rulesync 8.12.0 → 8.13.0

package/dist/cli/index.js

@@ -79,7 +79,7 @@ import {
   stringifyFrontmatter,
   toPosixPath,
   writeFileContent
-} from "../chunk-643VJ2QM.js";
+} from "../chunk-RLRAG4LZ.js";
 
 // src/cli/index.ts
 import { Command } from "commander";
@@ -658,32 +658,32 @@ async function convertFetchedFilesToRulesync(params) {
     {
       feature: "rules",
       getTargets: () => RulesProcessor.getToolTargets({ global: false }),
-      createProcessor: () => new RulesProcessor({ baseDir: tempDir, toolTarget: target, global: false, logger: logger5 })
+      createProcessor: () => new RulesProcessor({ outputRoot: tempDir, toolTarget: target, global: false, logger: logger5 })
     },
     {
       feature: "commands",
       getTargets: () => CommandsProcessor.getToolTargets({ global: false, includeSimulated: false }),
-      createProcessor: () => new CommandsProcessor({ baseDir: tempDir, toolTarget: target, global: false, logger: logger5 })
+      createProcessor: () => new CommandsProcessor({ outputRoot: tempDir, toolTarget: target, global: false, logger: logger5 })
     },
     {
       feature: "subagents",
       getTargets: () => SubagentsProcessor.getToolTargets({ global: false, includeSimulated: false }),
-      createProcessor: () => new SubagentsProcessor({ baseDir: tempDir, toolTarget: target, global: false, logger: logger5 })
+      createProcessor: () => new SubagentsProcessor({ outputRoot: tempDir, toolTarget: target, global: false, logger: logger5 })
     },
     {
       feature: "ignore",
       getTargets: () => IgnoreProcessor.getToolTargets(),
-      createProcessor: () => new IgnoreProcessor({ baseDir: tempDir, toolTarget: target, logger: logger5 })
+      createProcessor: () => new IgnoreProcessor({ outputRoot: tempDir, toolTarget: target, logger: logger5 })
     },
     {
       feature: "mcp",
       getTargets: () => McpProcessor.getToolTargets({ global: false }),
-      createProcessor: () => new McpProcessor({ baseDir: tempDir, toolTarget: target, global: false, logger: logger5 })
+      createProcessor: () => new McpProcessor({ outputRoot: tempDir, toolTarget: target, global: false, logger: logger5 })
     },
     {
       feature: "hooks",
       getTargets: () => HooksProcessor.getToolTargets({ global: false }),
-      createProcessor: () => new HooksProcessor({ baseDir: tempDir, toolTarget: target, global: false, logger: logger5 })
+      createProcessor: () => new HooksProcessor({ outputRoot: tempDir, toolTarget: target, global: false, logger: logger5 })
     }
   ];
   for (const config of featureConfigs) {
@@ -728,7 +728,7 @@ function isNotFoundError(error) {
   return false;
 }
 async function fetchFiles(params) {
-  const { source, options = {}, baseDir = process.cwd(), logger: logger5 } = params;
+  const { source, options = {}, outputRoot = process.cwd(), logger: logger5 } = params;
   const parsed = parseSource(source);
   if (parsed.provider === "gitlab") {
     throw new Error(
@@ -743,7 +743,7 @@ async function fetchFiles(params) {
   const target = options.target ?? "rulesync";
   checkPathTraversal({
     relativePath: outputDir,
-    intendedRootDir: baseDir
+    intendedRootDir: outputRoot
   });
   const token = GitHubClient.resolveToken(options.token);
   const client = new GitHubClient({ token });
@@ -766,7 +766,7 @@ async function fetchFiles(params) {
       enabledFeatures,
       target,
       outputDir,
-      baseDir,
+      outputRoot,
       conflictStrategy,
       logger: logger5
     });
@@ -793,7 +793,7 @@ async function fetchFiles(params) {
       skipped: 0
     };
   }
-  const outputBasePath = join(baseDir, outputDir);
+  const outputBasePath = join(outputRoot, outputDir);
   for (const { relativePath, size } of filesToFetch) {
     checkPathTraversal({
       relativePath,
@@ -907,7 +907,7 @@ async function fetchAndConvertToolFiles(params) {
     enabledFeatures,
     target,
     outputDir,
-    baseDir,
+    outputRoot,
     conflictStrategy: _conflictStrategy,
     logger: logger5
   } = params;
@@ -956,7 +956,7 @@ async function fetchAndConvertToolFiles(params) {
         logger5.debug(`Fetched to temp: ${toolRelativePath}`);
       })
     );
-    const outputBasePath = join(baseDir, outputDir);
+    const outputBasePath = join(outputRoot, outputDir);
     const { converted, convertedPaths } = await convertFetchedFilesToRulesync({
       tempDir,
       outputDir: outputBasePath,
@@ -1110,6 +1110,15 @@ async function fetchCommand(logger5, options) {
 }
 
 // src/cli/commands/generate.ts
+function sameDirSets(a, b) {
+  const aSet = new Set(a);
+  const bSet = new Set(b);
+  if (aSet.size !== bSet.size) return false;
+  for (const v of aSet) {
+    if (!bSet.has(v)) return false;
+  }
+  return true;
+}
 function logFeatureResult(logger5, params) {
   const { count, paths, featureName, isPreview, modePrefix } = params;
   if (count > 0) {
@@ -1124,18 +1133,33 @@ function logFeatureResult(logger5, params) {
   }
 }
 async function generateCommand(logger5, options) {
-  const config = await ConfigResolver.resolve(options);
+  const { baseDir, outputRoots, ...rest } = options;
+  if (baseDir !== void 0) {
+    logger5.warn(
+      "--base-dir is deprecated; use --output-roots instead. It will be removed in a future major release."
+    );
+  }
+  const outputRootsResolved = outputRoots !== void 0 && outputRoots.length > 0 ? outputRoots : baseDir;
+  if (baseDir !== void 0 && outputRoots !== void 0 && baseDir.length > 0 && outputRoots.length > 0 && !sameDirSets(outputRoots, baseDir)) {
+    logger5.warn(
+      `Both '--output-roots' and '--base-dir' were provided with differing values; using '--output-roots' (${JSON.stringify(outputRoots)}) and ignoring '--base-dir' (${JSON.stringify(baseDir)}).`
+    );
+  }
+  const config = await ConfigResolver.resolve(
+    { ...rest, outputRoots: outputRootsResolved },
+    { logger: logger5 }
+  );
   const check = config.getCheck();
   const isPreview = config.isPreviewMode();
   const modePrefix = isPreview ? "[DRY RUN]" : "";
   logger5.debug("Generating files...");
-  if (!await checkRulesyncDirExists({ baseDir: process.cwd() })) {
+  if (!await checkRulesyncDirExists({ inputRoot: config.getInputRoot() })) {
     throw new CLIError(
       ".rulesync directory not found. Run 'rulesync init' first.",
       ErrorCodes.RULESYNC_DIR_NOT_FOUND
     );
   }
-  logger5.debug(`Base directories: ${config.getBaseDirs().join(", ")}`);
+  logger5.debug(`Output roots: ${config.getOutputRoots().join(", ")}`);
   const features = config.getFeatures();
   if (features.includes("ignore")) {
     logger5.debug("Generating ignore files...");
@@ -1747,7 +1771,7 @@ async function importCommand(logger5, options) {
   if (options.targets.length > 1) {
     throw new CLIError("Only one tool can be imported at a time", ErrorCodes.IMPORT_FAILED);
   }
-  const config = await ConfigResolver.resolve(options);
+  const config = await ConfigResolver.resolve(options, { logger: logger5 });
   const tool = config.getTargets()[0];
   logger5.debug(`Importing files from ${tool}...`);
   const result = await importFromTool({ config, tool, logger: logger5 });
@@ -1805,7 +1829,7 @@ async function createConfigFile() {
         $schema: RULESYNC_CONFIG_SCHEMA_URL,
         targets: ["copilot", "cursor", "claudecode", "codexcli"],
         features: ["rules", "ignore", "mcp", "commands", "subagents", "skills", "hooks"],
-        baseDirs: ["."],
+        outputRoots: ["."],
         delete: true,
         verbose: false,
         silent: false,
@@ -2087,8 +2111,8 @@ var ApmLockSchema = z4.looseObject({
   dependencies: z4.array(ApmLockDependencySchema),
   mcp_servers: optional(z4.array(z4.string()))
 });
-function getApmLockPath(baseDir) {
-  return join4(baseDir, APM_LOCKFILE_FILE_NAME);
+function getApmLockPath(projectRoot) {
+  return join4(projectRoot, APM_LOCKFILE_FILE_NAME);
 }
 function createEmptyApmLock(params) {
   const base = params.existingLock ? { ...params.existingLock } : {};
@@ -2121,8 +2145,8 @@ ${issues}`);
   }
   return parsed.data;
 }
-async function readApmLock(baseDir) {
-  const path2 = getApmLockPath(baseDir);
+async function readApmLock(projectRoot) {
+  const path2 = getApmLockPath(projectRoot);
   if (!await fileExists(path2)) {
     return null;
   }
@@ -2130,7 +2154,7 @@ async function readApmLock(baseDir) {
   return parseApmLock(content);
 }
 async function writeApmLock(params) {
-  const path2 = getApmLockPath(params.baseDir);
+  const path2 = getApmLockPath(params.projectRoot);
   const content = serializeApmLock(params.lock);
   await writeFileContent(path2, content);
 }
@@ -2164,11 +2188,11 @@ var ApmManifestSchema = z5.looseObject({
     })
   )
 });
-function getApmManifestPath(baseDir) {
-  return join5(baseDir, APM_MANIFEST_FILE_NAME);
+function getApmManifestPath(projectRoot) {
+  return join5(projectRoot, APM_MANIFEST_FILE_NAME);
 }
-async function apmManifestExists(baseDir) {
-  return fileExists(getApmManifestPath(baseDir));
+async function apmManifestExists(projectRoot) {
+  return fileExists(getApmManifestPath(projectRoot));
 }
 function parseApmManifest(content) {
   const loaded = load2(content);
@@ -2190,8 +2214,8 @@ function parseApmManifest(content) {
     dependencies
   };
 }
-async function readApmManifest(baseDir) {
-  const path2 = getApmManifestPath(baseDir);
+async function readApmManifest(projectRoot) {
+  const path2 = getApmManifestPath(projectRoot);
   const content = await readFileContent(path2);
   return parseApmManifest(content);
 }
@@ -2344,13 +2368,13 @@ var APM_PRIMITIVES = [
   }
 ];
 async function installApm(params) {
-  const { baseDir, options = {}, logger: logger5 } = params;
-  const manifest = await readApmManifest(baseDir);
+  const { projectRoot, options = {}, logger: logger5 } = params;
+  const manifest = await readApmManifest(projectRoot);
   if (manifest.dependencies.length === 0) {
     logger5.warn("apm.yml has no dependencies.apm entries. Nothing to install.");
     return { dependenciesProcessed: 0, deployedFileCount: 0, failedDependencyCount: 0 };
   }
-  const existingLock = await readApmLock(baseDir);
+  const existingLock = await readApmLock(projectRoot);
   if (options.frozen) {
     if (!existingLock) {
       throw new Error(
@@ -2394,7 +2418,7 @@ async function installApm(params) {
       dep,
       client,
       semaphore,
-      baseDir,
+      projectRoot,
       existingLock,
       frozen,
       update: options.update ?? false,
@@ -2449,19 +2473,19 @@ async function installApm(params) {
         continue;
       }
       try {
-        checkPathTraversal({ relativePath, intendedRootDir: baseDir });
+        checkPathTraversal({ relativePath, intendedRootDir: projectRoot });
       } catch {
-        logger5.warn(`Refusing to remove stale apm file outside baseDir: "${relativePath}".`);
+        logger5.warn(`Refusing to remove stale apm file outside projectRoot: "${relativePath}".`);
         continue;
       }
-      const absolute = join6(baseDir, relativePath);
+      const absolute = join6(projectRoot, relativePath);
       await removeFile(absolute);
       logger5.debug(`Removed stale apm file: ${relativePath}`);
     }
   }
   if (!frozen) {
     newLock.generated_at = (/* @__PURE__ */ new Date()).toISOString();
-    await writeApmLock({ baseDir, lock: newLock });
+    await writeApmLock({ projectRoot, lock: newLock });
     if (failedCount === 0) {
       logger5.debug("rulesync-apm.lock.yaml updated.");
     } else {
@@ -2477,7 +2501,7 @@ async function installApm(params) {
   };
 }
 async function installDependency(params) {
-  const { dep, client, semaphore, baseDir, existingLock, frozen, update, logger: logger5 } = params;
+  const { dep, client, semaphore, projectRoot, existingLock, frozen, update, logger: logger5 } = params;
   const repoUrl = canonicalRepoUrl(dep);
   const locked = existingLock ? findApmLockDependency(existingLock, repoUrl) : void 0;
   let resolvedRef;
@@ -2521,7 +2545,7 @@ async function installDependency(params) {
       const deployRelative = toPosixPath(join6(primitive.deployDir, relativeToBase));
       checkPathTraversal({
         relativePath: deployRelative,
-        intendedRootDir: baseDir
+        intendedRootDir: projectRoot
       });
       const content = await withSemaphore(
         semaphore,
@@ -2536,7 +2560,7 @@ async function installDependency(params) {
       }
       deployed.push({ path: deployRelative, content });
       if (!frozen) {
-        await writeFileContent(join6(baseDir, deployRelative), content);
+        await writeFileContent(join6(projectRoot, deployRelative), content);
       }
     }
   }
@@ -2558,7 +2582,7 @@ async function installDependency(params) {
   }
   if (frozen) {
     for (const { path: deployRelative, content } of deployed) {
-      await writeFileContent(join6(baseDir, deployRelative), content);
+      await writeFileContent(join6(projectRoot, deployRelative), content);
     }
   }
   const lockEntry = {
@@ -2706,8 +2730,8 @@ var GhLockSchema = z6.looseObject({
   generated_at: z6.string(),
   installations: z6.array(GhLockInstallationSchema)
 });
-function getGhLockPath(baseDir) {
-  return join7(baseDir, GH_LOCKFILE_FILE_NAME);
+function getGhLockPath(projectRoot) {
+  return join7(projectRoot, GH_LOCKFILE_FILE_NAME);
 }
 function createEmptyGhLock(params) {
   const base = params?.existingLock ? { ...params.existingLock } : {};
@@ -2739,8 +2763,8 @@ ${issues}`);
   }
   return parsed.data;
 }
-async function readGhLock(baseDir) {
-  const path2 = getGhLockPath(baseDir);
+async function readGhLock(projectRoot) {
+  const path2 = getGhLockPath(projectRoot);
   if (!await fileExists(path2)) {
     return null;
   }
@@ -2748,7 +2772,7 @@ async function readGhLock(baseDir) {
   return parseGhLock(content);
 }
 async function writeGhLock(params) {
-  const path2 = getGhLockPath(params.baseDir);
+  const path2 = getGhLockPath(params.projectRoot);
   const content = serializeGhLock(params.lock);
   await writeFileContent(path2, content);
 }
@@ -2800,7 +2824,7 @@ function relativeInstallDirFor(params) {
 var SKILLS_REMOTE_DIR = "skills";
 var SKILL_FILE_NAME2 = "SKILL.md";
 async function installGh(params) {
-  const { baseDir, sources, options = {}, logger: logger5 } = params;
+  const { projectRoot, sources, options = {}, logger: logger5 } = params;
   if (sources.length === 0) {
     return { sourcesProcessed: 0, installedSkillCount: 0, failedSourceCount: 0 };
   }
@@ -2837,7 +2861,7 @@ async function installGh(params) {
       scope
     };
   });
-  const existingLock = await readGhLock(baseDir);
+  const existingLock = await readGhLock(projectRoot);
   const frozen = options.frozen ?? false;
   const update = options.update ?? false;
   if (frozen && !existingLock) {
@@ -2888,7 +2912,7 @@ async function installGh(params) {
       rs,
       client,
       semaphore,
-      baseDir,
+      projectRoot,
       existingLock,
       frozen,
       update,
@@ -2951,7 +2975,7 @@ async function installGh(params) {
         await removeStaleFile({
           relativePath: deployed,
           scope: prev.scope === "user" ? "user" : "project",
-          baseDir,
+          projectRoot,
           logger: logger5
         });
       }
@@ -2959,7 +2983,7 @@ async function installGh(params) {
   }
   if (!frozen) {
     newLock.generated_at = (/* @__PURE__ */ new Date()).toISOString();
-    await writeGhLock({ baseDir, lock: newLock });
+    await writeGhLock({ projectRoot, lock: newLock });
     if (failedCount === 0) {
       logger5.debug("rulesync-gh.lock.yaml updated.");
     } else {
@@ -2975,7 +2999,7 @@ async function installGh(params) {
   };
 }
 async function installSource(params) {
-  const { rs, client, semaphore, baseDir, existingLock, frozen, update, logger: logger5 } = params;
+  const { rs, client, semaphore, projectRoot, existingLock, frozen, update, logger: logger5 } = params;
   const { entry, owner, repo, agent, scope } = rs;
   const sourceKey = entry.source;
   let resolvedRef;
@@ -3050,7 +3074,7 @@ async function installSource(params) {
   }
   const results = [];
   const installRelDir = relativeInstallDirFor({ agent, scope });
-  const scopeRoot = scope === "user" ? getHomeDirectory() : baseDir;
+  const scopeRoot = scope === "user" ? getHomeDirectory() : projectRoot;
   const sourceUrl = `https://github.com/${owner}/${repo}`;
   const repository = `${owner}/${repo}`;
   const provenanceRef = usedTag ? resolvedRef : resolvedSha;
@@ -3166,12 +3190,12 @@ ${content}`;
   return results;
 }
 async function removeStaleFile(params) {
-  const { relativePath, scope, baseDir, logger: logger5 } = params;
+  const { relativePath, scope, projectRoot, logger: logger5 } = params;
   if (posix3.isAbsolute(relativePath) || relativePath.split(/[/\\]/).includes("..")) {
     logger5.warn(`Refusing to remove stale gh file with suspicious path: "${relativePath}".`);
     return;
   }
-  const scopeRoot = scope === "user" ? getHomeDirectory() : baseDir;
+  const scopeRoot = scope === "user" ? getHomeDirectory() : projectRoot;
   try {
     checkPathTraversal({ relativePath, intendedRootDir: scopeRoot });
   } catch {
@@ -3343,7 +3367,7 @@ async function fetchSkillFiles(params) {
 var MAX_WALK_DEPTH = 20;
 var MAX_TOTAL_FILES = 1e4;
 var MAX_TOTAL_SIZE = 100 * 1024 * 1024;
-async function walkDirectory(dir, baseDir, depth = 0, ctx = { totalFiles: 0, totalSize: 0 }, logger5) {
+async function walkDirectory(dir, outputRoot, depth = 0, ctx = { totalFiles: 0, totalSize: 0 }, logger5) {
   if (depth > MAX_WALK_DEPTH) {
     throw new GitClientError(
       `Directory tree exceeds max depth of ${MAX_WALK_DEPTH}: "${dir}". Aborting to prevent resource exhaustion.`
@@ -3358,7 +3382,7 @@ async function walkDirectory(dir, baseDir, depth = 0, ctx = { totalFiles: 0, tot
       continue;
     }
     if (await directoryExists(fullPath)) {
-      results.push(...await walkDirectory(fullPath, baseDir, depth + 1, ctx, logger5));
+      results.push(...await walkDirectory(fullPath, outputRoot, depth + 1, ctx, logger5));
     } else {
       const size = await getFileSize(fullPath);
       if (size > MAX_FILE_SIZE) {
@@ -3380,7 +3404,7 @@ async function walkDirectory(dir, baseDir, depth = 0, ctx = { totalFiles: 0, tot
         );
       }
       const content = await readFileContent(fullPath);
-      results.push({ relativePath: relative(baseDir, fullPath), content, size });
+      results.push({ relativePath: relative(outputRoot, fullPath), content, size });
     }
   }
   return results;
@@ -3434,7 +3458,7 @@ function createEmptyLock() {
 }
 async function readLockFile(params) {
   const { logger: logger5 } = params;
-  const lockPath = join11(params.baseDir, RULESYNC_SOURCES_LOCK_RELATIVE_FILE_PATH);
+  const lockPath = join11(params.projectRoot, RULESYNC_SOURCES_LOCK_RELATIVE_FILE_PATH);
   if (!await fileExists(lockPath)) {
     logger5.debug("No sources lockfile found, starting fresh.");
     return createEmptyLock();
@@ -3463,7 +3487,7 @@ async function readLockFile(params) {
 }
 async function writeLockFile(params) {
   const { logger: logger5 } = params;
-  const lockPath = join11(params.baseDir, RULESYNC_SOURCES_LOCK_RELATIVE_FILE_PATH);
+  const lockPath = join11(params.projectRoot, RULESYNC_SOURCES_LOCK_RELATIVE_FILE_PATH);
   const content = JSON.stringify(params.lock, null, 2) + "\n";
   await writeFileContent(lockPath, content);
   logger5.debug(`Wrote sources lockfile to ${lockPath}`);
@@ -3538,7 +3562,7 @@ function getLockedSkillNames(entry) {
 
 // src/lib/sources.ts
 async function resolveAndFetchSources(params) {
-  const { sources, baseDir, options = {}, logger: logger5 } = params;
+  const { sources, projectRoot, options = {}, logger: logger5 } = params;
   if (sources.length === 0) {
     return { fetchedSkillCount: 0, sourcesProcessed: 0 };
   }
@@ -3546,7 +3570,7 @@ async function resolveAndFetchSources(params) {
     logger5.info("Skipping source fetching.");
     return { fetchedSkillCount: 0, sourcesProcessed: 0 };
   }
-  let lock = options.updateSources ? createEmptyLock() : await readLockFile({ baseDir, logger: logger5 });
+  let lock = options.updateSources ? createEmptyLock() : await readLockFile({ projectRoot, logger: logger5 });
   if (options.frozen) {
     const missingKeys = [];
     for (const source of sources) {
@@ -3564,7 +3588,7 @@ async function resolveAndFetchSources(params) {
   const originalLockJson = JSON.stringify(lock);
   const token = GitHubClient.resolveToken(options.token);
   const client = new GitHubClient({ token });
-  const localSkillNames = await getLocalSkillDirNames(baseDir);
+  const localSkillNames = await getLocalSkillDirNames(projectRoot);
   let totalSkillCount = 0;
   const allFetchedSkillNames = /* @__PURE__ */ new Set();
   for (const sourceEntry of sources) {
@@ -3574,7 +3598,7 @@ async function resolveAndFetchSources(params) {
       if (transport === "git") {
         result = await fetchSourceViaGit({
           sourceEntry,
-          baseDir,
+          projectRoot,
           lock,
           localSkillNames,
           alreadyFetchedSkillNames: allFetchedSkillNames,
@@ -3586,7 +3610,7 @@ async function resolveAndFetchSources(params) {
         result = await fetchSource({
           sourceEntry,
           client,
-          baseDir,
+          projectRoot,
           lock,
           localSkillNames,
           alreadyFetchedSkillNames: allFetchedSkillNames,
@@ -3620,7 +3644,7 @@ async function resolveAndFetchSources(params) {
   }
   lock = { lockfileVersion: lock.lockfileVersion, sources: prunedSources };
   if (!options.frozen && JSON.stringify(lock) !== originalLockJson) {
-    await writeLockFile({ baseDir, lock, logger: logger5 });
+    await writeLockFile({ projectRoot, lock, logger: logger5 });
   } else {
     logger5.debug("Lockfile unchanged, skipping write.");
   }
@@ -3771,7 +3795,7 @@ async function fetchSource(params) {
   const {
     sourceEntry,
     client,
-    baseDir,
+    projectRoot,
     localSkillNames,
     alreadyFetchedSkillNames,
     updateSources,
@@ -3800,7 +3824,7 @@ async function fetchSource(params) {
     ref = resolvedSha;
     logger5.debug(`Resolved ${sourceKey} ref "${requestedRef}" to SHA: ${resolvedSha}`);
   }
-  const curatedDir = join12(baseDir, RULESYNC_CURATED_SKILLS_RELATIVE_DIR_PATH);
+  const curatedDir = join12(projectRoot, RULESYNC_CURATED_SKILLS_RELATIVE_DIR_PATH);
   if (locked && resolvedSha === locked.resolvedRef && !updateSources) {
     const allExist = await checkLockedSkillsExist(curatedDir, lockedSkillNames);
     if (allExist) {
@@ -3948,7 +3972,7 @@ async function fetchSource(params) {
 async function fetchSourceViaGit(params) {
   const {
     sourceEntry,
-    baseDir,
+    projectRoot,
     localSkillNames,
     alreadyFetchedSkillNames,
     updateSources,
@@ -3975,7 +3999,7 @@ async function fetchSourceViaGit(params) {
     requestedRef = def.ref;
     resolvedSha = def.sha;
   }
-  const curatedDir = join12(baseDir, RULESYNC_CURATED_SKILLS_RELATIVE_DIR_PATH);
+  const curatedDir = join12(projectRoot, RULESYNC_CURATED_SKILLS_RELATIVE_DIR_PATH);
   if (locked && resolvedSha === locked.resolvedRef && !updateSources) {
     if (await checkLockedSkillsExist(curatedDir, lockedSkillNames)) {
       return { skillCount: 0, fetchedSkillNames: lockedSkillNames, updatedLock: lock };
@@ -4057,8 +4081,8 @@ async function installCommand(logger5, options) {
   await runRulesyncInstall(logger5, options);
 }
 async function runRulesyncInstall(logger5, options) {
-  const baseDir = process.cwd();
-  const apmExists = await apmManifestExists(baseDir);
+  const projectRoot = process.cwd();
+  const apmExists = await apmManifestExists(projectRoot);
   const config = await ConfigResolver.resolve({
     configPath: options.configPath,
     verbose: options.verbose,
@@ -4083,7 +4107,7 @@ async function runRulesyncInstall(logger5, options) {
   logger5.debug(`Installing skills from ${sources.length} source(s)...`);
   const result = await resolveAndFetchSources({
     sources,
-    baseDir,
+    projectRoot,
     options: {
       updateSources: options.update,
       frozen: options.frozen,
@@ -4104,14 +4128,14 @@ async function runRulesyncInstall(logger5, options) {
   }
 }
 async function runApmInstall(logger5, options) {
-  const baseDir = process.cwd();
-  if (!await apmManifestExists(baseDir)) {
+  const projectRoot = process.cwd();
+  if (!await apmManifestExists(projectRoot)) {
     throw new Error(
       "--mode apm requires an apm.yml at the project root. Create one or drop --mode apm to fall back to rulesync mode."
     );
   }
   const result = await installApm({
-    baseDir,
+    projectRoot,
     options: {
       update: options.update,
       frozen: options.frozen,
@@ -4138,7 +4162,7 @@ async function runApmInstall(logger5, options) {
   }
 }
 async function runGhInstall(logger5, options) {
-  const baseDir = process.cwd();
+  const projectRoot = process.cwd();
   const config = await ConfigResolver.resolve({
     configPath: options.configPath,
     verbose: options.verbose,
@@ -4150,7 +4174,7 @@ async function runGhInstall(logger5, options) {
     return;
   }
   const result = await installGh({
-    baseDir,
+    projectRoot,
     sources,
     options: {
       update: options.update,
@@ -4273,7 +4297,7 @@ async function putCommand({
     }
     const fileContent = stringifyFrontmatter(body, frontmatter);
     const command = new RulesyncCommand({
-      baseDir: process.cwd(),
+      outputRoot: process.cwd(),
       relativeDirPath: RULESYNC_COMMANDS_RELATIVE_DIR_PATH,
       relativeFilePath: filename,
       frontmatter,
@@ -4418,7 +4442,7 @@ async function executeConvert(options) {
       features: options.features ?? ["*"],
       global: options.global,
       dryRun: options.dryRun,
-      // Always use default baseDirs (process.cwd()) and configPath
+      // Always use default outputRoots (process.cwd()) and configPath
       // verbose and silent are meaningless in MCP context
       verbose: false,
       silent: true
@@ -4486,7 +4510,7 @@ var generateOptionsSchema = z10.object({
 });
 async function executeGenerate(options = {}) {
   try {
-    const exists = await checkRulesyncDirExists({ baseDir: process.cwd() });
+    const exists = await checkRulesyncDirExists({ inputRoot: process.cwd() });
     if (!exists) {
       return {
         success: false,
@@ -4503,7 +4527,7 @@ async function executeGenerate(options = {}) {
       simulateCommands: options.simulateCommands,
       simulateSubagents: options.simulateSubagents,
       simulateSkills: options.simulateSkills,
-      // Always use default baseDirs (process.cwd()) and configPath
+      // Always use default outputRoots (process.cwd()) and configPath
       // verbose and silent are meaningless in MCP context
       verbose: false,
       silent: true
@@ -4603,19 +4627,19 @@ async function putHooksFile({ content }) {
     );
   }
   try {
-    const baseDir = process.cwd();
+    const outputRoot = process.cwd();
     const paths = RulesyncHooks.getSettablePaths();
     const relativeDirPath = paths.relativeDirPath;
     const relativeFilePath = paths.relativeFilePath;
-    const fullPath = join14(baseDir, relativeDirPath, relativeFilePath);
+    const fullPath = join14(outputRoot, relativeDirPath, relativeFilePath);
     const rulesyncHooks = new RulesyncHooks({
-      baseDir,
+      outputRoot,
       relativeDirPath,
       relativeFilePath,
       fileContent: content,
       validate: true
     });
-    await ensureDir(join14(baseDir, relativeDirPath));
+    await ensureDir(join14(outputRoot, relativeDirPath));
     await writeFileContent(fullPath, content);
     const relativePathFromCwd = join14(relativeDirPath, relativeFilePath);
     return {
@@ -4633,9 +4657,9 @@ async function putHooksFile({ content }) {
 }
 async function deleteHooksFile() {
   try {
-    const baseDir = process.cwd();
+    const outputRoot = process.cwd();
     const paths = RulesyncHooks.getSettablePaths();
-    const filePath = join14(baseDir, paths.relativeDirPath, paths.relativeFilePath);
+    const filePath = join14(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
     await removeFile(filePath);
     const relativePathFromCwd = join14(paths.relativeDirPath, paths.relativeFilePath);
     return {
@@ -4809,7 +4833,7 @@ async function executeImport(options) {
       // eslint-disable-next-line no-type-assertion/no-type-assertion
       features: options.features,
       global: options.global,
-      // Always use default baseDirs (process.cwd()) and configPath
+      // Always use default outputRoots (process.cwd()) and configPath
       // verbose and silent are meaningless in MCP context
       verbose: false,
       silent: true
@@ -4906,19 +4930,19 @@ async function putMcpFile({ content }) {
     );
   }
   try {
-    const baseDir = process.cwd();
+    const outputRoot = process.cwd();
     const paths = RulesyncMcp.getSettablePaths();
     const relativeDirPath = paths.recommended.relativeDirPath;
     const relativeFilePath = paths.recommended.relativeFilePath;
-    const fullPath = join16(baseDir, relativeDirPath, relativeFilePath);
+    const fullPath = join16(outputRoot, relativeDirPath, relativeFilePath);
     const rulesyncMcp = new RulesyncMcp({
-      baseDir,
+      outputRoot,
       relativeDirPath,
       relativeFilePath,
       fileContent: content,
       validate: true
     });
-    await ensureDir(join16(baseDir, relativeDirPath));
+    await ensureDir(join16(outputRoot, relativeDirPath));
     await writeFileContent(fullPath, content);
     const relativePathFromCwd = join16(relativeDirPath, relativeFilePath);
     return {
@@ -4936,14 +4960,18 @@ async function putMcpFile({ content }) {
 }
 async function deleteMcpFile() {
   try {
-    const baseDir = process.cwd();
+    const outputRoot = process.cwd();
     const paths = RulesyncMcp.getSettablePaths();
     const recommendedPath = join16(
-      baseDir,
+      outputRoot,
       paths.recommended.relativeDirPath,
       paths.recommended.relativeFilePath
     );
-    const legacyPath = join16(baseDir, paths.legacy.relativeDirPath, paths.legacy.relativeFilePath);
+    const legacyPath = join16(
+      outputRoot,
+      paths.legacy.relativeDirPath,
+      paths.legacy.relativeFilePath
+    );
     await removeFile(recommendedPath);
     await removeFile(legacyPath);
     const relativePathFromCwd = join16(
@@ -5042,19 +5070,19 @@ async function putPermissionsFile({ content }) {
     );
   }
   try {
-    const baseDir = process.cwd();
+    const outputRoot = process.cwd();
     const paths = RulesyncPermissions.getSettablePaths();
     const relativeDirPath = paths.relativeDirPath;
     const relativeFilePath = paths.relativeFilePath;
-    const fullPath = join17(baseDir, relativeDirPath, relativeFilePath);
+    const fullPath = join17(outputRoot, relativeDirPath, relativeFilePath);
     const rulesyncPermissions = new RulesyncPermissions({
-      baseDir,
+      outputRoot,
       relativeDirPath,
       relativeFilePath,
       fileContent: content,
       validate: true
     });
-    await ensureDir(join17(baseDir, relativeDirPath));
+    await ensureDir(join17(outputRoot, relativeDirPath));
     await writeFileContent(fullPath, content);
     const relativePathFromCwd = join17(relativeDirPath, relativeFilePath);
     return {
@@ -5072,9 +5100,9 @@ async function putPermissionsFile({ content }) {
 }
 async function deletePermissionsFile() {
   try {
-    const baseDir = process.cwd();
+    const outputRoot = process.cwd();
     const paths = RulesyncPermissions.getSettablePaths();
-    const filePath = join17(baseDir, paths.relativeDirPath, paths.relativeFilePath);
+    const filePath = join17(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
     await removeFile(filePath);
     const relativePathFromCwd = join17(paths.relativeDirPath, paths.relativeFilePath);
     return {
@@ -5212,7 +5240,7 @@ async function putRule({
       );
     }
     const rule = new RulesyncRule({
-      baseDir: process.cwd(),
+      outputRoot: process.cwd(),
       relativeDirPath: RULESYNC_RULES_RELATIVE_DIR_PATH,
       relativeFilePath: filename,
       frontmatter,
@@ -5419,7 +5447,7 @@ async function putSkill({
     }
     const aiDirFiles = otherFiles.map(mcpSkillFileToAiDirFile);
     const skill = new RulesyncSkill({
-      baseDir: process.cwd(),
+      outputRoot: process.cwd(),
       relativeDirPath: RULESYNC_SKILLS_RELATIVE_DIR_PATH,
       dirName,
       frontmatter,
@@ -5636,7 +5664,7 @@ async function putSubagent({
       );
     }
     const subagent = new RulesyncSubagent({
-      baseDir: process.cwd(),
+      outputRoot: process.cwd(),
       relativeDirPath: RULESYNC_SUBAGENTS_RELATIVE_DIR_PATH,
       relativeFilePath: filename,
       frontmatter,
@@ -6435,7 +6463,7 @@ function wrapCommand({
 }
 
 // src/cli/index.ts
-var getVersion = () => "8.12.0";
+var getVersion = () => "8.13.0";
 function wrapCommand2(name, errorCode, handler) {
   return wrapCommand({ name, errorCode, handler, getVersion });
 }
@@ -6552,8 +6580,12 @@ var main = async () => {
     `Comma-separated list of features to generate (${ALL_FEATURES.join(",")}) or '*' for all`,
     parseCommaSeparatedList
   ).option("--delete", "Delete all existing files in output directories before generating").option(
+    "-o, --output-roots <paths>",
+    "Output root directories to generate files into (comma-separated for multiple paths)",
+    parseCommaSeparatedList
+  ).option(
     "-b, --base-dir <paths>",
-    "Base directories to generate files (comma-separated for multiple paths)",
+    "[Deprecated] Use --output-roots instead. Output root directories (comma-separated for multiple paths)",
     parseCommaSeparatedList
   ).option("-V, --verbose", "Verbose output").option("-s, --silent", "Suppress all output").option("-c, --config <path>", "Path to configuration file").option("-g, --global", "Generate for global(user scope) configuration files").option(
     "--simulate-commands",
@@ -6564,6 +6596,9 @@ var main = async () => {
   ).option(
     "--simulate-skills",
     "Generate simulated skills. This feature is only available for copilot, cursor and codexcli."
+  ).option(
+    "--input-root <path>",
+    "Path to the directory containing .rulesync/ (parent of .rulesync/)"
   ).option("--dry-run", "Dry run: show changes without writing files").option("--check", "Check if files are up to date (exits with code 1 if changes needed)").action(
     wrapCommand2("generate", "GENERATION_FAILED", async (logger5, options) => {
       await generateCommand(logger5, options);