test(checkpoints): fix GIT_DIR test to match Dev Container scenario

The previous test set GIT_DIR after initializing the checkpoint service,
which didn't properly verify the fix. In real Dev Containers, GIT_DIR is
already set when Roo starts and creates the checkpoint service.

Changes:
- Initialize workspace repo before setting GIT_DIR (workspace already
  exists in real Dev Containers before GIT_DIR is set)
- Set GIT_DIR before creating the checkpoint service to properly test
  that sanitization works during service initialization
- Temporarily clear GIT_DIR when verifying external repo wasn't modified,
  then restore it to continue testing with GIT_DIR set

This ensures the test accurately simulates the Dev Container environment
and verifies that checkpoint operations are properly isolated despite
GIT_DIR being present during initialization.

Author: heyseth

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

@@ -825,67 +825,93 @@ describe.each([[RepoPerTaskCheckpointService, "RepoPerTaskCheckpointService"]])(
 			})
 
 			it("isolates checkpoint operations from GIT_DIR environment variable", async () => {
-				// This test verifies the fix for the issue where GIT_DIR environment variable
-				// causes checkpoint commits to go to the wrong repository
-
-				// Create a separate git directory to simulate GIT_DIR pointing elsewhere
-				const externalGitDir = path.join(tmpDir, `external-git-${Date.now()}`)
-				await fs.mkdir(externalGitDir, { recursive: true })
-				const externalGit = simpleGit(externalGitDir)
-				await externalGit.init()
-				await externalGit.addConfig("user.name", "External User")
-				await externalGit.addConfig("user.email", "[email protected]")
-
-				// Create and commit a file in the external repo
-				const externalFile = path.join(externalGitDir, "external.txt")
-				await fs.writeFile(externalFile, "External content")
-				await externalGit.add(".")
-				await externalGit.commit("External commit")
-
-				// Store the original commit count in the external repo
-				const externalLogBefore = await externalGit.log()
-				const externalCommitCountBefore = externalLogBefore.total
-
-				// Set GIT_DIR to point to the external repository
-				const originalGitDir = process.env.GIT_DIR
-				const externalDotGit = path.join(externalGitDir, ".git")
-				process.env.GIT_DIR = externalDotGit
+			// This test verifies the fix for the issue where GIT_DIR environment variable
+			// causes checkpoint commits to go to the wrong repository.
+			// In the real-world Dev Container scenario, GIT_DIR is set BEFORE Roo starts,
+			// so we need to set it BEFORE creating the checkpoint service.
+
+			// Create a separate git directory to simulate GIT_DIR pointing elsewhere
+			const externalGitDir = path.join(tmpDir, `external-git-${Date.now()}`)
+			await fs.mkdir(externalGitDir, { recursive: true })
+			const externalGit = simpleGit(externalGitDir)
+			await externalGit.init()
+			await externalGit.addConfig("user.name", "External User")
+			await externalGit.addConfig("user.email", "[email protected]")
+
+			// Create and commit a file in the external repo
+			const externalFile = path.join(externalGitDir, "external.txt")
+			await fs.writeFile(externalFile, "External content")
+			await externalGit.add(".")
+			await externalGit.commit("External commit")
+
+			// Store the original commit count in the external repo
+			const externalLogBefore = await externalGit.log()
+			const externalCommitCountBefore = externalLogBefore.total
+
+			// Initialize the workspace repo BEFORE setting GIT_DIR
+			// (In Dev Containers, the workspace repo already exists before GIT_DIR is set)
+			const testShadowDir = path.join(tmpDir, `shadow-git-dir-test-${Date.now()}`)
+			const testWorkspaceDir = path.join(tmpDir, `workspace-git-dir-test-${Date.now()}`)
+			const testRepo = await initWorkspaceRepo({ workspaceDir: testWorkspaceDir })
+
+			// Set GIT_DIR to point to the external repository BEFORE creating the service
+			// This simulates the Dev Container environment where GIT_DIR is already set
+			const originalGitDir = process.env.GIT_DIR
+			const externalDotGit = path.join(externalGitDir, ".git")
+			process.env.GIT_DIR = externalDotGit
+
+			try {
+				// Create a new checkpoint service with GIT_DIR already set
+				// This is the key difference - we're creating the service
+				// while GIT_DIR is set, just like in a real Dev Container
+				const testService = await klass.create({
+					taskId: `test-git-dir-${Date.now()}`,
+					shadowDir: testShadowDir,
+					workspaceDir: testWorkspaceDir,
+					log: () => {},
+				})
+				await testService.initShadowGit()
 
-				try {
-					// Make a change in the workspace and save a checkpoint
-					await fs.writeFile(testFile, "Modified with GIT_DIR set")
-					const commit = await service.saveCheckpoint("Checkpoint with GIT_DIR set")
-					expect(commit?.commit).toBeTruthy()
-
-					// Verify the checkpoint was saved in the shadow repo, not the external repo
-					const externalLogAfter = await externalGit.log()
-					const externalCommitCountAfter = externalLogAfter.total
-
-					// External repo should have the same number of commits (no new commits)
-					expect(externalCommitCountAfter).toBe(externalCommitCountBefore)
-
-					// Verify the checkpoint is accessible in the shadow repo
-					const diff = await service.getDiff({ to: commit!.commit })
-					expect(diff).toHaveLength(1)
-					expect(diff[0].paths.relative).toBe("test.txt")
-					expect(diff[0].content.after).toBe("Modified with GIT_DIR set")
-
-					// Verify we can restore the checkpoint
-					await fs.writeFile(testFile, "Another modification")
-					await service.restoreCheckpoint(commit!.commit)
-					expect(await fs.readFile(testFile, "utf-8")).toBe("Modified with GIT_DIR set")
-				} finally {
-					// Restore original GIT_DIR
-					if (originalGitDir !== undefined) {
-						process.env.GIT_DIR = originalGitDir
-					} else {
-						delete process.env.GIT_DIR
-					}
+				// Make a change in the workspace and save a checkpoint
+				const testWorkspaceFile = path.join(testWorkspaceDir, "test.txt")
+				await fs.writeFile(testWorkspaceFile, "Modified with GIT_DIR set")
+				const commit = await testService.saveCheckpoint("Checkpoint with GIT_DIR set")
+				expect(commit?.commit).toBeTruthy()
+
+				// Verify the checkpoint was saved in the shadow repo, not the external repo
+				// Temporarily clear GIT_DIR to check the external repo
+				delete process.env.GIT_DIR
+				const externalGitCheck = simpleGit(externalGitDir)
+				const externalLogAfter = await externalGitCheck.log()
+				const externalCommitCountAfter = externalLogAfter.total
+				// Restore GIT_DIR
+				process.env.GIT_DIR = externalDotGit
 
-					// Clean up external git directory
-					await fs.rm(externalGitDir, { recursive: true, force: true })
+				// External repo should have the same number of commits (no new commits)
+				expect(externalCommitCountAfter).toBe(externalCommitCountBefore)
+
+				// Verify the checkpoint is accessible in the shadow repo
+				const diff = await testService.getDiff({ to: commit!.commit })
+				expect(diff).toHaveLength(1)
+				expect(diff[0].paths.relative).toBe("test.txt")
+				expect(diff[0].content.after).toBe("Modified with GIT_DIR set")
+
+				// Verify we can restore the checkpoint
+				await fs.writeFile(testWorkspaceFile, "Another modification")
+				await testService.restoreCheckpoint(commit!.commit)
+				expect(await fs.readFile(testWorkspaceFile, "utf-8")).toBe("Modified with GIT_DIR set")
+			} finally {
+				// Restore original GIT_DIR
+				if (originalGitDir !== undefined) {
+					process.env.GIT_DIR = originalGitDir
+				} else {
+					delete process.env.GIT_DIR
 				}
-			})
+
+				// Clean up external git directory
+				await fs.rm(externalGitDir, { recursive: true, force: true })
+			}
+		})
 		})
 	},
 )