diff --git a/src/i18n/locales/ca/common.json b/src/i18n/locales/ca/common.json
index 33188fce193..f83bbcad2b9 100644
--- a/src/i18n/locales/ca/common.json
+++ b/src/i18n/locales/ca/common.json
@@ -39,6 +39,7 @@
 		"checkpoint_diff_with_next": "Canvis comparats amb el següent punt de control",
 		"checkpoint_diff_since_first": "Canvis des del primer punt de control",
 		"checkpoint_diff_to_current": "Canvis a l'espai de treball actual",
+		"nested_git_repos_excluded": "Punts de control activats. S'han exclòs {{count}} repositoris git niats: {{paths}}.",
 		"nested_git_repos_warning": "Els punts de control estan deshabilitats perquè s'ha detectat un repositori git niat a: {{path}}. Per utilitzar punts de control, si us plau elimina o reubica aquest repositori git niat.",
 		"no_workspace": "Si us plau, obre primer una carpeta de projecte",
 		"update_support_prompt": "Ha fallat l'actualització del missatge de suport",
diff --git a/src/i18n/locales/de/common.json b/src/i18n/locales/de/common.json
index 861d9da5768..c5c7bc30881 100644
--- a/src/i18n/locales/de/common.json
+++ b/src/i18n/locales/de/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Änderungen im Vergleich zum nächsten Checkpoint",
 		"checkpoint_diff_since_first": "Änderungen seit dem ersten Checkpoint",
 		"checkpoint_diff_to_current": "Änderungen am aktuellen Arbeitsbereich",
+		"nested_git_repos_excluded": "Checkpoints aktiviert. {{count}} verschachtelte Git-Repositorys ausgeschlossen: {{paths}}.",
 		"nested_git_repos_warning": "Checkpoints sind deaktiviert, da ein verschachteltes Git-Repository erkannt wurde unter: {{path}}. Um Checkpoints zu verwenden, entferne oder verschiebe bitte dieses verschachtelte Git-Repository.",
 		"no_workspace": "Bitte öffne zuerst einen Projektordner",
 		"update_support_prompt": "Fehler beim Aktualisieren der Support-Nachricht",
diff --git a/src/i18n/locales/en/common.json b/src/i18n/locales/en/common.json
index d65fe183679..9c5eaf44773 100644
--- a/src/i18n/locales/en/common.json
+++ b/src/i18n/locales/en/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Changes compared with next checkpoint",
 		"checkpoint_diff_since_first": "Changes since first checkpoint",
 		"checkpoint_diff_to_current": "Changes to current workspace",
+		"nested_git_repos_excluded": "Checkpoints enabled. Excluded {{count}} nested git repositories: {{paths}}.",
 		"nested_git_repos_warning": "Checkpoints are disabled because a nested git repository was detected at: {{path}}. To use checkpoints, please remove or relocate this nested git repository.",
 		"no_workspace": "Please open a project folder first",
 		"update_support_prompt": "Failed to update support prompt",
diff --git a/src/i18n/locales/es/common.json b/src/i18n/locales/es/common.json
index 82be83956b0..90d0aca8361 100644
--- a/src/i18n/locales/es/common.json
+++ b/src/i18n/locales/es/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Cambios comparados con el siguiente punto de control",
 		"checkpoint_diff_since_first": "Cambios desde el primer punto de control",
 		"checkpoint_diff_to_current": "Cambios en el espacio de trabajo actual",
+		"nested_git_repos_excluded": "Puntos de control habilitados. Se excluyeron {{count}} repositorios git anidados: {{paths}}.",
 		"nested_git_repos_warning": "Los puntos de control están deshabilitados porque se detectó un repositorio git anidado en: {{path}}. Para usar puntos de control, por favor elimina o reubica este repositorio git anidado.",
 		"no_workspace": "Por favor, abre primero una carpeta de proyecto",
 		"update_support_prompt": "Error al actualizar el mensaje de soporte",
diff --git a/src/i18n/locales/fr/common.json b/src/i18n/locales/fr/common.json
index 6fc05ff94a3..79a11b4959f 100644
--- a/src/i18n/locales/fr/common.json
+++ b/src/i18n/locales/fr/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Modifications comparées au prochain point de contrôle",
 		"checkpoint_diff_since_first": "Modifications depuis le premier point de contrôle",
 		"checkpoint_diff_to_current": "Modifications de l'espace de travail actuel",
+		"nested_git_repos_excluded": "Points de contrôle activés. {{count}} dépôts git imbriqués exclus : {{paths}}.",
 		"nested_git_repos_warning": "Les points de contrôle sont désactivés car un dépôt git imbriqué a été détecté à : {{path}}. Pour utiliser les points de contrôle, veuillez supprimer ou déplacer ce dépôt git imbriqué.",
 		"no_workspace": "Veuillez d'abord ouvrir un espace de travail",
 		"update_support_prompt": "Erreur lors de la mise à jour du prompt de support",
diff --git a/src/i18n/locales/hi/common.json b/src/i18n/locales/hi/common.json
index 528ed6d45f5..23eea21c42f 100644
--- a/src/i18n/locales/hi/common.json
+++ b/src/i18n/locales/hi/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "अगले चेकपॉइंट के साथ तुलना किए गए बदलाव",
 		"checkpoint_diff_since_first": "पहले चेकपॉइंट के बाद से बदलाव",
 		"checkpoint_diff_to_current": "वर्तमान कार्यक्षेत्र में बदलाव",
+		"nested_git_repos_excluded": "चेकपॉइंट सक्षम। {{count}} नेस्टेड git रिपॉजिटरी बहिष्कृत: {{paths}}।",
 		"nested_git_repos_warning": "चेकपॉइंट अक्षम हैं क्योंकि {{path}} पर नेस्टेड git रिपॉजिटरी का पता चला है। चेकपॉइंट का उपयोग करने के लिए, कृपया इस नेस्टेड git रिपॉजिटरी को हटाएं या स्थानांतरित करें।",
 		"no_workspace": "कृपया पहले प्रोजेक्ट फ़ोल्डर खोलें",
 		"update_support_prompt": "सपोर्ट प्रॉम्प्ट अपडेट करने में विफल",
diff --git a/src/i18n/locales/id/common.json b/src/i18n/locales/id/common.json
index cb1c3231fb8..f1e91a1599a 100644
--- a/src/i18n/locales/id/common.json
+++ b/src/i18n/locales/id/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Perubahan dibandingkan dengan checkpoint berikutnya",
 		"checkpoint_diff_since_first": "Perubahan sejak checkpoint pertama",
 		"checkpoint_diff_to_current": "Perubahan ke ruang kerja saat ini",
+		"nested_git_repos_excluded": "Checkpoint diaktifkan. {{count}} repositori git bersarang dikecualikan: {{paths}}.",
 		"nested_git_repos_warning": "Checkpoint dinonaktifkan karena repositori git bersarang terdeteksi di: {{path}}. Untuk menggunakan checkpoint, silakan hapus atau pindahkan repositori git bersarang ini.",
 		"no_workspace": "Silakan buka folder proyek terlebih dahulu",
 		"update_support_prompt": "Gagal memperbarui support prompt",
diff --git a/src/i18n/locales/it/common.json b/src/i18n/locales/it/common.json
index b4e522cb732..e97b112b08b 100644
--- a/src/i18n/locales/it/common.json
+++ b/src/i18n/locales/it/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Modifiche confrontate con il checkpoint successivo",
 		"checkpoint_diff_since_first": "Modifiche dal primo checkpoint",
 		"checkpoint_diff_to_current": "Modifiche all'area di lavoro corrente",
+		"nested_git_repos_excluded": "Checkpoint abilitati. Esclusi {{count}} repository git annidati: {{paths}}.",
 		"nested_git_repos_warning": "I checkpoint sono disabilitati perché è stato rilevato un repository git annidato in: {{path}}. Per utilizzare i checkpoint, rimuovi o sposta questo repository git annidato.",
 		"no_workspace": "Per favore, apri prima una cartella di progetto",
 		"update_support_prompt": "Errore durante l'aggiornamento del messaggio di supporto",
diff --git a/src/i18n/locales/ja/common.json b/src/i18n/locales/ja/common.json
index 7b63b6f7298..aa7194c2ac4 100644
--- a/src/i18n/locales/ja/common.json
+++ b/src/i18n/locales/ja/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "次のチェックポイントと比較した変更点",
 		"checkpoint_diff_since_first": "最初のチェックポイントからの変更点",
 		"checkpoint_diff_to_current": "現在のワークスペースへの変更点",
+		"nested_git_repos_excluded": "チェックポイントが有効です。{{count}} 個のネストされたgitリポジトリを除外しました: {{paths}}。",
 		"nested_git_repos_warning": "{{path}} でネストされたgitリポジトリが検出されたため、チェックポイントが無効になっています。チェックポイントを使用するには、このネストされたgitリポジトリを削除または移動してください。",
 		"no_workspace": "まずプロジェクトフォルダを開いてください",
 		"update_support_prompt": "サポートメッセージの更新に失敗しました",
diff --git a/src/i18n/locales/ko/common.json b/src/i18n/locales/ko/common.json
index fbde3225bb1..27d1baa8f32 100644
--- a/src/i18n/locales/ko/common.json
+++ b/src/i18n/locales/ko/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "다음 체크포인트와 비교한 변경 사항",
 		"checkpoint_diff_since_first": "첫 번째 체크포인트 이후의 변경 사항",
 		"checkpoint_diff_to_current": "현재 작업 공간으로의 변경 사항",
+		"nested_git_repos_excluded": "체크포인트가 활성화되었습니다. {{count}}개의 중첩된 git 저장소를 제외했습니다: {{paths}}.",
 		"nested_git_repos_warning": "{{path}}에서 중첩된 git 저장소가 감지되어 체크포인트가 비활성화되었습니다. 체크포인트를 사용하려면 이 중첩된 git 저장소를 제거하거나 이동해주세요.",
 		"no_workspace": "먼저 프로젝트 폴더를 열어주세요",
 		"update_support_prompt": "지원 프롬프트 업데이트에 실패했습니다",
diff --git a/src/i18n/locales/nl/common.json b/src/i18n/locales/nl/common.json
index eba274c96ec..51ae0aeefed 100644
--- a/src/i18n/locales/nl/common.json
+++ b/src/i18n/locales/nl/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Wijzigingen vergeleken met volgend checkpoint",
 		"checkpoint_diff_since_first": "Wijzigingen sinds eerste checkpoint",
 		"checkpoint_diff_to_current": "Wijzigingen in huidige werkruimte",
+		"nested_git_repos_excluded": "Checkpoints ingeschakeld. {{count}} geneste git-repositories uitgesloten: {{paths}}.",
 		"nested_git_repos_warning": "Checkpoints zijn uitgeschakeld omdat een geneste git-repository is gedetecteerd op: {{path}}. Om checkpoints te gebruiken, verwijder of verplaats deze geneste git-repository.",
 		"no_workspace": "Open eerst een projectmap",
 		"update_support_prompt": "Bijwerken van ondersteuningsprompt mislukt",
diff --git a/src/i18n/locales/pl/common.json b/src/i18n/locales/pl/common.json
index 20b568281bb..0f766bb55df 100644
--- a/src/i18n/locales/pl/common.json
+++ b/src/i18n/locales/pl/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Zmiany w porównaniu z następnym punktem kontrolnym",
 		"checkpoint_diff_since_first": "Zmiany od pierwszego punktu kontrolnego",
 		"checkpoint_diff_to_current": "Zmiany w bieżącym obszarze roboczym",
+		"nested_git_repos_excluded": "Punkty kontrolne włączone. Wykluczono {{count}} zagnieżdżonych repozytoriów git: {{paths}}.",
 		"nested_git_repos_warning": "Punkty kontrolne są wyłączone, ponieważ wykryto zagnieżdżone repozytorium git w: {{path}}. Aby używać punktów kontrolnych, usuń lub przenieś to zagnieżdżone repozytorium git.",
 		"no_workspace": "Najpierw otwórz folder projektu",
 		"update_support_prompt": "Nie udało się zaktualizować komunikatu wsparcia",
diff --git a/src/i18n/locales/pt-BR/common.json b/src/i18n/locales/pt-BR/common.json
index 38abc8c8047..936a326e92e 100644
--- a/src/i18n/locales/pt-BR/common.json
+++ b/src/i18n/locales/pt-BR/common.json
@@ -39,6 +39,7 @@
 		"checkpoint_diff_with_next": "Alterações comparadas com o próximo ponto de verificação",
 		"checkpoint_diff_since_first": "Alterações desde o primeiro ponto de verificação",
 		"checkpoint_diff_to_current": "Alterações no espaço de trabalho atual",
+		"nested_git_repos_excluded": "Checkpoints habilitados. {{count}} repositórios git aninhados excluídos: {{paths}}.",
 		"nested_git_repos_warning": "Os checkpoints estão desabilitados porque um repositório git aninhado foi detectado em: {{path}}. Para usar checkpoints, por favor remova ou realoque este repositório git aninhado.",
 		"no_workspace": "Por favor, abra primeiro uma pasta de projeto",
 		"update_support_prompt": "Falha ao atualizar o prompt de suporte",
diff --git a/src/i18n/locales/ru/common.json b/src/i18n/locales/ru/common.json
index d124f597318..1c908e10f43 100644
--- a/src/i18n/locales/ru/common.json
+++ b/src/i18n/locales/ru/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Изменения по сравнению со следующей контрольной точкой",
 		"checkpoint_diff_since_first": "Изменения с первой контрольной точки",
 		"checkpoint_diff_to_current": "Изменения в текущем рабочем пространстве",
+		"nested_git_repos_excluded": "Контрольные точки включены. Исключено {{count}} вложенных git-репозиториев: {{paths}}.",
 		"nested_git_repos_warning": "Контрольные точки отключены, поскольку обнаружен вложенный git-репозиторий в: {{path}}. Чтобы использовать контрольные точки, пожалуйста, удалите или переместите этот вложенный git-репозиторий.",
 		"no_workspace": "Пожалуйста, сначала откройте папку проекта",
 		"update_support_prompt": "Не удалось обновить промпт поддержки",
diff --git a/src/i18n/locales/tr/common.json b/src/i18n/locales/tr/common.json
index 00dcf6fc33d..d73ce085931 100644
--- a/src/i18n/locales/tr/common.json
+++ b/src/i18n/locales/tr/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Sonraki kontrol noktasıyla karşılaştırılan değişiklikler",
 		"checkpoint_diff_since_first": "İlk kontrol noktasından bu yana yapılan değişiklikler",
 		"checkpoint_diff_to_current": "Mevcut çalışma alanındaki değişiklikler",
+		"nested_git_repos_excluded": "Kontrol noktaları etkinleştirildi. {{count}} iç içe git deposu hariç tutuldu: {{paths}}.",
 		"nested_git_repos_warning": "{{path}} konumunda iç içe git deposu tespit edildiği için kontrol noktaları devre dışı bırakıldı. Kontrol noktalarını kullanmak için lütfen bu iç içe git deposunu kaldırın veya taşıyın.",
 		"no_workspace": "Lütfen önce bir proje klasörü açın",
 		"update_support_prompt": "Destek istemi güncellenemedi",
diff --git a/src/i18n/locales/vi/common.json b/src/i18n/locales/vi/common.json
index decd4ff53ef..92f49e0c328 100644
--- a/src/i18n/locales/vi/common.json
+++ b/src/i18n/locales/vi/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "Các thay đổi được so sánh với điểm kiểm tra tiếp theo",
 		"checkpoint_diff_since_first": "Các thay đổi kể từ điểm kiểm tra đầu tiên",
 		"checkpoint_diff_to_current": "Các thay đổi đối với không gian làm việc hiện tại",
+		"nested_git_repos_excluded": "Điểm kiểm tra đã bật. Đã loại trừ {{count}} kho git lồng nhau: {{paths}}.",
 		"nested_git_repos_warning": "Điểm kiểm tra bị vô hiệu hóa vì phát hiện kho git lồng nhau tại: {{path}}. Để sử dụng điểm kiểm tra, vui lòng xóa hoặc di chuyển kho git lồng nhau này.",
 		"no_workspace": "Vui lòng mở thư mục dự án trước",
 		"update_support_prompt": "Không thể cập nhật lời nhắc hỗ trợ",
diff --git a/src/i18n/locales/zh-CN/common.json b/src/i18n/locales/zh-CN/common.json
index 6df1f78b167..27b25185c2f 100644
--- a/src/i18n/locales/zh-CN/common.json
+++ b/src/i18n/locales/zh-CN/common.json
@@ -40,6 +40,7 @@
 		"checkpoint_diff_with_next": "与下一个存档点比较的更改",
 		"checkpoint_diff_since_first": "自第一个存档点以来的更改",
 		"checkpoint_diff_to_current": "对当前工作区的更改",
+		"nested_git_repos_excluded": "存档点已启用。已排除 {{count}} 个嵌套的 git 仓库：{{paths}}。",
 		"nested_git_repos_warning": "存档点已禁用，因为在 {{path}} 检测到嵌套的 git 仓库。要使用存档点，请移除或重新定位此嵌套的 git 仓库。",
 		"no_workspace": "请先打开项目文件夹",
 		"update_support_prompt": "更新支持消息失败",
diff --git a/src/i18n/locales/zh-TW/common.json b/src/i18n/locales/zh-TW/common.json
index be4a76fc5b9..7a1067ca669 100644
--- a/src/i18n/locales/zh-TW/common.json
+++ b/src/i18n/locales/zh-TW/common.json
@@ -35,6 +35,7 @@
 		"checkpoint_diff_with_next": "與下一個存檔點比較的變更",
 		"checkpoint_diff_since_first": "自第一個存檔點以來的變更",
 		"checkpoint_diff_to_current": "對目前工作區的變更",
+		"nested_git_repos_excluded": "存檔點已啟用。已排除 {{count}} 個巢狀的 git 儲存庫：{{paths}}。",
 		"nested_git_repos_warning": "存檔點已停用，因為在 {{path}} 偵測到巢狀的 git 儲存庫。要使用存檔點，請移除或重新配置此巢狀的 git 儲存庫。",
 		"no_workspace": "請先開啟專案資料夾",
 		"update_support_prompt": "更新支援訊息失敗",
diff --git a/src/services/checkpoints/ShadowCheckpointService.ts b/src/services/checkpoints/ShadowCheckpointService.ts
index fee08b2fa4b..8b4aa6f7b46 100644
--- a/src/services/checkpoints/ShadowCheckpointService.ts
+++ b/src/services/checkpoints/ShadowCheckpointService.ts
@@ -81,6 +81,8 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 
 	protected _checkpoints: string[] = []
 	protected _baseHash?: string
+	protected nestedRepoPaths: string[] = []
+	protected nestedRepoDetectionFailed = false
 
 	protected readonly dotGitDir: string
 	protected git?: SimpleGit
@@ -129,18 +131,30 @@ export abstract class ShadowCheckpointService extends EventEmitter {
 			throw new Error("Shadow git repo already initialized")
 		}
 
-		const nestedGitPath = await this.getNestedGitRepository()
+		// Detect nested git repos once at init. Stored as workspace-relative POSIX
+		// paths (e.g. "frontend", "packages/foo") for use in exclude patterns and
+		// pathspec excludes. Detection is intentionally not repeated on every save
+		// because ripgrep scans are expensive in large workspaces; instead, stageAll()
+		// enforces safety post-staging by scanning for gitlink entries.
+		this.nestedRepoPaths = await this.findNestedGitRepositories()
 
-		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: ${relativePath}. ` +
-					"Please remove or relocate nested git repositories to use the checkpoints feature.",
+		if (this.nestedRepoPaths.length > 0) {
+			const sortedPaths = [...this.nestedRepoPaths].sort()
+			this.log(
+				`[${this.constructor.name}#initShadowGit] found ${sortedPaths.length} nested git repositories, excluding from checkpoints: ${sortedPaths.join(", ")}`,
 			)
+			const maxDisplayPaths = 5
+			const shown = sortedPaths.slice(0, maxDisplayPaths)
+			const remaining = sortedPaths.length - shown.length
+			const displayPaths =
+				remaining > 0
+					? `${shown.join(", ")}, \u2026 (${remaining} more)`
+					: shown.join(", ")
+			const message = t("common:errors.nested_git_repos_excluded", {
+				count: String(sortedPaths.length),
+				paths: displayPaths,
+			})
+			vscode.window.showWarningMessage(message)
 		}
 
 		await fs.mkdir(this.checkpointsDir, { recursive: true })
@@ -206,67 +220,334 @@ 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 anchored exclude patterns for nested git repos so the shadow git
+		// ignores them entirely. Leading "/" anchors the pattern to the worktree
+		// root, preventing accidental matches at other directory depths.
+		for (const repoRel of this.nestedRepoPaths) {
+			patterns.push(`/${repoRel}/`)
+		}
+
 		await fs.writeFile(path.join(this.dotGitDir, "info", "exclude"), patterns.join("\n"))
 	}
 
+	private isIgnoredPathsAddError(error: unknown): boolean {
+		const msg = (error instanceof Error ? error.message : String(error)).toLowerCase()
+		return msg.includes("paths are ignored by one of your .gitignore files")
+	}
+
 	private async stageAll(git: SimpleGit) {
+		const addArgs: string[] = ["--ignore-errors", "--", "."]
+
+		// Add top-anchored pathspec excludes for each known nested repo.
+		for (const repoRel of this.nestedRepoPaths) {
+			addArgs.push(`:(exclude,top)${repoRel}/`)
+		}
+
 		try {
-			await git.add([".", "--ignore-errors"])
+			await git.add(addArgs)
 		} catch (error) {
+			if (!this.isIgnoredPathsAddError(error)) {
+				// Real failure (index corruption, disk full, lock file, etc.)
+				// must abort — proceeding would produce a bad checkpoint.
+				throw error
+			}
+
 			this.log(
-				`[${this.constructor.name}#stageAll] failed to add files to git: ${error instanceof Error ? error.message : String(error)}`,
+				`[${this.constructor.name}#stageAll] git add ignored-paths warning (expected): ${error instanceof Error ? error.message : String(error)}`,
+			)
+		}
+
+		// Safety enforcement runs outside the git-add catch so their
+		// throws propagate to saveCheckpoint() and abort the save.
+
+		// Post-staging safety layer 1: scan for gitlink entries (mode 160000)
+		// that indicate a nested repo slipped through despite the exclude file
+		// and pathspec. This catches repos added after init without requiring
+		// expensive re-detection on every save.
+		await this.purgeGitlinkEntries(git)
+
+		// Post-staging safety layer 2: when detection failed, walk parent
+		// directories of staged paths on the filesystem to find .git
+		// markers that reveal nested repos. This catches the case where
+		// nested repo source files were staged as regular files (the
+		// shadow repo's .git/ exclude hides the marker from git, so no
+		// gitlink is created and purgeGitlinkEntries cannot help). Gated
+		// on nestedRepoDetectionFailed to avoid filesystem walks on the
+		// normal path where the exclude file and pathspec are trustworthy.
+		if (this.nestedRepoDetectionFailed) {
+			await this.rejectStagedNestedRepoContent(git)
+		}
+	}
+
+	private async purgeGitlinkEntries(git: SimpleGit) {
+		const lsOutput = await git.raw(["ls-files", "--stage"])
+		const gitlinkPaths: string[] = []
+
+		for (const line of lsOutput.split("\n")) {
+			if (line.startsWith("160000 ")) {
+				// Format: "160000 <hash> <stage>\t<path>"
+				const tabIndex = line.indexOf("\t")
+				if (tabIndex !== -1) {
+					gitlinkPaths.push(line.substring(tabIndex + 1))
+				}
+			}
+		}
+
+		if (gitlinkPaths.length === 0) {
+			return
+		}
+
+		this.log(
+			`[${this.constructor.name}#purgeGitlinkEntries] removing ${gitlinkPaths.length} gitlink entries: ${gitlinkPaths.join(", ")}`,
+		)
+
+		for (const gitlinkPath of gitlinkPaths) {
+			await git.raw(["rm", "--cached", "--ignore-unmatch", "-r", "--", gitlinkPath])
+		}
+
+		// Triggered re-detection: a gitlink that was not in our known list
+		// means a nested repo appeared after init. Update the exclude set so
+		// subsequent saves are protected by the exclude file too.
+		const newPaths = gitlinkPaths.filter(
+			(p) => !this.nestedRepoPaths.includes(p),
+		)
+
+		if (newPaths.length > 0) {
+			this.log(
+				`[${this.constructor.name}#purgeGitlinkEntries] discovered ${newPaths.length} new nested repos, updating excludes: ${newPaths.join(", ")}`,
+			)
+			this.nestedRepoPaths = Array.from(new Set([...this.nestedRepoPaths, ...newPaths]))
+			await this.writeExcludeFile()
+		}
+
+		// Verify all gitlinks are gone. If any persist, staging is unsafe and
+		// the checkpoint save must be aborted.
+		const verifyOutput = await git.raw(["ls-files", "--stage"])
+		const remaining = verifyOutput.split("\n").filter((l) => l.startsWith("160000 "))
+		if (remaining.length > 0) {
+			throw new Error(
+				`Staging is unsafe: ${remaining.length} gitlink entries persist after purge. ` +
+					"Aborting checkpoint save.",
+			)
+		}
+	}
+
+	/**
+	 * Conservative fallback for when ripgrep-based detection failed. Walks
+	 * parent directories of staged paths on the filesystem to discover `.git`
+	 * markers (`.git/HEAD` for real repos, `.git` pointer files for
+	 * submodules/worktrees). Unstages any nested repo roots found and updates
+	 * the exclude list for subsequent saves. Throws if staged paths under a
+	 * nested repo root persist after removal.
+	 *
+	 * Only called when `nestedRepoDetectionFailed` is true, so the filesystem
+	 * walk cost is acceptable — it is the rare error-recovery path.
+	 */
+	private async rejectStagedNestedRepoContent(git: SimpleGit) {
+		const rawOutput = await git.raw(["diff", "--cached", "--name-only", "-z"])
+		const stagedPaths = rawOutput.split("\0").filter(Boolean)
+
+		if (stagedPaths.length === 0) {
+			return
+		}
+
+		// Walk unique ancestor directories of staged paths, checking for
+		// .git markers on the filesystem. The checkedDirs cache ensures each
+		// directory is stat'd at most once regardless of how many staged
+		// files share it.
+		const checkedDirs = new Set<string>()
+		const nestedRepoRoots = new Set<string>()
+
+		for (const filePath of stagedPaths) {
+			// Staged paths from git are POSIX-style; use path.posix to
+			// avoid platform-dependent separator drift on Windows.
+			let dir = path.posix.dirname(filePath)
+
+			while (dir && dir !== "." && dir !== "") {
+				if (checkedDirs.has(dir)) {
+					dir = path.posix.dirname(dir)
+					continue // skip stat calls but keep walking up — an earlier
+					// traversal may have found a deeper repo and broken out
+					// before checking this directory's ancestors
+				}
+
+				checkedDirs.add(dir)
+
+				// Check for .git directory (real nested repo).
+				// path.join is used here to build filesystem paths for stat calls.
+				const gitHeadPath = path.join(this.workspaceDir, dir, ".git", "HEAD")
+				if (await fileExistsAtPath(gitHeadPath)) {
+					nestedRepoRoots.add(dir)
+					break
+				}
+
+				// Check for .git pointer file (submodule / worktree).
+				const gitFilePath = path.join(this.workspaceDir, dir, ".git")
+				try {
+					const stat = await fs.stat(gitFilePath)
+					if (stat.isFile()) {
+						const content = await fs.readFile(gitFilePath, "utf8")
+						if (content.trimStart().startsWith("gitdir:")) {
+							nestedRepoRoots.add(dir)
+							break
+						}
+					}
+				} catch {
+					// Not a .git pointer file — continue walking up.
+				}
+
+				dir = path.posix.dirname(dir)
+			}
+		}
+
+		if (nestedRepoRoots.size === 0) {
+			return
+		}
+
+		const roots = Array.from(nestedRepoRoots)
+
+		this.log(
+			`[${this.constructor.name}#rejectStagedNestedRepoContent] detection fallback found ${roots.length} nested repos via filesystem: ${roots.join(", ")}`,
+		)
+
+		// Unstage nested repo contents.
+		for (const root of roots) {
+			await git.raw(["rm", "--cached", "--ignore-unmatch", "-r", "--", root + "/"])
+		}
+
+		// Update exclude list so subsequent saves are protected.
+		this.nestedRepoPaths = Array.from(new Set([...this.nestedRepoPaths, ...roots]))
+		await this.writeExcludeFile()
+
+		// Verify no staged paths remain under nested repo roots.
+		const verifyRaw = await git.raw(["diff", "--cached", "--name-only", "-z"])
+		const verifyPaths = verifyRaw.split("\0").filter(Boolean)
+		const leaked = verifyPaths.filter((p) => {
+			const pNorm = p.replace(/\\/g, "/")
+			return roots.some((r) => pNorm === r || pNorm.startsWith(r + "/"))
+		})
+
+		if (leaked.length > 0) {
+			throw new Error(
+				`Staging is unsafe: ${leaked.length} paths from nested repos persist after removal. ` +
+					"Aborting checkpoint save.",
 			)
 		}
 	}
 
-	private async getNestedGitRepository(): Promise<string | null> {
+	/**
+	 * Finds all nested git repositories inside the workspace.
+	 *
+	 * Returns workspace-relative POSIX paths (e.g. ["frontend", "packages/foo"])
+	 * suitable for use in gitignore patterns and pathspec excludes. Detection
+	 * covers both real `.git/` directories and `.git` pointer files used by
+	 * submodules and worktrees. The `--follow` flag is intentionally omitted to
+	 * avoid symlink false positives.
+	 *
+	 * On success, sets `nestedRepoDetectionFailed` to false. On error, sets it
+	 * to true and returns an empty array. When detection has failed, downstream
+	 * safety is enforced by `rejectStagedNestedRepoContent()` in `stageAll()`.
+	 */
+	private async findNestedGitRepositories(): 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]
-
-			const gitPaths = await executeRipgrep({ args, workspacePath: this.workspaceDir })
-
-			// Filter to only include nested git directories (not the root .git).
-			// Since we're searching for HEAD files, we expect type to be "file"
-			const nestedGitPaths = gitPaths.filter(({ type, path: filePath }) => {
-				// Check if it's a file and is a nested .git/HEAD (not at root)
-				if (type !== "file") return false
-
-				// Ensure it's a .git/HEAD file and not the root one
-				const normalizedPath = filePath.replace(/\\/g, "/")
-				return (
-					normalizedPath.includes(".git/HEAD") &&
-					!normalizedPath.startsWith(".git/") &&
-					normalizedPath !== ".git/HEAD"
-				)
-			})
+			// Search 1: real nested .git directories via their HEAD file.
+			const headArgs = ["--files", "--hidden", "-g", "**/.git/HEAD", this.workspaceDir]
+			const headResults = await executeRipgrep({ args: headArgs, workspacePath: this.workspaceDir })
 
-			if (nestedGitPaths.length > 0) {
-				// Get the first nested git repository path
-				// Remove .git/HEAD from the path to get the repository directory
-				const headPath = nestedGitPaths[0].path
+			// Search 2: .git pointer files (submodules / worktrees).
+			const pointerArgs = ["--files", "--hidden", "-g", "**/.git", this.workspaceDir]
+			const pointerResults = await executeRipgrep({ args: pointerArgs, workspacePath: this.workspaceDir })
 
-				// Use path module to properly extract the repository directory
-				// The HEAD file is at .git/HEAD, so we need to go up two directories
-				const gitDir = path.dirname(headPath) // removes HEAD, gives us .git
-				const repoDir = path.dirname(gitDir) // removes .git, gives us the repo directory
+			const repoPaths = new Set<string>()
 
-				const absolutePath = path.join(this.workspaceDir, repoDir)
+			// Process .git/HEAD results — each gives us a nested .git directory.
+			for (const { type, path: filePath } of headResults) {
+				if (type !== "file") {
+					continue
+				}
 
-				this.log(
-					`[${this.constructor.name}#getNestedGitRepository] found ${nestedGitPaths.length} nested git repositories, first at: ${repoDir}`,
-				)
-				return absolutePath
+				// Skip the workspace root's own .git/HEAD.
+				const normalized = filePath.replace(/\\/g, "/")
+				if (normalized === ".git/HEAD") {
+					continue
+				}
+
+				// Verify structure: basename must be HEAD, parent must be .git.
+				if (path.basename(filePath) !== "HEAD" || path.basename(path.dirname(filePath)) !== ".git") {
+					continue
+				}
+
+				// .git/HEAD → .git → repo directory
+				const repoDir = path.dirname(path.dirname(filePath))
+				const repoRel = repoDir.replace(/\\/g, "/")
+
+				// Skip if resolved to workspace root or outside workspace.
+				if (repoRel === "." || repoRel === "" || repoRel.startsWith("..")) {
+					continue
+				}
+
+				repoPaths.add(repoRel)
 			}
 
-			return null
+			// Process .git pointer file results — submodules store a file
+			// containing "gitdir: <path>" instead of a directory.
+			for (const { type, path: filePath } of pointerResults) {
+				if (type !== "file") {
+					continue
+				}
+
+				// Skip the workspace root's own .git.
+				const normalized = filePath.replace(/\\/g, "/")
+				if (normalized === ".git") {
+					continue
+				}
+
+				// Only consider entries where the basename is exactly ".git".
+				if (path.basename(filePath) !== ".git") {
+					continue
+				}
+
+				// Validate that this is a pointer file (contains "gitdir:").
+				const absPath = path.join(this.workspaceDir, filePath)
+				try {
+					const content = await fs.readFile(absPath, "utf8")
+					if (!content.trimStart().startsWith("gitdir:")) {
+						continue
+					}
+				} catch {
+					// Can't read the file — skip it.
+					continue
+				}
+
+				const repoDir = path.dirname(filePath)
+				const repoRel = repoDir.replace(/\\/g, "/")
+
+				if (repoRel === "." || repoRel === "" || repoRel.startsWith("..")) {
+					continue
+				}
+
+				repoPaths.add(repoRel)
+			}
+
+			const result = Array.from(repoPaths)
+
+			this.log(
+				`[${this.constructor.name}#findNestedGitRepositories] found ${result.length} nested git repositories: ${result.join(", ") || "(none)"}`,
+			)
+
+			this.nestedRepoDetectionFailed = false
+			return result
 		} catch (error) {
 			this.log(
-				`[${this.constructor.name}#getNestedGitRepository] failed to check for nested git repos: ${error instanceof Error ? error.message : String(error)}`,
+				`[${this.constructor.name}#findNestedGitRepositories] detection failed: ${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
+			// Fail-soft: detection failure is not fatal to init, but staging
+			// will run the conservative filesystem-based scan via
+			// rejectStagedNestedRepoContent() to prevent unsafe checkpoints.
+			this.nestedRepoDetectionFailed = true
+			return []
 		}
 	}
 
diff --git a/src/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts b/src/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts
index ee8f7bbdc9c..22564747b83 100644
--- a/src/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts
+++ b/src/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts
@@ -378,8 +378,8 @@ describe.each([[RepoPerTaskCheckpointService, "RepoPerTaskCheckpointService"]])(
 			})
 		})
 
-		describe(`${klass.name}#hasNestedGitRepositories`, () => {
-			it("throws error when nested git repositories are detected during initialization", async () => {
+		describe(`${klass.name}#nestedGitRepositories`, () => {
+			it("succeeds and excludes nested repos from checkpoints", 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()}`)
@@ -411,37 +411,44 @@ describe.each([[RepoPerTaskCheckpointService, "RepoPerTaskCheckpointService"]])(
 				await mainGit.add(".")
 				await mainGit.commit("Initial commit in main repo")
 
-				// Confirm nested git directory exists before initialization.
-				const nestedGitDir = path.join(nestedRepoPath, ".git")
-				const headFile = path.join(nestedGitDir, "HEAD")
-				await fs.writeFile(headFile, "HEAD")
-				expect(await fileExistsAtPath(nestedGitDir)).toBe(true)
-
 				vitest.spyOn(fileSearch, "executeRipgrep").mockImplementation(({ args }) => {
-					const searchPattern = args[4]
+					const searchPattern = args[3]
 
-					if (searchPattern.includes(".git/HEAD")) {
-						// Return the HEAD file path, not the .git directory
-						const headFilePath = path.join(path.relative(workspaceDir, nestedGitDir), "HEAD")
+					if (searchPattern === "**/.git/HEAD") {
 						return Promise.resolve([
 							{
-								path: headFilePath,
-								type: "file", // HEAD is a file, not a folder
+								path: "nested-project/.git/HEAD",
+								type: "file" as const,
 								label: "HEAD",
 							},
 						])
-					} else {
+					} else if (searchPattern === "**/.git") {
 						return Promise.resolve([])
 					}
+
+					return Promise.resolve([])
 				})
 
-				const service = new klass(taskId, shadowDir, workspaceDir, () => {})
+				const testService = 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:/,
-				)
+				// Initialization should succeed (not throw).
+				await expect(testService.initShadowGit()).resolves.not.toThrow()
+				expect(testService.isInitialized).toBe(true)
+
+				// Verify exclude file contains the nested repo pattern.
+				const excludePath = path.join(shadowDir, ".git", "info", "exclude")
+				const excludeContent = await fs.readFile(excludePath, "utf-8")
+				expect(excludeContent).toContain("/nested-project/")
+
+				// Save a checkpoint — nested repo files should not appear in diff.
+				await fs.writeFile(mainFile, "Modified main content")
+				const commit = await testService.saveCheckpoint("Checkpoint with nested repo")
+				expect(commit?.commit).toBeTruthy()
+
+				const diff = await testService.getDiff({ to: commit!.commit })
+				const diffPaths = diff.map((d) => d.paths.relative)
+				expect(diffPaths).toContain("main-file.txt")
+				expect(diffPaths).not.toContain("nested-project/nested-file.txt")
 
 				// Clean up.
 				vitest.restoreAllMocks()
@@ -468,21 +475,331 @@ describe.each([[RepoPerTaskCheckpointService, "RepoPerTaskCheckpointService"]])(
 				await mainGit.commit("Initial commit in main repo")
 
 				vitest.spyOn(fileSearch, "executeRipgrep").mockImplementation(() => {
-					// Return empty array to simulate no nested git repos found
 					return Promise.resolve([])
 				})
 
-				const service = new klass(taskId, shadowDir, workspaceDir, () => {})
+				const testService = new klass(taskId, shadowDir, workspaceDir, () => {})
 
-				// Verify that initialization succeeds when no nested git repos are detected
-				await expect(service.initShadowGit()).resolves.not.toThrow()
-				expect(service.isInitialized).toBe(true)
+				await expect(testService.initShadowGit()).resolves.not.toThrow()
+				expect(testService.isInitialized).toBe(true)
 
 				// Clean up.
 				vitest.restoreAllMocks()
 				await fs.rm(shadowDir, { recursive: true, force: true })
 				await fs.rm(workspaceDir, { recursive: true, force: true })
 			})
+
+			it("detects submodule .git pointer files", async () => {
+				const shadowDir = path.join(tmpDir, `${prefix}-submodule-${Date.now()}`)
+				const workspaceDir = path.join(tmpDir, `workspace-submodule-${Date.now()}`)
+
+				await fs.mkdir(workspaceDir, { recursive: true })
+				const mainGit = simpleGit(workspaceDir)
+				await mainGit.init()
+				await mainGit.addConfig("user.name", "Roo Code")
+				await mainGit.addConfig("user.email", "support@roocode.com")
+
+				// Create a submodule-style .git pointer file.
+				const submodulePath = path.join(workspaceDir, "libs", "shared")
+				await fs.mkdir(submodulePath, { recursive: true })
+				await fs.writeFile(
+					path.join(submodulePath, ".git"),
+					"gitdir: ../../.git/modules/libs/shared\n",
+				)
+				await fs.writeFile(path.join(submodulePath, "index.ts"), "export default {}")
+
+				const mainFile = path.join(workspaceDir, "main.ts")
+				await fs.writeFile(mainFile, "import shared from './libs/shared'")
+				await mainGit.add(".")
+				await mainGit.commit("Initial commit")
+
+				vitest.spyOn(fileSearch, "executeRipgrep").mockImplementation(({ args }) => {
+					const searchPattern = args[3]
+
+					if (searchPattern === "**/.git/HEAD") {
+						return Promise.resolve([])
+					} else if (searchPattern === "**/.git") {
+						return Promise.resolve([
+							{
+								path: "libs/shared/.git",
+								type: "file" as const,
+								label: ".git",
+							},
+						])
+					}
+
+					return Promise.resolve([])
+				})
+
+				const testService = new klass(taskId, shadowDir, workspaceDir, () => {})
+				await testService.initShadowGit()
+				expect(testService.isInitialized).toBe(true)
+
+				// Verify exclude file contains the submodule path.
+				const excludePath = path.join(shadowDir, ".git", "info", "exclude")
+				const excludeContent = await fs.readFile(excludePath, "utf-8")
+				expect(excludeContent).toContain("/libs/shared/")
+
+				// Clean up.
+				vitest.restoreAllMocks()
+				await fs.rm(shadowDir, { recursive: true, force: true })
+				await fs.rm(workspaceDir, { recursive: true, force: true })
+			})
+
+			it("detects multiple nested repos and excludes all", async () => {
+				const shadowDir = path.join(tmpDir, `${prefix}-multi-nested-${Date.now()}`)
+				const workspaceDir = path.join(tmpDir, `workspace-multi-nested-${Date.now()}`)
+
+				await fs.mkdir(workspaceDir, { recursive: true })
+				const mainGit = simpleGit(workspaceDir)
+				await mainGit.init()
+				await mainGit.addConfig("user.name", "Roo Code")
+				await mainGit.addConfig("user.email", "support@roocode.com")
+
+				const mainFile = path.join(workspaceDir, "root.txt")
+				await fs.writeFile(mainFile, "Root content")
+				await mainGit.add(".")
+				await mainGit.commit("Initial commit")
+
+				vitest.spyOn(fileSearch, "executeRipgrep").mockImplementation(({ args }) => {
+					const searchPattern = args[3]
+
+					if (searchPattern === "**/.git/HEAD") {
+						return Promise.resolve([
+							{ path: "frontend/.git/HEAD", type: "file" as const, label: "HEAD" },
+							{ path: "packages/api/.git/HEAD", type: "file" as const, label: "HEAD" },
+						])
+					} else if (searchPattern === "**/.git") {
+						return Promise.resolve([])
+					}
+
+					return Promise.resolve([])
+				})
+
+				const testService = new klass(taskId, shadowDir, workspaceDir, () => {})
+				await testService.initShadowGit()
+				expect(testService.isInitialized).toBe(true)
+
+				// Verify exclude file contains both nested repo patterns.
+				const excludePath = path.join(shadowDir, ".git", "info", "exclude")
+				const excludeContent = await fs.readFile(excludePath, "utf-8")
+				expect(excludeContent).toContain("/frontend/")
+				expect(excludeContent).toContain("/packages/api/")
+
+				// Clean up.
+				vitest.restoreAllMocks()
+				await fs.rm(shadowDir, { recursive: true, force: true })
+				await fs.rm(workspaceDir, { recursive: true, force: true })
+			})
+
+			it("no gitlink entries (mode 160000) remain after staging", async () => {
+				const shadowDir = path.join(tmpDir, `${prefix}-no-gitlink-${Date.now()}`)
+				const workspaceDir = path.join(tmpDir, `workspace-no-gitlink-${Date.now()}`)
+
+				await fs.mkdir(workspaceDir, { recursive: true })
+				const mainGit = simpleGit(workspaceDir)
+				await mainGit.init()
+				await mainGit.addConfig("user.name", "Roo Code")
+				await mainGit.addConfig("user.email", "support@roocode.com")
+
+				// Create a nested repo.
+				const nestedRepoPath = path.join(workspaceDir, "nested")
+				await fs.mkdir(nestedRepoPath, { recursive: true })
+				const nestedGit = simpleGit(nestedRepoPath)
+				await nestedGit.init()
+				await nestedGit.addConfig("user.name", "Roo Code")
+				await nestedGit.addConfig("user.email", "support@roocode.com")
+				await fs.writeFile(path.join(nestedRepoPath, "file.txt"), "nested content")
+				await nestedGit.add(".")
+				await nestedGit.commit("nested commit")
+
+				await fs.writeFile(path.join(workspaceDir, "root.txt"), "root content")
+				await mainGit.add(".")
+				await mainGit.commit("Initial commit")
+
+				vitest.spyOn(fileSearch, "executeRipgrep").mockImplementation(({ args }) => {
+					const searchPattern = args[3]
+
+					if (searchPattern === "**/.git/HEAD") {
+						return Promise.resolve([
+							{ path: "nested/.git/HEAD", type: "file" as const, label: "HEAD" },
+						])
+					} else if (searchPattern === "**/.git") {
+						return Promise.resolve([])
+					}
+
+					return Promise.resolve([])
+				})
+
+				const testService = new klass(taskId, shadowDir, workspaceDir, () => {})
+				await testService.initShadowGit()
+
+				// Save a checkpoint and then inspect the shadow git index.
+				await fs.writeFile(path.join(workspaceDir, "root.txt"), "modified root")
+				await testService.saveCheckpoint("Checkpoint")
+
+				// Inspect the shadow repo's index for gitlink entries.
+				const lsOutput = await simpleGit(shadowDir).raw(["ls-files", "--stage"])
+				const gitlinkLines = lsOutput.split("\n").filter((l: string) => l.startsWith("160000 "))
+				expect(gitlinkLines).toHaveLength(0)
+
+				// Clean up.
+				vitest.restoreAllMocks()
+				await fs.rm(shadowDir, { recursive: true, force: true })
+				await fs.rm(workspaceDir, { recursive: true, force: true })
+			})
+
+			it("restore does not touch nested repo directory", async () => {
+				const shadowDir = path.join(tmpDir, `${prefix}-restore-nested-${Date.now()}`)
+				const workspaceDir = path.join(tmpDir, `workspace-restore-nested-${Date.now()}`)
+
+				await fs.mkdir(workspaceDir, { recursive: true })
+				const mainGit = simpleGit(workspaceDir)
+				await mainGit.init()
+				await mainGit.addConfig("user.name", "Roo Code")
+				await mainGit.addConfig("user.email", "support@roocode.com")
+
+				// Create a nested repo with content.
+				const nestedRepoPath = path.join(workspaceDir, "nested")
+				await fs.mkdir(nestedRepoPath, { recursive: true })
+				const nestedGit = simpleGit(nestedRepoPath)
+				await nestedGit.init()
+				await nestedGit.addConfig("user.name", "Roo Code")
+				await nestedGit.addConfig("user.email", "support@roocode.com")
+				const nestedFile = path.join(nestedRepoPath, "nested-file.txt")
+				await fs.writeFile(nestedFile, "Original nested content")
+				await nestedGit.add(".")
+				await nestedGit.commit("nested commit")
+
+				// Create a main workspace file.
+				const mainFile = path.join(workspaceDir, "main.txt")
+				await fs.writeFile(mainFile, "Original main content")
+				await mainGit.add(".")
+				await mainGit.commit("Initial commit")
+
+				vitest.spyOn(fileSearch, "executeRipgrep").mockImplementation(({ args }) => {
+					const searchPattern = args[3]
+
+					if (searchPattern === "**/.git/HEAD") {
+						return Promise.resolve([
+							{ path: "nested/.git/HEAD", type: "file" as const, label: "HEAD" },
+						])
+					} else if (searchPattern === "**/.git") {
+						return Promise.resolve([])
+					}
+
+					return Promise.resolve([])
+				})
+
+				const testService = new klass(taskId, shadowDir, workspaceDir, () => {})
+				await testService.initShadowGit()
+
+				// Save checkpoint 1.
+				await fs.writeFile(mainFile, "Modified main content")
+				const commit1 = await testService.saveCheckpoint("Checkpoint 1")
+				expect(commit1?.commit).toBeTruthy()
+
+				// Modify nested repo file (should not be tracked).
+				await fs.writeFile(nestedFile, "Modified nested content")
+
+				// Restore to checkpoint 1 — nested repo should be untouched.
+				await testService.restoreCheckpoint(commit1!.commit)
+				expect(await fs.readFile(mainFile, "utf-8")).toBe("Modified main content")
+				// Nested file retains its modification since it's excluded.
+				expect(await fs.readFile(nestedFile, "utf-8")).toBe("Modified nested content")
+				expect(await fileExistsAtPath(path.join(nestedRepoPath, ".git"))).toBe(true)
+
+				// Clean up.
+				vitest.restoreAllMocks()
+				await fs.rm(shadowDir, { recursive: true, force: true })
+				await fs.rm(workspaceDir, { recursive: true, force: true })
+			})
+
+			it("aborts checkpoint save when detection failed and nested repo content is staged", async () => {
+				const shadowDir = path.join(tmpDir, `${prefix}-detect-fail-${Date.now()}`)
+				const workspaceDir = path.join(tmpDir, `workspace-detect-fail-${Date.now()}`)
+
+				await fs.mkdir(workspaceDir, { recursive: true })
+				const mainGit = simpleGit(workspaceDir)
+				await mainGit.init()
+				await mainGit.addConfig("user.name", "Roo Code")
+				await mainGit.addConfig("user.email", "support@roocode.com")
+
+				// Create a nested repo.
+				const nestedRepoPath = path.join(workspaceDir, "nested")
+				await fs.mkdir(nestedRepoPath, { recursive: true })
+				const nestedGit = simpleGit(nestedRepoPath)
+				await nestedGit.init()
+				await nestedGit.addConfig("user.name", "Roo Code")
+				await nestedGit.addConfig("user.email", "support@roocode.com")
+				await fs.writeFile(path.join(nestedRepoPath, "file.txt"), "nested content")
+				await nestedGit.add(".")
+				await nestedGit.commit("nested commit")
+
+				await fs.writeFile(path.join(workspaceDir, "root.txt"), "root content")
+				await mainGit.add(".")
+				await mainGit.commit("Initial commit")
+
+				// Simulate detection failure — ripgrep throws.
+				vitest.spyOn(fileSearch, "executeRipgrep").mockRejectedValue(
+					new Error("ripgrep not found"),
+				)
+
+				const logMessages: string[] = []
+				const testService = new klass(taskId, shadowDir, workspaceDir, (msg: string) =>
+					logMessages.push(msg),
+				)
+				await testService.initShadowGit()
+				expect(testService.isInitialized).toBe(true)
+
+				// Verify detection failure was logged.
+				expect(logMessages.some((m) => m.includes("detection failed"))).toBe(true)
+
+				// Attempting to save a checkpoint should trigger the
+				// conservative fallback and either safely exclude nested
+				// content or abort.
+				await fs.writeFile(path.join(workspaceDir, "root.txt"), "modified root")
+
+				// The save may succeed (if the fallback successfully removes
+				// nested content) or throw (if nested content persists).
+				// Either way, the checkpoint must not contain nested repo files.
+				try {
+					const commit = await testService.saveCheckpoint("Fallback test")
+					if (commit?.commit) {
+						const diff = await testService.getDiff({ to: commit.commit })
+						const diffPaths = diff.map((d) => d.paths.relative)
+						expect(diffPaths).not.toContain("nested/file.txt")
+					}
+				} catch (error) {
+					// Safety abort is acceptable — it means the fallback
+					// detected unsafe content and refused to proceed.
+					expect(error).toBeInstanceOf(Error)
+				}
+
+				// Clean up.
+				vitest.restoreAllMocks()
+				await fs.rm(shadowDir, { recursive: true, force: true })
+				await fs.rm(workspaceDir, { recursive: true, force: true })
+			})
+
+			it("aborts checkpoint save on real git add failure (not ignored-paths warning)", async () => {
+				// Ensure real staging failures (index corruption, disk full, etc.)
+				// still abort the save rather than producing a bad checkpoint.
+				await fs.writeFile(testFile, "Content that should not be checkpointed")
+
+				// Mock git.add to throw a real error (not an "ignored paths" warning).
+				const addSpy = vitest.spyOn(service["git"]!, "add").mockRejectedValueOnce(
+					new Error("fatal: index file corrupt"),
+				)
+
+				await expect(
+					service.saveCheckpoint("Should fail"),
+				).rejects.toThrow("fatal: index file corrupt")
+
+				// Verify the staging path was actually exercised.
+				expect(addSpy).toHaveBeenCalled()
+				addSpy.mockRestore()
+			})
 		})
 
 		describe(`${klass.name}#events`, () => {