Fix session save freeze and restore losing removed files

Save freeze fix:
- Added record_symlinks_batch() that inserts all symlinks in a single
  DB transaction instead of opening a new connection per file
- _save_session and _auto_save_session now use batch inserts
- With 1700 files this goes from 1700 connection cycles to 1

Removed files fix:
- _restore_files_from_session now filters by _removed_files so
  individually deleted files stay removed even when restoring from
  session data that pre-dates the removal

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

core/database.py

@@ -216,6 +216,31 @@ class DatabaseManager:
         except sqlite3.Error as e:
             raise DatabaseError(f"Failed to record symlink: {e}") from e
 
+    def record_symlinks_batch(
+        self,
+        session_id: int,
+        records: list[tuple[str, str, str, int]],
+    ) -> None:
+        """Record multiple symlinks in a single transaction.
+
+        Args:
+            session_id: The session these symlinks belong to.
+            records: List of (source, link, filename, seq) tuples.
+
+        Raises:
+            DatabaseError: If recording fails.
+        """
+        try:
+            with self._connect() as conn:
+                conn.executemany(
+                    """INSERT INTO symlinks
+                       (session_id, source_path, link_path, original_filename, sequence_number)
+                       VALUES (?, ?, ?, ?, ?)""",
+                    [(session_id, src, lnk, fname, seq) for src, lnk, fname, seq in records]
+                )
+        except sqlite3.Error as e:
+            raise DatabaseError(f"Failed to record symlinks: {e}") from e
+
     def get_sessions(self) -> list[SessionRecord]:
         """List all sessions with link counts.
 

ui/main_window.py

@@ -3166,17 +3166,18 @@ class SequenceLinkerUI(QWidget):
             self._save_session_settings(session_id, save_effective_types=True)
 
             # Save the file list so the exact sequence can be restored
+            records = []
             for i, (source_dir, filename, folder_idx, file_idx) in enumerate(files):
                 source_path = source_dir / filename
                 ext = source_path.suffix
                 link_name = f"seq{folder_idx + 1:02d}_{file_idx:04d}{ext}"
-                self.db.record_symlink(
-                    session_id=session_id,
-                    source=str(source_path.resolve()),
-                    link=str(Path(dest) / link_name),
-                    filename=filename,
-                    seq=i,
-                )
+                records.append((
+                    str(source_path.resolve()),
+                    str(Path(dest) / link_name),
+                    filename,
+                    i,
+                ))
+            self.db.record_symlinks_batch(session_id, records)
         except Exception:
             pass  # Best-effort save on close
 
@@ -3200,19 +3201,20 @@ class SequenceLinkerUI(QWidget):
 
             self._save_session_settings(session_id, save_effective_types=True)
 
-            # Save the exact file list
+            # Save the exact file list in a single transaction
             files = self._get_files_in_order()
+            records = []
             for i, (source_dir, filename, folder_idx, file_idx) in enumerate(files):
                 source_path = source_dir / filename
                 ext = source_path.suffix
                 link_name = f"seq{folder_idx + 1:02d}_{file_idx:04d}{ext}"
-                self.db.record_symlink(
-                    session_id=session_id,
-                    source=str(source_path.resolve()),
-                    link=str(Path(dest) / link_name),
-                    filename=filename,
-                    seq=i,
-                )
+                records.append((
+                    str(source_path.resolve()),
+                    str(Path(dest) / link_name),
+                    filename,
+                    i,
+                ))
+            self.db.record_symlinks_batch(session_id, records)
 
             main_count = sum(
                 1 for i, f in enumerate(self.source_folders)
@@ -3667,8 +3669,11 @@ class SequenceLinkerUI(QWidget):
             # Sort files by their sequence index
             sorted_files = sorted(file_list, key=lambda x: x[0])
 
-            # Folder existence already verified in _try_resume_session;
-            # only recheck individual files if the folder has changed on disk.
+            # Filter out individually removed files
+            removed = self._removed_files.get(folder_path, set())
+            if removed:
+                sorted_files = [(idx, fname) for idx, fname in sorted_files if fname not in removed]
+
             if not sorted_files:
                 continue