fix(dolt): auto-commit pending changes before pull to prevent merge errors (GH#2474)

Store initialization (schema init, molecule loading, metadata writes) can dirty
the working set before the user's pull command runs. Dolt refuses to merge with
uncommitted changes, causing 'cannot merge with uncommitted changes' errors.
Repeated failed attempts can corrupt Dolt journals in server mode.

Fix: auto-commit any pending changes before executing pull in both Pull() and
PullFrom(). Uses existing Commit() which gracefully handles 'nothing to commit'
when the working set is already clean.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: steveyegge

internal/storage/dolt/federation.go

@@ -38,6 +38,16 @@ func (s *DoltStore) PushTo(ctx context.Context, peer string) error {
 // For git-protocol remotes, uses CLI `dolt pull` to avoid MySQL connection timeouts.
 // Returns any merge conflicts if present.
 func (s *DoltStore) PullFrom(ctx context.Context, peer string) ([]storage.Conflict, error) {
+	// GH#2474: Auto-commit pending changes before pull to prevent
+	// "cannot merge with uncommitted changes" errors.
+	if !s.readOnly {
+		if err := s.Commit(ctx, "auto-commit before pull"); err != nil {
+			if !isDoltNothingToCommit(err) {
+				return nil, fmt.Errorf("failed to commit pending changes before pull: %w", err)
+			}
+		}
+	}
+
 	var conflicts []storage.Conflict
 	if s.isPeerGitProtocolRemote(ctx, peer) {
 		err := s.withPeerCredentials(ctx, peer, func(creds *remoteCredentials) error {

internal/storage/dolt/store.go

@@ -1491,6 +1491,20 @@ func (s *DoltStore) Pull(ctx context.Context) (retErr error) {
 		)...),
 	)
 	defer func() { endSpan(span, retErr) }()
+
+	// GH#2474: Auto-commit pending changes before pull to prevent
+	// "cannot merge with uncommitted changes" errors. Store initialization
+	// (schema init, molecule loading, metadata writes) can dirty the working
+	// set before the user's pull command runs.
+	if !s.readOnly {
+		if err := s.Commit(ctx, "auto-commit before pull"); err != nil {
+			// "nothing to commit" is fine — working set is already clean
+			if !isDoltNothingToCommit(err) {
+				return fmt.Errorf("failed to commit pending changes before pull: %w", err)
+			}
+		}
+	}
+
 	creds := s.mainRemoteCredentials()
 	// Git-protocol remotes: use CLI to avoid MySQL connection timeout during transfer.
 	// Must check before remoteUser — Hosted Dolt SSH remotes have remoteUser set