fix: preserve untracked files during checkpoint rollback

Fixes #9530 - Rollback no longer deletes files that were not created or tracked by Roo Code.

Previously, git clean -d -f was removing ALL untracked files during rollback, including files manually created by users outside of Roo Code. This fix removes the git clean command, allowing git reset --hard to handle the rollback properly, which only affects tracked files.

- Removed git clean command from restoreCheckpoint method
- Added test to verify manually created files are preserved during rollback
- All existing tests pass

src/services/checkpoints/ShadowCheckpointService.ts

@@ -342,7 +342,7 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 			}
 
 			const start = Date.now()
-			await this.git.clean("f", ["-d", "-f"])
+			// Only reset tracked files to checkpoint state, preserve untracked files
 			await this.git.reset(["--hard", commitHash])
 
 			// Remove all checkpoints after the specified commitHash.

src/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts

@@ -267,6 +267,48 @@ describe.each([[RepoPerTaskCheckpointService, "RepoPerTaskCheckpointService"]])(
 				expect(await fs.readFile(testFile, "utf-8")).toBe("Changed tracked file")
 			})
 
+			it("preserves manually created files during rollback (fixes issue #9530)", async () => {
+				// This test simulates the exact scenario from the bug report:
+				// 1. Create a checkpoint
+				// 2. User manually creates a file outside of Roo Code
+				// 3. Rollback to the checkpoint
+				// 4. The manually created file should NOT be deleted
+
+				// Create initial checkpoint
+				await fs.writeFile(testFile, "Initial content")
+				const commit1 = await service.saveCheckpoint("Initial checkpoint")
+				expect(commit1?.commit).toBeTruthy()
+
+				// Make some changes and create another checkpoint
+				await fs.writeFile(testFile, "Modified by Roo Code")
+				const commit2 = await service.saveCheckpoint("Second checkpoint")
+				expect(commit2?.commit).toBeTruthy()
+
+				// Simulate user manually creating a file AFTER all checkpoints
+				// This file is never tracked by any checkpoint
+				const manuallyCreatedFile = path.join(service.workspaceDir, "manually-created.txt")
+				await fs.writeFile(manuallyCreatedFile, "I was created manually, not by Roo Code!")
+
+				// Now rollback to the first checkpoint
+				await service.restoreCheckpoint(commit1!.commit)
+
+				// The tracked file should be restored to its initial state
+				expect(await fs.readFile(testFile, "utf-8")).toBe("Initial content")
+
+				// IMPORTANT: The manually created file should still exist
+				// This is the fix for issue #9530 - manually created files should not be deleted
+				expect(await fs.readFile(manuallyCreatedFile, "utf-8")).toBe("I was created manually, not by Roo Code!")
+
+				// Rollback to the second checkpoint
+				await service.restoreCheckpoint(commit2!.commit)
+
+				// The tracked file should be at its second state
+				expect(await fs.readFile(testFile, "utf-8")).toBe("Modified by Roo Code")
+
+				// The manually created file should still persist
+				expect(await fs.readFile(manuallyCreatedFile, "utf-8")).toBe("I was created manually, not by Roo Code!")
+			})
+
 			it("handles file deletions correctly", async () => {
 				await fs.writeFile(testFile, "I am tracked!")
 				const untrackedFile = path.join(service.workspaceDir, "new.txt")