test: fix Phase 2 migration schema tests

- Update test_domains_schema to expect two_factor column
- Fix test_run_migrations_idempotent for migration 002
- Update test_get_applied_migrations_after_running to check both migrations
- Update test_initialize_full_setup to verify both migrations
- Add test coverage strategy documentation to report

All 189 tests now passing.

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

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

tests/unit/test_database.py

@@ -138,8 +138,9 @@ class TestDatabaseMigrations:
 
             migrations = db.get_applied_migrations()
 
-            # Migration 001 should be applied
+            # Both migrations should be applied
             assert 1 in migrations
+            assert 2 in migrations
 
     def test_run_migrations_creates_tables(self):
         """Test run_migrations creates expected tables."""
@@ -174,10 +175,15 @@ class TestDatabaseMigrations:
 
             engine = db.get_engine()
             with engine.connect() as conn:
-                # Check migration was recorded only once
+                # Check migrations were recorded correctly (001 and 002)
                 result = conn.execute(text("SELECT COUNT(*) FROM migrations"))
                 count = result.fetchone()[0]
-                assert count == 1
+                assert count == 2
+
+                # Verify both migrations are present
+                result = conn.execute(text("SELECT version FROM migrations ORDER BY version"))
+                versions = [row[0] for row in result]
+                assert versions == [1, 2]
 
     def test_initialize_full_setup(self):
         """Test initialize performs full database setup."""
@@ -190,9 +196,10 @@ class TestDatabaseMigrations:
             # Verify database is healthy
             assert db.check_health() is True
 
-            # Verify migrations ran
+            # Verify all migrations ran
             migrations = db.get_applied_migrations()
             assert 1 in migrations
+            assert 2 in migrations
 
             # Verify tables exist
             engine = db.get_engine()
@@ -253,6 +260,7 @@ class TestMigrationSchemaCorrectness:
                     "verified",
                     "created_at",
                     "verified_at",
+                    "two_factor",
                 }
 
                 assert columns == expected_columns