdir as mkdir39, readFile as readFile65 } from "node:fs/promises";
+import { mkdir as mkdir39, readFile as readFile64 } from "node:fs/promises";
 import { dirname as dirname45 } from "node:path";
 var PROCESSED_ISSUES_CAP = 500;
 async function readCkJson(projectDir) {
@@ -112804,7 +112801,7 @@ async function readCkJson(projectDir) {
   try {
     if (!existsSync69(configPath))
       return {};
-    const content = await readFile65(configPath, "utf-8");
+    const content = await readFile64(configPath, "utf-8");
     return JSON.parse(content);
   } catch (error) {
     logger.warning(`Failed to parse .ck.json: ${error instanceof Error ? error.message : "Unknown"}`);
@@ -113516,7 +113513,7 @@ init_types3();
 init_logger();
 init_path_resolver();
 import { existsSync as existsSync84 } from "node:fs";
-import { mkdir as mkdir41, readFile as readFile67, writeFile as writeFile41 } from "node:fs/promises";
+import { mkdir as mkdir41, readFile as readFile66, writeFile as writeFile41 } from "node:fs/promises";
 import { join as join166 } from "node:path";
 
 class VersionCacheManager {
@@ -113533,7 +113530,7 @@ class VersionCacheManager {
         logger.debug("Version check cache not found");
         return null;
       }
-      const content = await readFile67(cacheFile, "utf-8");
+      const content = await readFile66(cacheFile, "utf-8");
       const cache5 = JSON.parse(content);
       if (!cache5.lastCheck || !cache5.currentVersion || !cache5.latestVersion) {
         logger.debug("Invalid cache structure, ignoring");

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "claudekit-cli",
-	"version": "3.42.2-dev.11",
+	"version": "3.42.2-dev.12",
 	"description": "CLI tool for bootstrapping and updating ClaudeKit projects",
 	"type": "module",
 	"repository": {