diff --git a/pkg/cli/add_command.go b/pkg/cli/add_command.go
index 44758f6049a..5dc8dcd16b6 100644
--- a/pkg/cli/add_command.go
+++ b/pkg/cli/add_command.go
@@ -82,6 +82,8 @@ type AddOptions struct {
 	// the workflow frontmatter, enabling GitHub Actions token auth for Copilot.
 	// Set by the add-wizard when the user selects org-billing auth instead of a PAT.
 	AddCopilotRequestsPermission bool
+	// initializedFiles contains files created by add-wizard after its clean-tree check.
+	initializedFiles []string
 }
 
 // AddWorkflowsResult contains the result of adding workflows
@@ -262,7 +264,7 @@ func AddResolvedWorkflows(ctx context.Context, workflowStrings []string, resolve
 		}
 
 		// Check no other changes are present
-		if err := checkCleanWorkingDirectory(opts.Verbose); err != nil {
+		if err := checkCleanWorkingDirectoryIgnoring(opts.Verbose, opts.initializedFiles); err != nil {
 			return nil, fmt.Errorf("working directory is not clean: %w", err)
 		}
 	}
diff --git a/pkg/cli/add_command_test.go b/pkg/cli/add_command_test.go
index f22ae73c02f..5b7d6f110cb 100644
--- a/pkg/cli/add_command_test.go
+++ b/pkg/cli/add_command_test.go
@@ -462,6 +462,51 @@ func TestEnsureAddRepositoryInitialized(t *testing.T) {
 	})
 }
 
+// TestEnsureAddRepositoryInitializedWithDetails_AbsolutePaths verifies that
+// ensureAddRepositoryInitializedWithDetails returns absolute paths for files
+// that were actually written by init, and skips files that init deliberately
+// does not create (e.g. .gitattributes when --no-gitattributes is used).
+func TestEnsureAddRepositoryInitializedWithDetails_AbsolutePaths(t *testing.T) {
+	repoDir := t.TempDir()
+
+	originalFindGitRoot := addFindGitRoot
+	originalInitRepository := addInitRepository
+	originalMissingInitMarkers := addMissingInitMarkers
+	t.Cleanup(func() {
+		addFindGitRoot = originalFindGitRoot
+		addInitRepository = originalInitRepository
+		addMissingInitMarkers = originalMissingInitMarkers
+	})
+
+	// Use a marker whose isBootstrapInitMarkerSatisfied check uses the default
+	// branch (file exists and size > 0), so the test does not need to reproduce
+	// marker-specific content such as a SKILL.md or MCP config.
+	writtenMarker := ".vscode/settings.json"
+	skippedMarker := ".gitattributes"
+
+	addFindGitRoot = func() (string, error) { return repoDir, nil }
+	addMissingInitMarkers = func(string, string) ([]string, error) {
+		return []string{writtenMarker, skippedMarker}, nil
+	}
+	addInitRepository = func(InitOptions) error {
+		// Simulate init: create the settings.json marker but skip .gitattributes.
+		p := filepath.Join(repoDir, filepath.FromSlash(writtenMarker))
+		if err := os.MkdirAll(filepath.Dir(p), 0755); err != nil {
+			return err
+		}
+		return os.WriteFile(p, []byte(`{}`), 0644)
+	}
+
+	files, err := ensureAddRepositoryInitializedWithDetails("", false, true)
+	require.NoError(t, err)
+
+	// Only the actually-written file should be returned.
+	require.Len(t, files, 1)
+	// The returned path must be absolute.
+	require.True(t, filepath.IsAbs(files[0]), "expected absolute path, got %q", files[0])
+	require.Equal(t, filepath.Join(repoDir, filepath.FromSlash(writtenMarker)), files[0])
+}
+
 func TestAddResolvedWorkflows_IgnoresBootstrapRequireOwnerTypeDuringInstall(t *testing.T) {
 	originalCheckOwnerType := bootstrapCheckOwnerType
 	t.Cleanup(func() {
diff --git a/pkg/cli/add_init.go b/pkg/cli/add_init.go
index ff9ad8d0bbc..95f2d54d649 100644
--- a/pkg/cli/add_init.go
+++ b/pkg/cli/add_init.go
@@ -3,6 +3,7 @@ package cli
 import (
 	"errors"
 	"fmt"
+	"path/filepath"
 
 	"github.com/github/gh-aw/pkg/gitutil"
 )
@@ -35,7 +36,6 @@ func ensureAddRepositoryInitializedWithDetails(engineOverride string, verbose bo
 		if len(missingMarkers) == 0 {
 			return nil
 		}
-		initializedFiles = append(initializedFiles, missingMarkers...)
 
 		addLog.Printf("Repository missing init markers; running init: %v", missingMarkers)
 		if err := addInitRepository(InitOptions{
@@ -53,6 +53,21 @@ func ensureAddRepositoryInitializedWithDetails(engineOverride string, verbose bo
 			return fmt.Errorf("failed to initialize repository for agentic workflows: %w", err)
 		}
 
+		// Record only the files that were actually written by init (some markers,
+		// e.g. .gitattributes with --no-gitattributes, may intentionally be skipped).
+		// Use absolute paths so callers don't need to resolve against gitRoot.
+		for _, marker := range missingMarkers {
+			ok, statErr := isBootstrapInitMarkerSatisfied(".", marker)
+			if statErr != nil || !ok {
+				continue
+			}
+			absPath, pathErr := filepath.Abs(marker)
+			if pathErr != nil {
+				return fmt.Errorf("failed to resolve path for initialized file %s: %w", marker, pathErr)
+			}
+			initializedFiles = append(initializedFiles, absPath)
+		}
+
 		return nil
 	})
 	if err != nil {
diff --git a/pkg/cli/add_interactive_git.go b/pkg/cli/add_interactive_git.go
index 9a0d99aa00a..7f8f22db316 100644
--- a/pkg/cli/add_interactive_git.go
+++ b/pkg/cli/add_interactive_git.go
@@ -56,6 +56,7 @@ func (c *AddInteractiveConfig) createWorkflowPRAndConfigureSecret(ctx context.Co
 		StopAfter:                    c.StopAfter,
 		DisableSecurityScanner:       c.DisableSecurityScanner,
 		AddCopilotRequestsPermission: c.UseCopilotRequests,
+		initializedFiles:             initFiles,
 	}
 	result, err := AddResolvedWorkflows(ctx, c.WorkflowSpecs, c.resolvedWorkflows, opts)
 	if err != nil {
diff --git a/pkg/cli/add_workflow_pr.go b/pkg/cli/add_workflow_pr.go
index 1bd62c28be0..d5a32bbc616 100644
--- a/pkg/cli/add_workflow_pr.go
+++ b/pkg/cli/add_workflow_pr.go
@@ -76,6 +76,9 @@ func addWorkflowsWithPR(ctx context.Context, workflows []*ResolvedWorkflow, opts
 
 	// Create file tracker for rollback capability
 	tracker := NewFileTracker()
+	for _, initializedFile := range opts.initializedFiles {
+		tracker.TrackCreated(initializedFile)
+	}
 
 	// Ensure we switch back to original branch on exit
 	defer func() {
diff --git a/pkg/cli/git.go b/pkg/cli/git.go
index fc08c490135..b2b7d115983 100644
--- a/pkg/cli/git.go
+++ b/pkg/cli/git.go
@@ -558,9 +558,38 @@ func hasPendingChanges() (bool, error) {
 
 // checkCleanWorkingDirectory checks if there are uncommitted changes
 func checkCleanWorkingDirectory(verbose bool) error {
+	return checkCleanWorkingDirectoryIgnoring(verbose, nil)
+}
+
+// checkCleanWorkingDirectoryIgnoring checks for uncommitted changes except for
+// the provided paths (which may be absolute or repository-relative).
+func checkCleanWorkingDirectoryIgnoring(verbose bool, ignoredPaths []string) error {
 	console.LogVerbose(verbose, "Checking for uncommitted changes...")
 
-	cmd := exec.Command("git", "status", "--porcelain")
+	args := []string{"status", "--porcelain", "--untracked-files=all"}
+	if len(ignoredPaths) > 0 {
+		gitRoot, err := gitutil.FindGitRoot()
+		if err != nil {
+			return fmt.Errorf("failed to find git root for path resolution: %w", err)
+		}
+		args = append(args, "--", ":(top)**")
+		for _, ignoredPath := range ignoredPaths {
+			cleaned := filepath.Clean(ignoredPath)
+			// Convert absolute paths to paths relative to the git root so they
+			// work correctly as :(top,...) pathspecs.
+			if filepath.IsAbs(cleaned) {
+				rel, relErr := filepath.Rel(gitRoot, cleaned)
+				if relErr != nil {
+					return fmt.Errorf("failed to resolve %s relative to git root: %w", ignoredPath, relErr)
+				}
+				cleaned = rel
+			}
+			path := filepath.ToSlash(strings.TrimPrefix(cleaned, "."+string(filepath.Separator)))
+			args = append(args, ":(top,literal,exclude)"+path)
+		}
+	}
+
+	cmd := exec.Command("git", args...)
 	output, err := cmd.Output()
 	if err != nil {
 		return fmt.Errorf("failed to check git status: %w", err)
diff --git a/pkg/cli/git_test.go b/pkg/cli/git_test.go
index 2dd2b62e53d..b5a74562541 100644
--- a/pkg/cli/git_test.go
+++ b/pkg/cli/git_test.go
@@ -79,6 +79,88 @@ func TestGetCurrentBranchNotInRepo(t *testing.T) {
 	assert.Error(t, err, "getCurrentBranch should return an error when not in a git repository")
 }
 
+func TestCheckCleanWorkingDirectoryIgnoring(t *testing.T) {
+	tmpDir := testutil.TempDir(t, "test-*")
+
+	originalDir, err := os.Getwd()
+	require.NoError(t, err)
+	defer func() {
+		require.NoError(t, os.Chdir(originalDir))
+	}()
+
+	require.NoError(t, os.Chdir(tmpDir))
+	require.NoError(t, exec.Command("git", "init").Run())
+	require.NoError(t, exec.Command("git", "config", "user.name", "Test User").Run())
+	require.NoError(t, exec.Command("git", "config", "user.email", "test@example.com").Run())
+
+	generatedFile := filepath.Join(".github", "skills", "agentic-workflows", "SKILL.md")
+	require.NoError(t, os.MkdirAll(filepath.Dir(generatedFile), 0755))
+	require.NoError(t, os.WriteFile(generatedFile, []byte("generated"), 0644))
+
+	require.NoError(t, checkCleanWorkingDirectoryIgnoring(false, []string{generatedFile}))
+	require.ErrorContains(t, checkCleanWorkingDirectory(false), "working directory has uncommitted changes")
+
+	// Staged (but not committed) init file should also be excluded.
+	require.NoError(t, exec.Command("git", "add", generatedFile).Run())
+	require.NoError(t, checkCleanWorkingDirectoryIgnoring(false, []string{generatedFile}))
+	require.ErrorContains(t, checkCleanWorkingDirectory(false), "working directory has uncommitted changes")
+
+	require.NoError(t, exec.Command("git", "commit", "-m", "initial commit").Run())
+	require.NoError(t, os.WriteFile(generatedFile, []byte("updated"), 0644))
+
+	require.NoError(t, checkCleanWorkingDirectoryIgnoring(false, []string{generatedFile}))
+	require.ErrorContains(t, checkCleanWorkingDirectory(false), "working directory has uncommitted changes")
+
+	require.NoError(t, os.WriteFile("README.md", []byte("user file"), 0644))
+	require.ErrorContains(
+		t,
+		checkCleanWorkingDirectoryIgnoring(false, []string{generatedFile}),
+		"working directory has uncommitted changes",
+	)
+}
+
+// TestCheckCleanWorkingDirectoryIgnoringAbsolutePaths verifies that absolute
+// paths are accepted when the current directory is a subdirectory of the repo.
+// This is the case when the wizard is invoked from a nested directory and
+// ensureAddRepositoryInitializedWithDetails returns absolute paths.
+func TestCheckCleanWorkingDirectoryIgnoringAbsolutePaths(t *testing.T) {
+	repoDir := testutil.TempDir(t, "test-*")
+
+	originalDir, err := os.Getwd()
+	require.NoError(t, err)
+	defer func() {
+		require.NoError(t, os.Chdir(originalDir))
+	}()
+
+	require.NoError(t, os.Chdir(repoDir))
+	require.NoError(t, exec.Command("git", "init").Run())
+	require.NoError(t, exec.Command("git", "config", "user.name", "Test User").Run())
+	require.NoError(t, exec.Command("git", "config", "user.email", "test@example.com").Run())
+
+	// Create the init file at the repo root.
+	generatedFile := filepath.Join(".github", "skills", "agentic-workflows", "SKILL.md")
+	require.NoError(t, os.MkdirAll(filepath.Dir(generatedFile), 0755))
+	require.NoError(t, os.WriteFile(generatedFile, []byte("generated"), 0644))
+	absGenerated := filepath.Join(repoDir, generatedFile)
+
+	// Create a subdirectory and cd into it to simulate a nested invocation.
+	subDir := filepath.Join(repoDir, "subdir")
+	require.NoError(t, os.MkdirAll(subDir, 0755))
+	require.NoError(t, os.Chdir(subDir))
+
+	// Passing the absolute path from a nested CWD should still exclude the file.
+	require.NoError(t, checkCleanWorkingDirectoryIgnoring(false, []string{absGenerated}))
+	require.ErrorContains(t, checkCleanWorkingDirectory(false), "working directory has uncommitted changes")
+
+	// An unrelated untracked file must still be detected even when the init file is excluded.
+	require.NoError(t, os.WriteFile(filepath.Join(repoDir, "README.md"), []byte("user file"), 0644))
+	require.ErrorContains(
+		t,
+		checkCleanWorkingDirectoryIgnoring(false, []string{absGenerated}),
+		"working directory has uncommitted changes",
+	)
+}
+
 func TestCreateAndSwitchBranch(t *testing.T) {
 	tmpDir := testutil.TempDir(t, "test-*")