diff --git a/src/cli/commands/generate.ts b/src/cli/commands/generate.ts
index 799460e98..1914c00be 100644
--- a/src/cli/commands/generate.ts
+++ b/src/cli/commands/generate.ts
@@ -120,6 +120,17 @@ export async function generateCommand(logger: Logger, options: GenerateOptions):
   }
 
   if (totalGenerated === 0) {
+    if (check) {
+      if (result.hasDiff) {
+        throw new CLIError(
+          "Files are not up to date. Run 'rulesync generate' to update.",
+          ErrorCodes.GENERATION_FAILED,
+        );
+      }
+      logger.success("✓ All files are up to date.");
+      return;
+    }
+
     const enabledFeatures = features.join(", ");
     logger.info(`✓ All files are up to date (${enabledFeatures})`);
     return;
diff --git a/src/features/commands/commands-processor.test.ts b/src/features/commands/commands-processor.test.ts
index 152531d75..3f4e2dd1d 100644
--- a/src/features/commands/commands-processor.test.ts
+++ b/src/features/commands/commands-processor.test.ts
@@ -1221,7 +1221,7 @@ describe("CommandsProcessor", () => {
       }
     });
 
-    it("should filter out non-deletable files when forDeletion is true", async () => {
+    it("should include non-deletable files for orphan detection when forDeletion is true", async () => {
       processor = new CommandsProcessor({ logger, baseDir: testDir, toolTarget: "claudecode" });
 
       mockFindFilesByGlobs.mockResolvedValue([
@@ -1239,8 +1239,15 @@ describe("CommandsProcessor", () => {
       );
 
       const filesToDelete = await processor.loadToolFiles({ forDeletion: true });
-      expect(filesToDelete).toHaveLength(1);
-      expect(filesToDelete[0]?.getRelativeFilePath()).toBe("deletable.md");
+      // Should return all files for orphan detection, regardless of isDeletable()
+      // isDeletable() will be checked during actual deletion in removeOrphanAiFiles
+      expect(filesToDelete).toHaveLength(2);
+      const deletable = filesToDelete.find((f) => f.getRelativeFilePath() === "deletable.md");
+      const nonDeletable = filesToDelete.find(
+        (f) => f.getRelativeFilePath() === "non-deletable.md",
+      );
+      expect(deletable?.isDeletable()).toBe(true);
+      expect(nonDeletable?.isDeletable()).toBe(false);
     });
 
     it("should reject path traversal in loadToolFiles", async () => {
diff --git a/src/features/commands/commands-processor.ts b/src/features/commands/commands-processor.ts
index 535167849..525a3ac36 100644
--- a/src/features/commands/commands-processor.ts
+++ b/src/features/commands/commands-processor.ts
@@ -453,16 +453,15 @@ export class CommandsProcessor extends FeatureProcessor {
     const commandFilePaths = await findFilesByGlobs(globPattern);
 
     if (forDeletion) {
-      const toolCommands = commandFilePaths
-        .map((path) =>
-          factory.class.forDeletion({
-            baseDir: this.baseDir,
-            relativeDirPath: paths.relativeDirPath,
-            relativeFilePath: this.safeRelativePath(baseDirFull, path),
-            global: this.global,
-          }),
-        )
-        .filter((cmd) => cmd.isDeletable());
+      const toolCommands = commandFilePaths.map((path) =>
+        factory.class.forDeletion({
+          baseDir: this.baseDir,
+          relativeDirPath: paths.relativeDirPath,
+          relativeFilePath: this.safeRelativePath(baseDirFull, path),
+          global: this.global,
+        }),
+      );
+      // Don't filter by isDeletable() here; it will be checked during actual deletion
 
       this.logger.debug(
         `Successfully loaded ${toolCommands.length} ${paths.relativeDirPath} commands`,
diff --git a/src/features/hooks/hooks-processor.test.ts b/src/features/hooks/hooks-processor.test.ts
index b3d5003b0..d6b80d794 100644
--- a/src/features/hooks/hooks-processor.test.ts
+++ b/src/features/hooks/hooks-processor.test.ts
@@ -173,10 +173,13 @@ describe("HooksProcessor", () => {
       expect(files[0]?.getRelativeFilePath()).toBe("hooks.json");
     });
 
-    it("should return empty array for claudecode when forDeletion (not deletable)", async () => {
+    it("should return file for claudecode when forDeletion (not deletable) for orphan detection", async () => {
       const processor = new HooksProcessor({ logger, baseDir: testDir, toolTarget: "claudecode" });
       const files = await processor.loadToolFiles({ forDeletion: true });
-      expect(files).toHaveLength(0);
+      // Should return file even if not deletable, for orphan detection
+      // isDeletable() will be checked during actual deletion in removeOrphanAiFiles
+      expect(files).toHaveLength(1);
+      expect(files[0].isDeletable()).toBe(false);
     });
   });
 
diff --git a/src/features/hooks/hooks-processor.ts b/src/features/hooks/hooks-processor.ts
index d7ffc06c6..475b61a5f 100644
--- a/src/features/hooks/hooks-processor.ts
+++ b/src/features/hooks/hooks-processor.ts
@@ -272,11 +272,9 @@ export class HooksProcessor extends FeatureProcessor {
           relativeFilePath: paths.relativeFilePath,
           global: this.global,
         });
-        const list = toolHooks.isDeletable?.() !== false ? [toolHooks] : [];
-        this.logger.debug(
-          `Successfully loaded ${list.length} ${this.toolTarget} hooks files for deletion`,
-        );
-        return list;
+        // Return the file for orphan detection; isDeletable() will be checked during actual deletion
+        this.logger.debug(`Successfully loaded 1 ${this.toolTarget} hooks file for deletion check`);
+        return [toolHooks];
       }
 
       const toolHooks = await factory.class.fromFile({
diff --git a/src/features/ignore/ignore-processor.test.ts b/src/features/ignore/ignore-processor.test.ts
index cf85ffee8..898b0c078 100644
--- a/src/features/ignore/ignore-processor.test.ts
+++ b/src/features/ignore/ignore-processor.test.ts
@@ -405,7 +405,7 @@ describe("IgnoreProcessor", () => {
   });
 
   describe("loadToolFiles with forDeletion: true", () => {
-    it("should filter out non-deletable files when loading for deletion", async () => {
+    it("should include non-deletable files for orphan detection when loading for deletion", async () => {
       await ensureDir(join(testDir, ".claude"));
       await writeFileContent(
         join(testDir, ".claude", "settings.json"),
@@ -423,9 +423,11 @@ describe("IgnoreProcessor", () => {
       expect(allFiles).toHaveLength(1);
       expect(allFiles[0]?.isDeletable()).toBe(false);
 
-      // Load tool files for deletion (should exclude non-deletable files)
-      const filesToDelete = await processor.loadToolFiles({ forDeletion: true });
-      expect(filesToDelete).toHaveLength(0);
+      // Load tool files for deletion checking - should include all files for orphan detection
+      // isDeletable() will be checked during actual deletion in removeOrphanAiFiles
+      const filesForDeletionCheck = await processor.loadToolFiles({ forDeletion: true });
+      expect(filesForDeletionCheck).toHaveLength(1);
+      expect(filesForDeletionCheck[0]?.isDeletable()).toBe(false);
     });
 
     it("should treat claudecode-legacy ignore files the same as claudecode", async () => {
@@ -450,8 +452,11 @@ describe("IgnoreProcessor", () => {
       expect(allFiles[0]).toBeInstanceOf(ClaudecodeIgnore);
       expect(allFiles[0]?.isDeletable()).toBe(false);
 
-      const filesToDelete = await processor.loadToolFiles({ forDeletion: true });
-      expect(filesToDelete).toHaveLength(0);
+      // loadToolFiles({ forDeletion: true }) should still include non-deletable files
+      // for orphan detection; isDeletable() is checked during actual deletion
+      const filesForDeletionCheck = await processor.loadToolFiles({ forDeletion: true });
+      expect(filesForDeletionCheck).toHaveLength(1);
+      expect(filesForDeletionCheck[0]?.isDeletable()).toBe(false);
     });
 
     it("should return deletable files with correct paths", async () => {
diff --git a/src/features/ignore/ignore-processor.ts b/src/features/ignore/ignore-processor.ts
index 47692ed45..ba9719b37 100644
--- a/src/features/ignore/ignore-processor.ts
+++ b/src/features/ignore/ignore-processor.ts
@@ -156,8 +156,8 @@ export class IgnoreProcessor extends FeatureProcessor {
           relativeFilePath: paths.relativeFilePath,
         });
 
-        const toolIgnores = toolIgnore.isDeletable() ? [toolIgnore] : [];
-        return toolIgnores;
+        // Return the file for orphan detection; isDeletable() will be checked during actual deletion
+        return [toolIgnore];
       }
 
       const toolIgnores = await this.loadToolIgnores();
diff --git a/src/features/mcp/mcp-processor.test.ts b/src/features/mcp/mcp-processor.test.ts
index 825f611e1..ede4db7b2 100644
--- a/src/features/mcp/mcp-processor.test.ts
+++ b/src/features/mcp/mcp-processor.test.ts
@@ -1177,7 +1177,7 @@ describe("McpProcessor", () => {
       expect(filesToDelete).toEqual([]);
     });
 
-    it("should filter out non-deletable files in global mode", async () => {
+    it("should include non-deletable files for orphan detection in global mode", async () => {
       // Mock forDeletion to return non-deletable instance
       (vi.mocked(ClaudecodeMcp).forDeletion as ReturnType<typeof vi.fn>).mockImplementation(
         (params: { relativeFilePath: string }) => ({
@@ -1196,8 +1196,10 @@ describe("McpProcessor", () => {
 
       const filesToDelete = await processor.loadToolFiles({ forDeletion: true });
 
-      // loadToolFiles with forDeletion: true should filter out non-deletable files
-      expect(filesToDelete).toHaveLength(0);
+      // loadToolFiles with forDeletion: true should include all files for orphan detection
+      // isDeletable() will be checked during actual deletion in removeOrphanAiFiles
+      expect(filesToDelete).toHaveLength(1);
+      expect(filesToDelete[0].isDeletable()).toBe(false);
     });
 
     it("should not filter out deletable files in local mode", async () => {
diff --git a/src/features/mcp/mcp-processor.ts b/src/features/mcp/mcp-processor.ts
index dc29e6cc8..c46426336 100644
--- a/src/features/mcp/mcp-processor.ts
+++ b/src/features/mcp/mcp-processor.ts
@@ -378,9 +378,9 @@ export class McpProcessor extends FeatureProcessor {
           global: this.global,
         });
 
-        const toolMcps = toolMcp.isDeletable() ? [toolMcp] : [];
-        this.logger.debug(`Successfully loaded ${toolMcps.length} ${this.toolTarget} MCP files`);
-        return toolMcps;
+        // Return the file for orphan detection; isDeletable() will be checked during actual deletion
+        this.logger.debug(`Successfully loaded 1 ${this.toolTarget} MCP file for deletion check`);
+        return [toolMcp];
       }
 
       const toolMcps = [
diff --git a/src/features/rules/rules-processor.ts b/src/features/rules/rules-processor.ts
index 2886c85c1..479dcde42 100644
--- a/src/features/rules/rules-processor.ts
+++ b/src/features/rules/rules-processor.ts
@@ -940,7 +940,8 @@ export class RulesProcessor extends FeatureProcessor {
       };
 
       /**
-       * Build deletion rules from discovered file paths: resolve dir, check traversal, create forDeletion, filter isDeletable.
+       * Build deletion rules from discovered file paths: resolve dir, check traversal, create forDeletion.
+       * Don't filter by isDeletable() here; it will be checked during actual deletion.
        *
        * Two modes:
        * - Root mode (no opts): `relativeFilePath` = `basename(filePath)`, traversal checks `relativeDirPath` against `this.baseDir`.
@@ -953,26 +954,24 @@ export class RulesProcessor extends FeatureProcessor {
       ): ToolRule[] => {
         const isNonRoot = opts !== undefined;
         const effectiveBaseDir = isNonRoot ? opts.baseDirOverride : this.baseDir;
-        return filePaths
-          .map((filePath) => {
-            const relativeDirPath = isNonRoot
-              ? opts.relativeDirPathOverride
-              : resolveRelativeDirPath(filePath);
-            const relativeFilePath = isNonRoot
-              ? relative(effectiveBaseDir, filePath)
-              : basename(filePath);
-            checkPathTraversal({
-              relativePath: isNonRoot ? relativeFilePath : relativeDirPath,
-              intendedRootDir: effectiveBaseDir,
-            });
-            return factory.class.forDeletion({
-              baseDir: this.baseDir,
-              relativeDirPath,
-              relativeFilePath,
-              global: this.global,
-            });
-          })
-          .filter((rule) => rule.isDeletable());
+        return filePaths.map((filePath) => {
+          const relativeDirPath = isNonRoot
+            ? opts.relativeDirPathOverride
+            : resolveRelativeDirPath(filePath);
+          const relativeFilePath = isNonRoot
+            ? relative(effectiveBaseDir, filePath)
+            : basename(filePath);
+          checkPathTraversal({
+            relativePath: isNonRoot ? relativeFilePath : relativeDirPath,
+            intendedRootDir: effectiveBaseDir,
+          });
+          return factory.class.forDeletion({
+            baseDir: this.baseDir,
+            relativeDirPath,
+            relativeFilePath,
+            global: this.global,
+          });
+        });
       };
 
       const findFilesWithFallback = async (
diff --git a/src/features/subagents/subagents-processor.ts b/src/features/subagents/subagents-processor.ts
index 9675b99d2..460999523 100644
--- a/src/features/subagents/subagents-processor.ts
+++ b/src/features/subagents/subagents-processor.ts
@@ -376,16 +376,15 @@ export class SubagentsProcessor extends FeatureProcessor {
     );
 
     if (forDeletion) {
-      const toolSubagents = subagentFilePaths
-        .map((path) =>
-          factory.class.forDeletion({
-            baseDir: this.baseDir,
-            relativeDirPath: paths.relativeDirPath,
-            relativeFilePath: basename(path),
-            global: this.global,
-          }),
-        )
-        .filter((subagent) => subagent.isDeletable());
+      const toolSubagents = subagentFilePaths.map((path) =>
+        factory.class.forDeletion({
+          baseDir: this.baseDir,
+          relativeDirPath: paths.relativeDirPath,
+          relativeFilePath: basename(path),
+          global: this.global,
+        }),
+      );
+      // Don't filter by isDeletable() here; it will be checked during actual deletion
 
       this.logger.debug(
         `Successfully loaded ${toolSubagents.length} ${paths.relativeDirPath} subagents`,
diff --git a/src/lib/generate.test.ts b/src/lib/generate.test.ts
index 1a6a5c457..79be45168 100644
--- a/src/lib/generate.test.ts
+++ b/src/lib/generate.test.ts
@@ -365,6 +365,32 @@ describe("generate", () => {
       expect(result.mcpCount).toBe(0);
       expect(McpProcessor).not.toHaveBeenCalled();
     });
+
+    it("should remove orphan MCP files when delete option is enabled and source is empty", async () => {
+      mockConfig.getFeatures.mockReturnValue(["mcp"]);
+      mockConfig.getDelete.mockReturnValue(true);
+
+      const existingFiles = [{ file: "existing", getFilePath: () => "/path/to/existing" }];
+      const mockProcessor = {
+        loadToolFiles: vi.fn().mockResolvedValue(existingFiles),
+        removeOrphanAiFiles: vi.fn().mockResolvedValue(1),
+        loadRulesyncFiles: vi.fn().mockResolvedValue([]),
+        convertRulesyncFilesToToolFiles: vi.fn(),
+        writeAiFiles: vi.fn(),
+      };
+      vi.mocked(McpProcessor).mockImplementation(function () {
+        return mockProcessor as unknown as McpProcessor;
+      });
+
+      const result = await generate({ logger, config: mockConfig as never });
+
+      expect(result.mcpCount).toBe(0);
+      expect(result.hasDiff).toBe(true);
+      expect(mockProcessor.convertRulesyncFilesToToolFiles).not.toHaveBeenCalled();
+      expect(mockProcessor.writeAiFiles).not.toHaveBeenCalled();
+      expect(mockProcessor.loadToolFiles).toHaveBeenCalledWith({ forDeletion: true });
+      expect(mockProcessor.removeOrphanAiFiles).toHaveBeenCalledWith(existingFiles, []);
+    });
   });
 
   describe("commands feature", () => {
diff --git a/src/lib/generate.ts b/src/lib/generate.ts
index 820171ef8..fa81c457a 100644
--- a/src/lib/generate.ts
+++ b/src/lib/generate.ts
@@ -349,13 +349,22 @@ async function generateMcpCore(params: {
       });
 
       const rulesyncFiles = await processor.loadRulesyncFiles();
-      const toolFiles = await processor.convertRulesyncFilesToToolFiles(rulesyncFiles);
+      let result;
 
-      const result = await processFeatureGeneration({
-        config,
-        processor,
-        toolFiles,
-      });
+      if (rulesyncFiles.length === 0) {
+        result = await processEmptyFeatureGeneration({
+          config,
+          processor,
+        });
+      } else {
+        const toolFiles = await processor.convertRulesyncFilesToToolFiles(rulesyncFiles);
+
+        result = await processFeatureGeneration({
+          config,
+          processor,
+          toolFiles,
+        });
+      }
 
       totalCount += result.count;
       allPaths.push(...result.paths);
diff --git a/src/types/feature-processor.test.ts b/src/types/feature-processor.test.ts
index 39d12f152..08ac7abc5 100644
--- a/src/types/feature-processor.test.ts
+++ b/src/types/feature-processor.test.ts
@@ -23,6 +23,7 @@ function createMockFile(filePath: string): AiFile {
     getFilePath: () => filePath,
     getFileContent: () => "content",
     getRelativePathFromCwd: () => filePath,
+    isDeletable: () => true,
   } as AiFile;
 }
 
diff --git a/src/types/feature-processor.ts b/src/types/feature-processor.ts
index 01004f1a6..588d7436f 100644
--- a/src/types/feature-processor.ts
+++ b/src/types/feature-processor.ts
@@ -97,6 +97,11 @@ export abstract class FeatureProcessor {
     const orphanFiles = existingFiles.filter((f) => !generatedPaths.has(f.getFilePath()));
 
     for (const aiFile of orphanFiles) {
+      // Skip files that are not deletable (e.g., shared config files)
+      if (!aiFile.isDeletable()) {
+        continue;
+      }
+
       const filePath = aiFile.getFilePath();
       if (this.dryRun) {
         this.logger.info(`[DRY RUN] Would delete: ${filePath}`);
@@ -105,6 +110,7 @@ export abstract class FeatureProcessor {
       }
     }
 
+    // Return count of all orphan files, including non-deletable ones, for check mode
     return orphanFiles.length;
   }
 }