fix: allow checkpoints with nested git repos by excluding them

- Modified ShadowCheckpointService to exclude nested git repos instead of disabling checkpoints
- Added getNestedGitRepositories method to find all nested repos
- Updated writeExcludeFile to add nested repos to exclude patterns
- Added info messages to notify users when nested repos are excluded
- Updated tests to reflect new behavior
- Fixes #8433

src/i18n/locales/en/common.json

@@ -142,7 +142,9 @@
 		"image_copied_to_clipboard": "Image data URI copied to clipboard",
 		"image_saved": "Image saved to {{path}}",
 		"mode_exported": "Mode '{{mode}}' exported successfully",
-		"mode_imported": "Mode imported successfully"
+		"mode_imported": "Mode imported successfully",
+		"nested_git_repo_excluded": "Nested git repository at '{{path}}' will be excluded from checkpoints",
+		"nested_git_repos_excluded": "{{count}} nested git repositories will be excluded from checkpoints"
 	},
 	"answers": {
 		"yes": "Yes",

src/services/checkpoints/ShadowCheckpointService.ts

@@ -70,20 +70,6 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 			throw new Error("Shadow git repo already initialized")
 		}
 
-		const nestedGitPath = await this.getNestedGitRepository()
-
-		if (nestedGitPath) {
-			// Show persistent error message with the offending path
-			const relativePath = path.relative(this.workspaceDir, nestedGitPath)
-			const message = t("common:errors.nested_git_repos_warning", { path: relativePath })
-			vscode.window.showErrorMessage(message)
-
-			throw new Error(
-				`Checkpoints are disabled because a nested git repository was detected at: ${relativePath}. ` +
-					"Please remove or relocate nested git repositories to use the checkpoints feature.",
-			)
-		}
-
 		await fs.mkdir(this.checkpointsDir, { recursive: true })
 		const git = simpleGit(this.checkpointsDir)
 		const gitVersion = await git.version()
@@ -102,6 +88,7 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 				)
 			}
 
+			// Write exclude file which will include nested git repos
 			await this.writeExcludeFile()
 			this.baseHash = await git.revparse(["HEAD"])
 		} else {
@@ -111,6 +98,7 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 			await git.addConfig("commit.gpgSign", "false") // Disable commit signing for shadow repo.
 			await git.addConfig("user.name", "Roo Code")
 			await git.addConfig("user.email", "noreply@example.com")
+			// Write exclude file which will include nested git repos
 			await this.writeExcludeFile()
 			await this.stageAll(git)
 			const { commit } = await git.commit("initial commit", { "--allow-empty": null })
@@ -147,6 +135,16 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 	protected async writeExcludeFile() {
 		await fs.mkdir(path.join(this.dotGitDir, "info"), { recursive: true })
 		const patterns = await getExcludePatterns(this.workspaceDir)
+
+		// Add nested git repositories to exclude patterns
+		const nestedGitPaths = await this.getNestedGitRepositories()
+		for (const gitPath of nestedGitPaths) {
+			const relativePath = path.relative(this.workspaceDir, gitPath)
+			// Add the directory and all its contents to exclude patterns
+			patterns.push(relativePath + "/")
+			this.log(`[${this.constructor.name}#writeExcludeFile] excluding nested git repo: ${relativePath}`)
+		}
+
 		await fs.writeFile(path.join(this.dotGitDir, "info", "exclude"), patterns.join("\n"))
 	}
 
@@ -160,7 +158,7 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 		}
 	}
 
-	private async getNestedGitRepository(): Promise<string | null> {
+	private async getNestedGitRepositories(): Promise<string[]> {
 		try {
 			// Find all .git/HEAD files that are not at the root level.
 			const args = ["--files", "--hidden", "--follow", "-g", "**/.git/HEAD", this.workspaceDir]
@@ -182,10 +180,10 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 				)
 			})
 
-			if (nestedGitPaths.length > 0) {
-				// Get the first nested git repository path
+			const repoDirs: string[] = []
+			for (const gitPath of nestedGitPaths) {
 				// Remove .git/HEAD from the path to get the repository directory
-				const headPath = nestedGitPaths[0].path
+				const headPath = gitPath.path
 
 				// Use path module to properly extract the repository directory
 				// The HEAD file is at .git/HEAD, so we need to go up two directories
@@ -193,21 +191,35 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 				const repoDir = path.dirname(gitDir) // removes .git, gives us the repo directory
 
 				const absolutePath = path.join(this.workspaceDir, repoDir)
-
-				this.log(
-					`[${this.constructor.name}#getNestedGitRepository] found ${nestedGitPaths.length} nested git repositories, first at: ${repoDir}`,
-				)
-				return absolutePath
+				repoDirs.push(absolutePath)
 			}
 
-			return null
+			if (repoDirs.length > 0) {
+				this.log(
+					`[${this.constructor.name}#getNestedGitRepositories] found ${repoDirs.length} nested git repositories`,
+				)
+
+				// Show informational message to user
+				if (repoDirs.length === 1) {
+					const relativePath = path.relative(this.workspaceDir, repoDirs[0])
+					vscode.window.showInformationMessage(
+						t("common:info.nested_git_repo_excluded", { path: relativePath }),
+					)
+				} else {
+					vscode.window.showInformationMessage(
+						t("common:info.nested_git_repos_excluded", { count: repoDirs.length }),
+					)
+				}
+			}
+
+			return repoDirs
 		} catch (error) {
 			this.log(
-				`[${this.constructor.name}#getNestedGitRepository] failed to check for nested git repos: ${error instanceof Error ? error.message : String(error)}`,
+				`[${this.constructor.name}#getNestedGitRepositories] failed to check for nested git repos: ${error instanceof Error ? error.message : String(error)}`,
 			)
 
-			// If we can't check, assume there are no nested repos to avoid blocking the feature.
-			return null
+			// If we can't check, return empty array to avoid blocking the feature.
+			return []
 		}
 	}
 

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

@@ -379,7 +379,7 @@ describe.each([[RepoPerTaskCheckpointService, "RepoPerTaskCheckpointService"]])(
 		})
 
 		describe(`${klass.name}#hasNestedGitRepositories`, () => {
-			it("throws error when nested git repositories are detected during initialization", async () => {
+			it("excludes nested git repositories from checkpoints instead of throwing error", async () => {
 				// Create a new temporary workspace and service for this test.
 				const shadowDir = path.join(tmpDir, `${prefix}-nested-git-${Date.now()}`)
 				const workspaceDir = path.join(tmpDir, `workspace-nested-git-${Date.now()}`)
@@ -437,11 +437,25 @@ describe.each([[RepoPerTaskCheckpointService, "RepoPerTaskCheckpointService"]])(
 
 				const service = new klass(taskId, shadowDir, workspaceDir, () => {})
 
-				// Verify that initialization throws an error when nested git repos are detected
-				// The error message now includes the specific path of the nested repository
-				await expect(service.initShadowGit()).rejects.toThrowError(
-					/Checkpoints are disabled because a nested git repository was detected at:/,
-				)
+				// Verify that initialization succeeds and excludes nested git repos
+				await expect(service.initShadowGit()).resolves.not.toThrow()
+				expect(service.isInitialized).toBe(true)
+
+				// Verify that the nested git repo is excluded by checking the exclude file
+				const excludesPath = path.join(service.checkpointsDir, ".git", "info", "exclude")
+				const excludeContent = await fs.readFile(excludesPath, "utf-8")
+				expect(excludeContent).toContain("nested-project/")
+
+				// Verify that changes in the nested repo are not tracked
+				await fs.writeFile(nestedFile, "Modified content in nested repo")
+				const checkpoint = await service.saveCheckpoint("Test checkpoint")
+				// Should not create a checkpoint since nested repo changes are excluded
+				expect(checkpoint?.commit).toBeFalsy()
+
+				// Verify that changes in the main repo are still tracked
+				await fs.writeFile(mainFile, "Modified content in main repo")
+				const mainCheckpoint = await service.saveCheckpoint("Main repo checkpoint")
+				expect(mainCheckpoint?.commit).toBeTruthy()
 
 				// Clean up.
 				vitest.restoreAllMocks()