docs: fix deployment ordering and add __init__.py to spec

- Fix migration diagram: runs after container starts, not before
- Add -c app/alembic.ini flag to migration command
- Add __init__.py to repository structure tree

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: baijum

docs/deployment.md

@@ -78,16 +78,16 @@ If the health check fails, traffic stays on the previous version.
 
 ## Database Migrations
 
-Migrations run automatically as part of the deployment pipeline, **before** the new application container starts.
+Migrations run automatically as part of the deployment pipeline, **after the application container starts, by executing alembic inside the running container**.
 
 ```
 Deploy started
       │
       ▼
-Run database migrations
+Start containers
       │
       ▼
-Start new application container
+Run migrations (inside container)
       │
       ▼
 Health check
@@ -96,7 +96,7 @@ Health check
 Migration command:
 
 ```bash
-docker compose exec app alembic upgrade head
+docker compose exec app alembic -c app/alembic.ini upgrade head
 ```
 
 ### Safe Migration Rules

docs/spec.md

@@ -20,6 +20,7 @@ Each application lives in its own GitHub repository under the `towlion` organiza
 ```
 repo/
   app/                          # FastAPI backend
+    __init__.py                 # Package marker (required)
     Dockerfile                  # Backend container image
     main.py                     # Application entry point
   frontend/                     # Next.js frontend (optional)