fix(setup): preserve symlinks in atomicWriteFile

Add ResolveForWrite helper that resolves symlinks before writing,
so atomic writes go to the symlink target instead of replacing
the symlink itself.

internal/utils/path.go

@@ -69,6 +69,23 @@ func FindMoleculesJSONLInDir(dbDir string) string {
 	return ""
 }
 
+// ResolveForWrite returns the path to write to, resolving symlinks.
+// If path is a symlink, returns the resolved target path.
+// If path doesn't exist, returns path unchanged (new file).
+func ResolveForWrite(path string) (string, error) {
+	info, err := os.Lstat(path)
+	if err != nil {
+		if os.IsNotExist(err) {
+			return path, nil
+		}
+		return "", err
+	}
+	if info.Mode()&os.ModeSymlink != 0 {
+		return filepath.EvalSymlinks(path)
+	}
+	return path, nil
+}
+
 // CanonicalizePath converts a path to its canonical form by:
 // 1. Converting to absolute path
 // 2. Resolving symlinks

internal/utils/path_test.go

@@ -179,3 +179,54 @@ func TestCanonicalizePathSymlink(t *testing.T) {
 		}
 	}
 }
+
+func TestResolveForWrite(t *testing.T) {
+	t.Run("regular file", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		file := filepath.Join(tmpDir, "regular.txt")
+		if err := os.WriteFile(file, []byte("test"), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		got, err := ResolveForWrite(file)
+		if err != nil {
+			t.Fatalf("unexpected error: %v", err)
+		}
+		if got != file {
+			t.Errorf("got %q, want %q", got, file)
+		}
+	})
+
+	t.Run("symlink", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		target := filepath.Join(tmpDir, "target.txt")
+		if err := os.WriteFile(target, []byte("test"), 0644); err != nil {
+			t.Fatal(err)
+		}
+		link := filepath.Join(tmpDir, "link.txt")
+		if err := os.Symlink(target, link); err != nil {
+			t.Fatal(err)
+		}
+
+		got, err := ResolveForWrite(link)
+		if err != nil {
+			t.Fatalf("unexpected error: %v", err)
+		}
+		if got != target {
+			t.Errorf("got %q, want %q", got, target)
+		}
+	})
+
+	t.Run("non-existent", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		newFile := filepath.Join(tmpDir, "new.txt")
+
+		got, err := ResolveForWrite(newFile)
+		if err != nil {
+			t.Fatalf("unexpected error: %v", err)
+		}
+		if got != newFile {
+			t.Errorf("got %q, want %q", got, newFile)
+		}
+	})
+}