fix: Add Alembic migration 0104 for missing embedding + audit_log columns

Two critical bugs found by API integration tests:
1. contacts.embedding (vector(768)) — ORM model updated in Phase 5.3 but
   plugin migration 0002_embeddings.sql was never run as Alembic migration.
   Also adds embedding columns to mails, companies, files, calendar_entries, tags.
2. audit_log.created_at, updated_at, deleted_at — AuditLog inherits TenantMixin
   which expects these columns, but they were never added to the DB table.
   Also adds to deletion_log.

Migration uses IF NOT EXISTS checks for all columns/indexes.
Alembic head: 0103 → 0104

alembic/versions/0104_add_embedding_and_audit_timestamps.py

@@ -0,0 +1,99 @@
+"""Add embedding column to contacts + timestamp columns to audit_log.
+
+Fixes two issues found by API integration tests:
+1. contacts.embedding (vector(768)) — ORM model was updated in Phase 5.3 but
+   the plugin migration 0002_embeddings.sql was never run as an Alembic migration.
+2. audit_log.created_at, updated_at, deleted_at — AuditLog model inherits TenantMixin
+   which expects these columns, but they were never added to the DB table.
+
+Revision ID: 0104
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+revision = "0104"
+down_revision = "0103"
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+
+    # 1. Add embedding column to contacts (if not exists)
+    result = conn.execute(sa.text(
+        "SELECT column_name FROM information_schema.columns "
+        "WHERE table_name = 'contacts' AND column_name = 'embedding'"
+    ))
+    if result.fetchone() is None:
+        op.execute("ALTER TABLE contacts ADD COLUMN embedding vector(768)")
+        op.execute(
+            "CREATE INDEX IF NOT EXISTS ix_contacts_embedding "
+            "ON contacts USING hnsw(embedding vector_cosine_ops)"
+        )
+
+    # 2. Add embedding columns to other tables (from plugin migration 0002)
+    for table in ["mails", "companies", "files", "calendar_entries"]:
+        result = conn.execute(sa.text(
+            f"SELECT column_name FROM information_schema.columns "
+            f"WHERE table_name = '{table}' AND column_name = 'embedding'"
+        ))
+        if result.fetchone() is None:
+            op.execute(f"ALTER TABLE {table} ADD COLUMN embedding vector(768)")
+            op.execute(
+                f"CREATE INDEX IF NOT EXISTS ix_{table}_embedding "
+                f"ON {table} USING hnsw(embedding vector_cosine_ops)"
+            )
+
+    # Tags use 384-dim embeddings
+    result = conn.execute(sa.text(
+        "SELECT column_name FROM information_schema.columns "
+        "WHERE table_name = 'tags' AND column_name = 'embedding'"
+    ))
+    if result.fetchone() is None:
+        op.execute("ALTER TABLE tags ADD COLUMN embedding vector(384)")
+        op.execute(
+            "CREATE INDEX IF NOT EXISTS ix_tags_embedding "
+            "ON tags USING hnsw(embedding vector_cosine_ops)"
+        )
+
+    # 3. Add timestamp columns to audit_log (if not exists)
+    for col in ["created_at", "updated_at", "deleted_at"]:
+        result = conn.execute(sa.text(
+            f"SELECT column_name FROM information_schema.columns "
+            f"WHERE table_name = 'audit_log' AND column_name = '{col}'"
+        ))
+        if result.fetchone() is None:
+            op.execute(
+                f"ALTER TABLE audit_log ADD COLUMN {col} "
+                f"TIMESTAMPTZ DEFAULT NOW()"
+            )
+
+    # 4. Add timestamp columns to deletion_log (if not exists)
+    for col in ["created_at", "updated_at", "deleted_at"]:
+        result = conn.execute(sa.text(
+            f"SELECT column_name FROM information_schema.columns "
+            f"WHERE table_name = 'deletion_log' AND column_name = '{col}'"
+        ))
+        if result.fetchone() is None:
+            op.execute(
+                f"ALTER TABLE deletion_log ADD COLUMN {col} "
+                f"TIMESTAMPTZ DEFAULT NOW()"
+            )
+
+
+def downgrade() -> None:
+    # Drop embedding columns
+    for table in ["contacts", "mails", "companies", "files", "calendar_entries"]:
+        op.execute(f"DROP INDEX IF EXISTS ix_{table}_embedding")
+        op.execute(f"ALTER TABLE {table} DROP COLUMN IF EXISTS embedding")
+
+    op.execute("DROP INDEX IF EXISTS ix_tags_embedding")
+    op.execute("ALTER TABLE tags DROP COLUMN IF EXISTS embedding")
+
+    # Drop timestamp columns from audit_log
+    for col in ["created_at", "updated_at", "deleted_at"]:
+        op.execute(f"ALTER TABLE audit_log DROP COLUMN IF EXISTS {col}")
+
+    # Drop timestamp columns from deletion_log
+    for col in ["created_at", "updated_at", "deleted_at"]:
+        op.execute(f"ALTER TABLE deletion_log DROP COLUMN IF EXISTS {col}")