diff --git a/cmd/git.go b/cmd/git.go
index 489cd4e..4254d4d 100644
--- a/cmd/git.go
+++ b/cmd/git.go
@@ -34,16 +34,12 @@ var gitCmd = &cobra.Command{
 	Short: "Run any arbitrary command. Use with caution.",
 	Long: `Run any arbitrary command. Use with caution.
 
-Be wary of how pda! version control operates before using this.
-Regular data is stored in "PDA_DATA/pda/stores" as a store; the
-Git repository is in "PDA_DATA/pda/vcs" and contains a plaintext
-replica of the store data.
+The Git repository lives directly in the stores directory
+("PDA_DATA/pda/stores"). Store files (*.ndjson) are tracked
+by Git as-is.
 
-The regular sync command (or auto-syncing) exports pda! data into
-plaintext in the Git repository. If you manually modify the
-repository without using the built-in commands, or exporting your
-data to the Git folder in the correct format first, you may desync
-your repository.
+If you manually modify files without using the built-in
+commands, you may desync your repository.
 
 Generally prefer "pda sync".`,
 	Args:               cobra.ArbitraryArgs,
diff --git a/cmd/init.go b/cmd/init.go
index d0259b2..07c64a9 100644
--- a/cmd/init.go
+++ b/cmd/init.go
@@ -40,7 +40,7 @@ var initCmd = &cobra.Command{
 }
 
 func init() {
-	initCmd.Flags().Bool("clean", false, "Remove existing VCS directory before initialising")
+	initCmd.Flags().Bool("clean", false, "Remove .git from stores directory before initialising")
 	rootCmd.AddCommand(initCmd)
 }
 
@@ -55,66 +55,74 @@ func vcsInit(cmd *cobra.Command, args []string) error {
 	if err != nil {
 		return err
 	}
+
+	hasRemote := len(args) == 1
+
 	if clean {
-		entries, err := os.ReadDir(repoDir)
-		if err == nil && len(entries) > 0 {
-			fmt.Printf("remove existing VCS directory '%s'? (y/n)\n", repoDir)
+		gitDir := filepath.Join(repoDir, ".git")
+		if _, err := os.Stat(gitDir); err == nil {
+			fmt.Printf("remove .git from '%s'? (y/n)\n", repoDir)
 			var confirm string
 			if _, err := fmt.Scanln(&confirm); err != nil {
-				return fmt.Errorf("cannot clean vcs dir: %w", err)
+				return fmt.Errorf("cannot clean git dir: %w", err)
 			}
 			if strings.ToLower(confirm) != "y" {
-				return fmt.Errorf("aborted cleaning vcs dir")
+				return fmt.Errorf("aborted cleaning git dir")
+			}
+			if err := os.RemoveAll(gitDir); err != nil {
+				return fmt.Errorf("cannot clean git dir: %w", err)
 			}
-		}
-		if err := os.RemoveAll(repoDir); err != nil {
-			return fmt.Errorf("cannot clean vcs dir: %w", err)
 		}
 
-		dbs, err := store.AllStores()
-		if err == nil && len(dbs) > 0 {
-			fmt.Printf("remove all existing stores? (y/n)\n")
-			var confirm string
-			if _, err := fmt.Scanln(&confirm); err != nil {
-				return fmt.Errorf("cannot clean stores: %w", err)
-			}
-			if strings.ToLower(confirm) != "y" {
-				return fmt.Errorf("aborted cleaning stores")
-			}
-			if err := wipeAllStores(store); err != nil {
-				return fmt.Errorf("cannot clean stores: %w", err)
+		if hasRemote {
+			dbs, err := store.AllStores()
+			if err == nil && len(dbs) > 0 {
+				fmt.Printf("remove all existing stores and .gitignore? (required for clone) (y/n)\n")
+				var confirm string
+				if _, err := fmt.Scanln(&confirm); err != nil {
+					return fmt.Errorf("cannot clean stores: %w", err)
+				}
+				if strings.ToLower(confirm) != "y" {
+					return fmt.Errorf("aborted cleaning stores")
+				}
+				if err := wipeAllStores(store); err != nil {
+					return fmt.Errorf("cannot clean stores: %w", err)
+				}
+				gi := filepath.Join(repoDir, ".gitignore")
+				if err := os.Remove(gi); err != nil && !os.IsNotExist(err) {
+					return fmt.Errorf("cannot remove .gitignore: %w", err)
+				}
 			}
 		}
 	}
-	if err := os.MkdirAll(filepath.Join(repoDir), 0o750); err != nil {
-		return err
-	}
 
 	gitDir := filepath.Join(repoDir, ".git")
-	if _, err := os.Stat(gitDir); os.IsNotExist(err) {
-		if len(args) == 1 {
-			remote := args[0]
-			fmt.Printf("running: git clone %s %s\n", remote, repoDir)
-			if err := runGit("", "clone", remote, repoDir); err != nil {
-				return err
-			}
-		} else {
-			fmt.Printf("running: git init\n")
-			if err := runGit(repoDir, "init"); err != nil {
-				return err
-			}
-		}
-	} else {
+	if _, err := os.Stat(gitDir); err == nil {
 		fmt.Println("vcs already initialised; use --clean to reinitialise")
 		return nil
 	}
 
-	if err := writeGitignore(repoDir); err != nil {
-		return err
+	if hasRemote {
+		// git clone requires the target directory to be empty
+		entries, err := os.ReadDir(repoDir)
+		if err == nil && len(entries) > 0 {
+			return fmt.Errorf("stores directory is not empty; use --clean with a remote to wipe and clone")
+		}
+
+		remote := args[0]
+		fmt.Printf("running: git clone %s %s\n", remote, repoDir)
+		if err := runGit("", "clone", remote, repoDir); err != nil {
+			return err
+		}
+	} else {
+		if err := os.MkdirAll(repoDir, 0o750); err != nil {
+			return err
+		}
+		fmt.Printf("running: git init\n")
+		if err := runGit(repoDir, "init"); err != nil {
+			return err
+		}
 	}
 
-	if len(args) == 0 {
-		return nil
-	}
-	return restoreAllSnapshots(store, repoDir)
+	return writeGitignore(repoDir)
 }
diff --git a/cmd/sync.go b/cmd/sync.go
index 222ee3c..b5b696e 100644
--- a/cmd/sync.go
+++ b/cmd/sync.go
@@ -44,7 +44,6 @@ func init() {
 }
 
 func sync(manual bool) error {
-	store := &Store{}
 	repoDir, err := ensureVCSInitialized()
 	if err != nil {
 		return err
@@ -89,18 +88,12 @@ func sync(manual bool) error {
 						return err
 					}
 				}
-				if err := pullRemote(repoDir, remoteInfo); err != nil {
-					return err
-				}
-				return restoreAllSnapshots(store, repoDir)
+				return pullRemote(repoDir, remoteInfo)
 			}
 		}
 	}
 
-	if err := exportAllStores(store, repoDir); err != nil {
-		return err
-	}
-	if err := runGit(repoDir, "add", storeDirName); err != nil {
+	if err := runGit(repoDir, "add", "-A"); err != nil {
 		return err
 	}
 	changed, err := repoHasStagedChanges(repoDir)
diff --git a/cmd/vcs.go b/cmd/vcs.go
index 757a996..9a82706 100644
--- a/cmd/vcs.go
+++ b/cmd/vcs.go
@@ -9,22 +9,10 @@ import (
 	"path/filepath"
 	"strconv"
 	"strings"
-
-	gap "github.com/muesli/go-app-paths"
 )
 
-const storeDirName = "stores"
-
 func vcsRepoRoot() (string, error) {
-	scope := gap.NewVendorScope(gap.User, "pda", "vcs")
-	dir, err := scope.DataPath("")
-	if err != nil {
-		return "", err
-	}
-	if err := os.MkdirAll(dir, 0o750); err != nil {
-		return "", err
-	}
-	return dir, nil
+	return (&Store{}).path()
 }
 
 func ensureVCSInitialized() (string, error) {
@@ -47,10 +35,8 @@ func writeGitignore(repoDir string) error {
 		content := strings.Join([]string{
 			"# generated by pda",
 			"*",
-			"!/",
 			"!.gitignore",
-			"!" + storeDirName + "/",
-			"!" + storeDirName + "/*",
+			"!*.ndjson",
 			"",
 		}, "\n")
 		if err := os.WriteFile(path, []byte(content), 0o640); err != nil {
@@ -66,71 +52,6 @@ func writeGitignore(repoDir string) error {
 	return nil
 }
 
-// snapshotDB copies a store's .ndjson file into the VCS directory.
-func snapshotDB(store *Store, repoDir, db string) error {
-	targetDir := filepath.Join(repoDir, storeDirName)
-	if err := os.MkdirAll(targetDir, 0o750); err != nil {
-		return err
-	}
-
-	srcPath, err := store.storePath(db)
-	if err != nil {
-		return err
-	}
-
-	data, err := os.ReadFile(srcPath)
-	if err != nil {
-		if os.IsNotExist(err) {
-			return nil
-		}
-		return err
-	}
-
-	target := filepath.Join(targetDir, db+".ndjson")
-	return os.WriteFile(target, data, 0o640)
-}
-
-// exportAllStores copies every store's .ndjson file to repoDir/stores
-// and removes stale snapshot files for deleted stores.
-func exportAllStores(store *Store, repoDir string) error {
-	stores, err := store.AllStores()
-	if err != nil {
-		return err
-	}
-
-	targetDir := filepath.Join(repoDir, storeDirName)
-	if err := os.MkdirAll(targetDir, 0o750); err != nil {
-		return err
-	}
-
-	current := make(map[string]struct{})
-	for _, db := range stores {
-		current[db] = struct{}{}
-		if err := snapshotDB(store, repoDir, db); err != nil {
-			return fmt.Errorf("snapshot %q: %w", db, err)
-		}
-	}
-
-	entries, err := os.ReadDir(targetDir)
-	if err != nil {
-		return err
-	}
-	for _, e := range entries {
-		if e.IsDir() || filepath.Ext(e.Name()) != ".ndjson" {
-			continue
-		}
-		dbName := strings.TrimSuffix(e.Name(), ".ndjson")
-		if _, ok := current[dbName]; ok {
-			continue
-		}
-		if err := os.Remove(filepath.Join(targetDir, e.Name())); err != nil && !os.IsNotExist(err) {
-			return err
-		}
-	}
-
-	return nil
-}
-
 func runGit(dir string, args ...string) error {
 	cmd := exec.Command("git", args...)
 	cmd.Dir = dir
@@ -288,66 +209,6 @@ func currentBranch(dir string) (string, error) {
 	return branch, nil
 }
 
-// restoreAllSnapshots copies .ndjson files from VCS snapshot dir into store paths,
-// and removes local stores that are not in the snapshot.
-func restoreAllSnapshots(store *Store, repoDir string) error {
-	targetDir := filepath.Join(repoDir, storeDirName)
-	entries, err := os.ReadDir(targetDir)
-	if err != nil {
-		if os.IsNotExist(err) {
-			fmt.Printf("no existing stores found, not restoring")
-			return nil
-		}
-		return err
-	}
-	snapshotDBs := make(map[string]struct{})
-
-	for _, e := range entries {
-		if e.IsDir() {
-			continue
-		}
-		if filepath.Ext(e.Name()) != ".ndjson" {
-			continue
-		}
-		dbName := strings.TrimSuffix(e.Name(), ".ndjson")
-		snapshotDBs[dbName] = struct{}{}
-
-		srcPath := filepath.Join(targetDir, e.Name())
-		data, err := os.ReadFile(srcPath)
-		if err != nil {
-			return fmt.Errorf("restore %q: %w", dbName, err)
-		}
-
-		dstPath, err := store.storePath(dbName)
-		if err != nil {
-			return fmt.Errorf("restore %q: %w", dbName, err)
-		}
-
-		if err := os.WriteFile(dstPath, data, 0o640); err != nil {
-			return fmt.Errorf("restore %q: %w", dbName, err)
-		}
-	}
-
-	localDBs, err := store.AllStores()
-	if err != nil {
-		return err
-	}
-	for _, db := range localDBs {
-		if _, ok := snapshotDBs[db]; ok {
-			continue
-		}
-		p, err := store.storePath(db)
-		if err != nil {
-			return err
-		}
-		if err := os.Remove(p); err != nil && !os.IsNotExist(err) {
-			return fmt.Errorf("remove store '%s': %w", db, err)
-		}
-	}
-
-	return nil
-}
-
 func wipeAllStores(store *Store) error {
 	dbs, err := store.AllStores()
 	if err != nil {