diff --git a/file/AGENTS.md b/file/AGENTS.md
index b932e03..1416bc9 100644
--- a/file/AGENTS.md
+++ b/file/AGENTS.md
@@ -39,13 +39,32 @@ way POSIX tools expect, without that newline leaking into the mod content and ap
 spurious character in TTS. The two halves are a matched pair — changing one without the other adds
 or eats a newline on every round trip.
 
-## `Clear` and its safety check
-
-`DirOps.Clear()` deletes and recreates a directory. Because it is destructive, `preClearCheck`
-first walks the tree and refuses if it finds a file whose extension is not in `allowedExtensions`
-(`.json`, `.gmnotes`, `.luascriptstate`, `.ttslua`, `.xml`). The intent is that the objects
-directory should only ever contain files this tool generated, so anything unrecognized means the
-path is wrong and deleting would destroy someone's work.
+## `Clear` and its safety checks
+
+`DirOps.Clear()` deletes and recreates a directory. Because it is destructive it runs two guards
+before touching anything.
+
+**Ownership marker.** After a successful clear, `Clear` drops a hidden sentinel file
+(`.ttsmm-managed`, the `managedMarker` constant) into the directory. On the next run that marker is
+proof the tool created the directory, so deleting it is safe. `Clear` refuses unless one of:
+
+- the directory does not exist,
+- the directory is empty,
+- the directory already contains the marker, or
+- the directory has no marker but every file passes the legacy extension allowlist
+  (`allowedExtensions`: `.json`, `.gmnotes`, `.luascriptstate`, `.ttslua`, `.xml`) — backward
+  compatibility for trees written before the marker existed; they clear once and gain a marker
+  going forward.
+
+A non-empty directory with no marker and unrecognized content (a mistargeted `--moddir` pointed at,
+say, `$HOME`) is refused with an error explaining how to proceed. This also resolves the older
+`.DS_Store`/`.gitkeep` false-positive, since a tool-created directory carries a marker and the
+extension check no longer gates it.
+
+**Path guard.** Independent of contents, `pathGuard` resolves the target to an absolute, cleaned
+path and refuses the filesystem root, the user's home directory, any ancestor of home, and
+suspiciously shallow single-segment paths — targets that are almost always a typo rather than a mod
+tree.
 
 ## `conversions.go`
 
diff --git a/file/dirops.go b/file/dirops.go
index 455bef2..902bc04 100644
--- a/file/dirops.go
+++ b/file/dirops.go
@@ -6,6 +6,7 @@ import (
 	"os"
 	"path"
 	"path/filepath"
+	"strings"
 	"time"
 )
 
@@ -18,6 +19,12 @@ var allowedExtensions = map[string]struct{}{
 	".xml":            {},
 }
 
+// managedMarker is the hidden ownership marker (sentinel) this tool drops into any
+// directory it manages. Its presence is proof that the directory was created by
+// TTSModManager, which is what makes deleting the directory's contents safe. See the
+// "Clear and its safety check" section of AGENTS.md.
+const managedMarker = ".ttsmm-managed"
+
 // DirCreator abstracts folder creation
 type DirCreator interface {
 	CreateDir(relpath string, suggestion string) (string, error)
@@ -89,12 +96,119 @@ func (d *DirOps) preClearCheck() error {
 	return walkErr
 }
 
+// pathGuard refuses to operate on paths that are almost certainly a mistargeted
+// --moddir rather than a real objects directory: the filesystem root, the user's home
+// directory (or any ancestor of it), or any suspiciously shallow path. Deleting any of
+// these would destroy unrelated user data.
+func pathGuard(target string) error {
+	abs, err := filepath.Abs(target)
+	if err != nil {
+		return fmt.Errorf("could not resolve absolute path of %s: %w", target, err)
+	}
+	abs = filepath.Clean(abs)
+
+	// Refuse the filesystem root.
+	if abs == filepath.Clean(string(filepath.Separator)) {
+		return fmt.Errorf("refusing to clear filesystem root %q", abs)
+	}
+
+	// Refuse the home directory and any ancestor of it.
+	if home, herr := os.UserHomeDir(); herr == nil && home != "" {
+		home = filepath.Clean(home)
+		if abs == home {
+			return fmt.Errorf("refusing to clear home directory %q", abs)
+		}
+		// An ancestor of home (e.g. /home, / on some systems) is even more dangerous.
+		// abs is a strict ancestor when the path from abs down to home never climbs out.
+		if rel, rerr := filepath.Rel(abs, home); rerr == nil && rel != "." && !startsWithParent(rel) {
+			return fmt.Errorf("refusing to clear %q, an ancestor of your home directory %q", abs, home)
+		}
+	}
+
+	// Refuse suspiciously shallow paths: a single segment below the root such as
+	// "/objects" is far more likely a typo than a real mod tree.
+	trimmed := strings.Trim(abs, string(filepath.Separator))
+	if trimmed == "" {
+		return fmt.Errorf("refusing to clear filesystem root %q", abs)
+	}
+	if !strings.ContainsRune(trimmed, filepath.Separator) {
+		return fmt.Errorf("refusing to clear suspiciously shallow path %q; pass a --moddir at least two levels deep", abs)
+	}
+
+	return nil
+}
+
+// startsWithParent reports whether a filepath.Rel result indicates the target is an
+// ancestor of home (the relative path from target to home does not need to climb out).
+func startsWithParent(rel string) bool {
+	return rel == ".." || strings.HasPrefix(rel, ".."+string(filepath.Separator))
+}
+
+// isClearable decides whether it is safe to delete the contents of d.base. Deletion is
+// allowed when the directory:
+//   - does not exist, or
+//   - is empty, or
+//   - already contains our ownership marker (proof this tool created it), or
+//   - passes the legacy extension allowlist (backward compatibility for trees written
+//     by versions predating the marker).
+//
+// Anything else - a non-empty directory of unrecognized files with no marker, such as a
+// mistargeted $HOME - is refused.
+func (d *DirOps) isClearable() error {
+	entries, err := os.ReadDir(d.base)
+	if err != nil {
+		if os.IsNotExist(err) {
+			return nil // absent: nothing to destroy
+		}
+		return fmt.Errorf("reading directory %s: %w", d.base, err)
+	}
+
+	if len(entries) == 0 {
+		return nil // empty: nothing to destroy
+	}
+
+	// Marker present: this tool created the directory, so clearing is safe.
+	for _, e := range entries {
+		if !e.IsDir() && e.Name() == managedMarker {
+			return nil
+		}
+	}
+
+	// Backward compatibility: a directory that predates the marker but contains only
+	// recognized content is still ours to clear (and gains a marker going forward).
+	if err := d.preClearCheck(); err != nil {
+		return fmt.Errorf(
+			"%s is not empty, has no %s ownership marker, and contains unrecognized content: %w; "+
+				"refusing to delete it in case --moddir is pointed at the wrong place. "+
+				"If this really is a mod objects directory, remove the offending file or the whole directory by hand and re-run",
+			d.base, managedMarker, err)
+	}
+	return nil
+}
+
+// writeMarker drops the ownership marker into d.base so future Clear calls recognize the
+// directory as one this tool manages.
+func (d *DirOps) writeMarker() error {
+	marker := filepath.Join(d.base, managedMarker)
+	content := []byte("This directory is managed by TTSModManager. It may be deleted and recreated by reverse mode.\n")
+	if err := os.WriteFile(marker, content, 0644); err != nil {
+		return fmt.Errorf("error writing ownership marker %s: %w", marker, err)
+	}
+	return nil
+}
+
 // Clear removes all contents from the base directory and recreates it.
 func (d *DirOps) Clear() error {
 	log.Println("Performing safety check...")
 	startTime := time.Now()
 
-	if err := d.preClearCheck(); err != nil {
+	// Path guard: refuse obviously dangerous targets regardless of contents.
+	if err := pathGuard(d.base); err != nil {
+		return fmt.Errorf("pre-clear safety check failed, operation aborted: %w", err)
+	}
+
+	// Ownership guard: refuse to delete a directory this tool does not appear to own.
+	if err := d.isClearable(); err != nil {
 		return fmt.Errorf("pre-clear safety check failed, operation aborted: %w", err)
 	}
 
@@ -111,6 +225,11 @@ func (d *DirOps) Clear() error {
 		return fmt.Errorf("error recreating directory %s: %w", d.base, err)
 	}
 
+	// Drop the ownership marker so this directory is recognized as ours next time.
+	if err := d.writeMarker(); err != nil {
+		return err
+	}
+
 	log.Printf("Cleared and recreated directory: %s", d.base)
 	return nil
 }
@@ -128,6 +247,11 @@ func (d *DirOps) ListFilesAndFolders(relpath string) ([]string, []string, error)
 		if entry.IsDir() {
 			folnames = append(folnames, filepath.Join(relpath, entry.Name()))
 		} else {
+			// Hide the ownership marker: it is an internal file/ bookkeeping detail and
+			// must not be seen as mod content by the rest of the pipeline.
+			if entry.Name() == managedMarker {
+				continue
+			}
 			fnames = append(fnames, filepath.Join(relpath, entry.Name()))
 		}
 	}
diff --git a/file/dirops_test.go b/file/dirops_test.go
index 3ae9b80..40a8481 100644
--- a/file/dirops_test.go
+++ b/file/dirops_test.go
@@ -114,8 +114,12 @@ func TestClearRemovesAndRecreates(t *testing.T) {
 	if err != nil {
 		t.Fatalf("ReadDir() after Clear: %v", err)
 	}
-	if len(entries) != 0 {
-		t.Errorf("expected empty directory after Clear, found %d entries", len(entries))
+	// Clear now drops the ownership marker into the recreated dir (#96),
+	// so the only permitted entry is that marker.
+	for _, e := range entries {
+		if e.Name() != managedMarker {
+			t.Errorf("expected only the ownership marker after Clear, found %q", e.Name())
+		}
 	}
 }
 
@@ -162,3 +166,124 @@ func TestListFilesAndFolders(t *testing.T) {
 		t.Errorf("folders want != got:\n%v\n", diff)
 	}
 }
+
+// --- ownership-marker + path-guard tests (#96) ---
+
+func writeFile(t *testing.T, p, content string) {
+	t.Helper()
+	if err := os.WriteFile(p, []byte(content), 0644); err != nil {
+		t.Fatalf("could not write %s: %v", p, err)
+	}
+}
+
+func markerExists(dir string) bool {
+	_, err := os.Stat(filepath.Join(dir, managedMarker))
+	return err == nil
+}
+
+// (a) An unmarked, non-empty directory containing a disallowed file is refused, and its
+// contents are left untouched.
+func TestClearRefusesUnmarkedForeignContent(t *testing.T) {
+	dir := t.TempDir()
+	victim := filepath.Join(dir, "important.txt")
+	writeFile(t, victim, "the user's real data")
+
+	d := NewDirOps(dir)
+	if err := d.Clear(); err == nil {
+		t.Fatalf("expected Clear to refuse an unmarked directory with foreign content, got nil")
+	}
+
+	if _, err := os.Stat(victim); err != nil {
+		t.Fatalf("Clear deleted the user's file despite refusing: %v", err)
+	}
+}
+
+// (b) A directory that already carries the ownership marker clears successfully, and the
+// marker is present afterwards.
+func TestClearAllowsMarkedDirectory(t *testing.T) {
+	dir := t.TempDir()
+	writeFile(t, filepath.Join(dir, managedMarker), "managed")
+	// Even foreign content is fine once the marker proves we own the directory.
+	writeFile(t, filepath.Join(dir, "leftover.bin"), "stale")
+
+	d := NewDirOps(dir)
+	if err := d.Clear(); err != nil {
+		t.Fatalf("expected Clear to succeed on a marked directory, got %v", err)
+	}
+
+	if _, err := os.Stat(filepath.Join(dir, "leftover.bin")); !os.IsNotExist(err) {
+		t.Fatalf("expected old content to be removed, stat err = %v", err)
+	}
+	if !markerExists(dir) {
+		t.Fatalf("expected marker to be re-written after Clear")
+	}
+}
+
+// (c) An empty directory, and an absent directory, both clear and gain a marker.
+func TestClearEmptyAndAbsentGetMarker(t *testing.T) {
+	t.Run("empty", func(t *testing.T) {
+		dir := t.TempDir()
+		d := NewDirOps(dir)
+		if err := d.Clear(); err != nil {
+			t.Fatalf("expected Clear to succeed on empty directory, got %v", err)
+		}
+		if !markerExists(dir) {
+			t.Fatalf("expected marker after clearing empty directory")
+		}
+	})
+
+	t.Run("absent", func(t *testing.T) {
+		dir := filepath.Join(t.TempDir(), "does-not-exist-yet")
+		d := NewDirOps(dir)
+		if err := d.Clear(); err != nil {
+			t.Fatalf("expected Clear to succeed on absent directory, got %v", err)
+		}
+		if !markerExists(dir) {
+			t.Fatalf("expected marker after creating absent directory")
+		}
+	})
+}
+
+// Backward compatibility: an unmarked directory whose files all pass the legacy
+// extension allowlist still clears (and gains a marker going forward).
+func TestClearAllowsLegacyRecognizedContent(t *testing.T) {
+	dir := t.TempDir()
+	writeFile(t, filepath.Join(dir, "obj.json"), "{}")
+	writeFile(t, filepath.Join(dir, "script.ttslua"), "-- lua")
+
+	d := NewDirOps(dir)
+	if err := d.Clear(); err != nil {
+		t.Fatalf("expected Clear to succeed on legacy recognized content, got %v", err)
+	}
+	if !markerExists(dir) {
+		t.Fatalf("expected marker after clearing legacy directory")
+	}
+}
+
+// (d) The path guard refuses the filesystem root and the home directory outright.
+func TestPathGuardRefusesDangerousTargets(t *testing.T) {
+	if err := pathGuard(string(filepath.Separator)); err == nil {
+		t.Fatalf("expected path guard to refuse filesystem root")
+	}
+
+	home, err := os.UserHomeDir()
+	if err != nil || home == "" {
+		t.Skip("no home directory available on this platform")
+	}
+	if err := pathGuard(home); err == nil {
+		t.Fatalf("expected path guard to refuse home directory %q", home)
+	}
+
+	// Clear must also refuse the home directory, not just the raw guard.
+	d := NewDirOps(home)
+	if err := d.Clear(); err == nil {
+		t.Fatalf("expected Clear to refuse home directory %q", home)
+	}
+}
+
+// The path guard refuses suspiciously shallow single-segment paths.
+func TestPathGuardRefusesShallowPaths(t *testing.T) {
+	if err := pathGuard(string(filepath.Separator) + "objects"); err == nil {
+		t.Fatalf("expected path guard to refuse a single-segment path")
+	}
+}