Phase 5: Alembic baseline, per-site deploy, ADRs to docs/adr

Migration runner ready and a sister site can deploy from a clean
checkout with one .env file.

ADRs relocated (migrations/adr/ -> docs/adr/):
- migrations/ is now Alembic territory, not docs.
- All cross-references updated: CLAUDE.md, docs/PLUGIN-HOOKS.md,
  docs/PLUGIN-QUICKSTART.md.

Alembic initialized (migrations/):
- env.py, script.py.mako, alembic.ini copied from Flask-Migrate
  templates so `flask db migrate` and `flask db upgrade` work without
  a one-time `flask db init` (which would clash with the existing
  migrations/ directory).
- Baseline migration generated via autogenerate, captures all 47
  tables (core models + 6 plugins) as the upgrade target. Ready for
  per-site `flask db upgrade` from an empty schema.

Deploy artifacts:
- Dockerfile: python:3.12-slim base, gunicorn server, non-root user,
  healthcheck against /api/auth/login. Single image bundles all six
  plugins; sites enable via `flask plugin install <name>`.
- docker-compose.yml: MySQL 8 + API container, healthcheck-gated
  startup, env-driven secrets that fail loud on missing values
  (`${SECRET_KEY:?}` form).
- .env.example: full env-var inventory with comments. Calls out
  required vs optional. Matches what ProductionConfig.validate
  enforces.

docs/DEPLOY.md:
- Step-by-step per-site runbook: clone, configure .env, bring up
  stack, run migrations, seed reference data, install plugins,
  create admin, front with TLS, backups, updates.
- Common-issues table.
- Cross-links to ADR-004 (per-site rationale), ADR-003 (plugin
  distribution), and the config source.

Skills:
- migrating-asset-schema: Alembic + one-shot data migration policy.
  Rules: additive first, renames are three steps, destructive ops
  need rollback, equipment migration filter per ADR-001 + ADR-005.
- hardening-flask-config: production validation, CORS allowlist
  policy, JWT cookie hardening, per-site deploy isolation per ADR-004.

CLAUDE.md updated to reflect the post-Phase-5 state. No tests added
this commit; the Alembic baseline is exercised by the existing
db.create_all-based test suite (tests do not touch the migration
runner; that's by design until per-plugin migrations land).

Test count unchanged: 101 passing.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

migrations/env.py

@@ -0,0 +1,113 @@
+import logging
+from logging.config import fileConfig
+
+from flask import current_app
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+logger = logging.getLogger('alembic.env')
+
+
+def get_engine():
+    try:
+        # this works with Flask-SQLAlchemy<3 and Alchemical
+        return current_app.extensions['migrate'].db.get_engine()
+    except (TypeError, AttributeError):
+        # this works with Flask-SQLAlchemy>=3
+        return current_app.extensions['migrate'].db.engine
+
+
+def get_engine_url():
+    try:
+        return get_engine().url.render_as_string(hide_password=False).replace(
+            '%', '%%')
+    except AttributeError:
+        return str(get_engine().url).replace('%', '%%')
+
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+config.set_main_option('sqlalchemy.url', get_engine_url())
+target_db = current_app.extensions['migrate'].db
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def get_metadata():
+    if hasattr(target_db, 'metadatas'):
+        return target_db.metadatas[None]
+    return target_db.metadata
+
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url, target_metadata=get_metadata(), literal_binds=True
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+
+    # this callback is used to prevent an auto-migration from being generated
+    # when there are no changes to the schema
+    # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
+    def process_revision_directives(context, revision, directives):
+        if getattr(config.cmd_opts, 'autogenerate', False):
+            script = directives[0]
+            if script.upgrade_ops.is_empty():
+                directives[:] = []
+                logger.info('No changes in schema detected.')
+
+    conf_args = current_app.extensions['migrate'].configure_args
+    if conf_args.get("process_revision_directives") is None:
+        conf_args["process_revision_directives"] = process_revision_directives
+
+    connectable = get_engine()
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=get_metadata(),
+            **conf_args
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()