fix: Handle partially migrated databases in migration 002 detection

CRITICAL HOTFIX for production deployment failure

Problem:
- Production database had migration 001 applied but not migration 002
- Migration 002's tables (tokens, authorization_codes) already existed from SCHEMA_SQL
- Smart detection only checked when migration_count == 0 (fresh database)
- For partially migrated databases (count > 0), tried to run full migration
- This failed with "table already exists" error

Solution:
- Always check migration 002's state, regardless of migration_count
- If tables exist with correct structure, skip table creation
- Create missing indexes only
- Mark migration as applied

Testing:
- Manual verification with production scenario: SUCCESS
- 561 automated tests passing
- test_run_migrations_partial_applied confirms fix works

Impact:
- Fixes deployment on partially migrated production databases
- No impact on fresh or fully migrated databases
- Backwards compatible with all database states

Version: 1.0.0-rc.2 → 1.0.0-rc.3

Generated with Claude Code

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

starpunk/__init__.py

@@ -153,5 +153,5 @@ def create_app(config=None):
 
 # Package version (Semantic Versioning 2.0.0)
 # See docs/standards/versioning-strategy.md for details
-__version__ = "1.0.0-rc.2"
-__version_info__ = (1, 0, 0, "rc", 2)
+__version__ = "1.0.0-rc.3"
+__version_info__ = (1, 0, 0, "rc", 3)

starpunk/migrations.py

@@ -370,14 +370,20 @@ def run_migrations(db_path, logger=None):
         # Get already-applied migrations
         applied = get_applied_migrations(conn)
 
-        # Apply pending migrations (using smart detection for fresh databases)
+        # Apply pending migrations (using smart detection for fresh databases and migration 002)
         pending_count = 0
         skipped_count = 0
         for migration_name, migration_path in migration_files:
             if migration_name not in applied:
-                # For fresh databases (migration_count == 0), check if migration is actually needed
-                # Some migrations may have been included in SCHEMA_SQL
-                if migration_count == 0 and not is_migration_needed(conn, migration_name):
+                # Check if migration is actually needed
+                # For fresh databases (migration_count == 0), check all migrations
+                # For migration 002, ALWAYS check (handles partially migrated databases)
+                should_check_needed = (
+                    migration_count == 0 or
+                    migration_name == "002_secure_tokens_and_authorization_codes.sql"
+                )
+
+                if should_check_needed and not is_migration_needed(conn, migration_name):
                     # Special handling for migration 002: if tables exist but indexes don't,
                     # create just the indexes
                     if migration_name == "002_secure_tokens_and_authorization_codes.sql":