diff --git a/src/integrations/checkpoints/CheckpointTracker.ts b/src/integrations/checkpoints/CheckpointTracker.ts
index 09aabbbc16..e7e6ab381d 100644
--- a/src/integrations/checkpoints/CheckpointTracker.ts
+++ b/src/integrations/checkpoints/CheckpointTracker.ts
@@ -1,7 +1,7 @@
 import fs from "fs/promises"
 import os from "os"
 import * as path from "path"
-import simpleGit from "simple-git"
+import simpleGit, { SimpleGit } from "simple-git"
 import * as vscode from "vscode"
 import { ClineProvider } from "../../core/webview/ClineProvider"
 import { fileExistsAtPath } from "../../utils/fs"
@@ -221,10 +221,8 @@ class CheckpointTracker {
 			await git.addConfig("user.name", "Cline Checkpoint")
 			await git.addConfig("user.email", "noreply@example.com")
 
+			await this.addAllFiles(git)
 			// Initial commit (--allow-empty ensures it works even with no files)
-			await this.renameNestedGitRepos(true)
-			await git.add(".")
-			await this.renameNestedGitRepos(false)
 			await git.commit("initial commit", { "--allow-empty": null })
 
 			return gitPath
@@ -251,9 +249,7 @@ class CheckpointTracker {
 		try {
 			const gitPath = await this.getShadowGitPath()
 			const git = simpleGit(path.dirname(gitPath))
-			await this.renameNestedGitRepos(true)
-			await git.add(".")
-			await this.renameNestedGitRepos(false)
+			await this.addAllFiles(git)
 			const result = await git.commit("checkpoint", {
 				"--allow-empty": null,
 			})
@@ -316,9 +312,7 @@ class CheckpointTracker {
 		}
 
 		// Stage all changes so that untracked files appear in diff summary
-		await this.renameNestedGitRepos(true)
-		await git.add(".")
-		await this.renameNestedGitRepos(false)
+		await this.addAllFiles(git)
 
 		const diffSummary = rhsHash ? await git.diffSummary([`${baseHash}..${rhsHash}`]) : await git.diffSummary([baseHash])
 
@@ -365,8 +359,19 @@ class CheckpointTracker {
 		return result
 	}
 
+	private async addAllFiles(git: SimpleGit) {
+		await this.renameNestedGitRepos(true)
+		try {
+			await git.add(".")
+		} catch (error) {
+			console.error("Failed to add files to git:", error)
+		} finally {
+			await this.renameNestedGitRepos(false)
+		}
+	}
+
 	// Since we use git to track checkpoints, we need to temporarily disable nested git repos to work around git's requirement of using submodules for nested repos.
-	async renameNestedGitRepos(disable: boolean) {
+	private async renameNestedGitRepos(disable: boolean) {
 		// Find all .git directories that are not at the root level
 		const gitPaths = await globby("**/.git" + (disable ? "" : GIT_DISABLED_SUFFIX), {
 			cwd: this.cwd,