diff --git a/docs/src/content/docs/reference/safe-outputs-pull-requests.md b/docs/src/content/docs/reference/safe-outputs-pull-requests.md
index 68a28e72a58..9006f76e546 100644
--- a/docs/src/content/docs/reference/safe-outputs-pull-requests.md
+++ b/docs/src/content/docs/reference/safe-outputs-pull-requests.md
@@ -457,12 +457,15 @@ Protection covers three categories:
 
 - `.github/` — covers all GitHub Actions workflows, Dependabot config, and other repository-level security settings.
 - `.agents/` — covers generic agent instruction and configuration files stored in the `.agents/` directory.
+- `.githooks/` — covers repository-tracked git hook scripts.
+- `.husky/` — covers Husky-managed git hook scripts.
 
-**4. Repository access control files** — matched by filename anywhere in the repository:
+**4. Repository governance files** — matched by filename anywhere in the repository:
 
 | File | Description |
 |------|-------------|
 | `CODEOWNERS` | Governs required code reviewers; valid at the repository root, `.github/`, or `docs/` |
+| `DESIGN.md` | Defines persistent design-system guidance for coding agents |
 
 > [!NOTE]
-> Runtime manifests and access control files (`CODEOWNERS`) are matched by **basename only** (the filename without its directory path), so they are protected regardless of where they appear in the repository. Path-prefix rules (`.github/`, `.agents/`, `.claude/`, `.codex/`) match the full relative path from the repository root.
+> Runtime manifests and governance files (`CODEOWNERS`, `DESIGN.md`) are matched by **basename only** (the filename without its directory path), so they are protected regardless of where they appear in the repository. Path-prefix rules (`.github/`, `.agents/`, `.githooks/`, `.husky/`, `.claude/`, `.codex/`) match the full relative path from the repository root.
diff --git a/pkg/workflow/compiler_safe_outputs_config_test.go b/pkg/workflow/compiler_safe_outputs_config_test.go
index b395cafd290..6be7faf69b6 100644
--- a/pkg/workflow/compiler_safe_outputs_config_test.go
+++ b/pkg/workflow/compiler_safe_outputs_config_test.go
@@ -2255,7 +2255,7 @@ func TestProtectedFilesExclude(t *testing.T) {
 			name:               "exclude AGENTS.md from create-pull-request",
 			excludeFiles:       []string{"AGENTS.md"},
 			wantExcludedFromPF: []string{"AGENTS.md"},
-			wantPresentInPF:    []string{"package.json", "go.mod", "CODEOWNERS"},
+			wantPresentInPF:    []string{"package.json", "go.mod", "CODEOWNERS", "DESIGN.md"},
 		},
 		{
 			name:               "exclude multiple files",
@@ -2388,4 +2388,17 @@ func TestProtectedFilesExcludePushToPRBranch(t *testing.T) {
 	}
 	assert.NotContains(t, pfStrings, "AGENTS.md", "AGENTS.md should be excluded from protected_files")
 	assert.Contains(t, pfStrings, "package.json", "package.json should still be in protected_files")
+
+	ppRaw, ok := pushConfig["protected_path_prefixes"]
+	require.True(t, ok, "should have protected_path_prefixes field")
+	ppAny, ok := ppRaw.([]any)
+	require.True(t, ok, "protected_path_prefixes should be a slice")
+	ppStrings := make([]string, 0, len(ppAny))
+	for _, v := range ppAny {
+		if s, ok := v.(string); ok {
+			ppStrings = append(ppStrings, s)
+		}
+	}
+	assert.Contains(t, ppStrings, ".githooks/", ".githooks/ should be in protected_path_prefixes by default")
+	assert.Contains(t, ppStrings, ".husky/", ".husky/ should be in protected_path_prefixes by default")
 }
diff --git a/pkg/workflow/runtime_definitions.go b/pkg/workflow/runtime_definitions.go
index dd9502baf0d..71d36860f1c 100644
--- a/pkg/workflow/runtime_definitions.go
+++ b/pkg/workflow/runtime_definitions.go
@@ -187,6 +187,7 @@ func init() {
 // that files placed at the repo root or in "docs/" are equally protected.
 var securityConfigFiles = []string{
 	"CODEOWNERS", // Governs required reviewers; valid at repo root, .github/, or docs/
+	"DESIGN.md",  // Captures design-system source of truth consumed by coding agents
 }
 
 // getAllManifestFiles returns the deduplicated union of all manifest file names
@@ -212,8 +213,9 @@ func getAllManifestFiles(extra ...string) []string {
 // additionally protected by filename (see securityConfigFiles) so that root-
 // and docs/-level placements are covered too.
 // ".agents/" covers generic agent instruction and configuration files.
+// ".githooks/" and ".husky/" cover repository-tracked git hook scripts.
 func getProtectedPathPrefixes(extra ...string) []string {
-	return mergeUnique([]string{".github/", ".agents/"}, extra...)
+	return mergeUnique([]string{".github/", ".agents/", ".githooks/", ".husky/"}, extra...)
 }
 
 // excludeFromSlice returns a new slice containing the items from base
diff --git a/pkg/workflow/safe_outputs_config_generation_test.go b/pkg/workflow/safe_outputs_config_generation_test.go
index 26ffde8a690..20088c5a8ee 100644
--- a/pkg/workflow/safe_outputs_config_generation_test.go
+++ b/pkg/workflow/safe_outputs_config_generation_test.go
@@ -549,9 +549,12 @@ func TestGenerateSafeOutputsConfigCreatePullRequestIncludesEngineManifests(t *te
 	protectedFiles := parseStringSliceAny(prConfig["protected_files"], nil)
 	assert.Contains(t, protectedFiles, "CLAUDE.md", "CLAUDE.md should be protected for Claude engine workflows")
 	assert.Contains(t, protectedFiles, "AGENTS.md", "AGENTS.md should be protected for Claude engine workflows")
+	assert.Contains(t, protectedFiles, "DESIGN.md", "DESIGN.md should be protected by default")
 
 	protectedPathPrefixes := parseStringSliceAny(prConfig["protected_path_prefixes"], nil)
 	assert.Contains(t, protectedPathPrefixes, ".claude/", ".claude/ should be protected for Claude engine workflows")
+	assert.Contains(t, protectedPathPrefixes, ".githooks/", ".githooks/ should be protected by default")
+	assert.Contains(t, protectedPathPrefixes, ".husky/", ".husky/ should be protected by default")
 }
 
 func TestGenerateSafeOutputsConfigCreatePullRequestAppliesProtectedFilesExclude(t *testing.T) {