diff --git a/src/core/checkpoints/index.ts b/src/core/checkpoints/index.ts
index bc842c9f18..6233862be1 100644
--- a/src/core/checkpoints/index.ts
+++ b/src/core/checkpoints/index.ts
@@ -18,7 +18,11 @@ import { CheckpointServiceOptions, RepoPerTaskCheckpointService } from "../../se
 
 export async function getCheckpointService(
 	task: Task,
-	{ interval = 250, timeout = 15_000 }: { interval?: number; timeout?: number } = {},
+	{
+		interval = 250,
+		timeout = 15_000,
+		isInitialCall = false,
+	}: { interval?: number; timeout?: number; isInitialCall?: boolean } = {},
 ) {
 	if (!task.enableCheckpoints) {
 		return undefined
@@ -67,13 +71,14 @@ export async function getCheckpointService(
 		}
 
 		if (task.checkpointServiceInitializing) {
-			await pWaitFor(
-				() => {
-					console.log("[Task#getCheckpointService] waiting for service to initialize")
-					return !!task.checkpointService && !!task?.checkpointService?.isInitialized
-				},
-				{ interval, timeout },
-			)
+			// If this is the initial call from initiateTaskLoop, don't apply a timeout
+			// to allow large repositories to complete initialization
+			const waitOptions = isInitialCall ? { interval } : { interval, timeout }
+
+			await pWaitFor(() => {
+				console.log("[Task#getCheckpointService] waiting for service to initialize")
+				return !!task.checkpointService && !!task?.checkpointService?.isInitialized
+			}, waitOptions)
 			if (!task?.checkpointService) {
 				task.enableCheckpoints = false
 				return undefined
diff --git a/src/core/task/Task.ts b/src/core/task/Task.ts
index c5be865731..ca8906da6c 100644
--- a/src/core/task/Task.ts
+++ b/src/core/task/Task.ts
@@ -1661,7 +1661,8 @@ export class Task extends EventEmitter<TaskEvents> implements TaskLike {
 
 	private async initiateTaskLoop(userContent: Anthropic.Messages.ContentBlockParam[]): Promise<void> {
 		// Kicks off the checkpoints initialization process in the background.
-		getCheckpointService(this)
+		// Pass isInitialCall=true to avoid timeout for large repositories
+		getCheckpointService(this, { isInitialCall: true })
 
 		let nextUserContent = userContent
 		let includeFileDetails = true
diff --git a/src/services/checkpoints/ShadowCheckpointService.ts b/src/services/checkpoints/ShadowCheckpointService.ts
index ba56b8abc6..68f43dc333 100644
--- a/src/services/checkpoints/ShadowCheckpointService.ts
+++ b/src/services/checkpoints/ShadowCheckpointService.ts
@@ -145,7 +145,9 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 
 	private async stageAll(git: SimpleGit) {
 		try {
-			await git.add(".")
+			// Use --ignore-errors to continue even if some files can't be added (e.g., permission issues)
+			// This prevents the operation from failing in large repositories with problematic files
+			await git.add([".", "--ignore-errors"])
 		} catch (error) {
 			this.log(
 				`[${this.constructor.name}#stageAll] failed to add files to git: ${error instanceof Error ? error.message : String(error)}`,