fix: add database schema migration for simulation_run_id column

Add automatic schema migration to handle existing databases that don't
have the simulation_run_id column in the positions table.

Problem:
- v0.3.0-alpha.3 databases lack simulation_run_id column
- CREATE TABLE IF NOT EXISTS doesn't add new columns to existing tables
- Index creation fails with "no such column: simulation_run_id"

Solution:
- Add _migrate_schema() function to detect and migrate old schemas
- Check if positions table exists and inspect its columns
- ALTER TABLE to add simulation_run_id if missing
- Run migration before creating indexes

This allows seamless upgrades from alpha.3 to alpha.4 without manual
database deletion or migration scripts.

Fixes docker compose startup error:
  sqlite3.OperationalError: no such column: simulation_run_id

Generated with [Claude Code](https://claude.com/claude-code)

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

api/database.py

@@ -203,6 +203,9 @@ def initialize_database(db_path: str = "data/jobs.db") -> None:
         )
     """)
 
+    # Run schema migrations for existing databases
+    _migrate_schema(cursor)
+
     # Create indexes for performance
     _create_indexes(cursor)
 
@@ -210,6 +213,21 @@ def initialize_database(db_path: str = "data/jobs.db") -> None:
     conn.close()
 
 
+def _migrate_schema(cursor: sqlite3.Cursor) -> None:
+    """Migrate existing database schema to latest version."""
+    # Check if positions table exists and has simulation_run_id column
+    cursor.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='positions'")
+    if cursor.fetchone():
+        cursor.execute("PRAGMA table_info(positions)")
+        columns = [row[1] for row in cursor.fetchall()]
+
+        if 'simulation_run_id' not in columns:
+            # Add simulation_run_id column to existing positions table
+            cursor.execute("""
+                ALTER TABLE positions ADD COLUMN simulation_run_id TEXT
+            """)
+
+
 def _create_indexes(cursor: sqlite3.Cursor) -> None:
     """Create database indexes for query performance."""