Phase 1 MVP - Complete implementation

- Auth: register, login, JWT with refresh tokens, blocklist
- Projects/Folders/Documents CRUD with soft deletes
- Tags CRUD and assignment
- FTS5 search with highlights and tag filtering
- ADR-001, ADR-002, ADR-003 compliant
- Security fixes applied (JWT_SECRET_KEY, exception handler, cookie secure)
- 25 tests passing

alembic/env.py

@@ -0,0 +1,58 @@
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config, pool
+
+from alembic import context
+
+# this is the Alembic Config object
+config = context.config
+
+# Interpret the config file for Python logging.
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+# Import models for autogenerate
+import sys
+from pathlib import Path
+sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
+
+from app.database import Base
+from app.models import agent, project, folder, document, tag, refresh_token
+
+target_metadata = Base.metadata
+
+
+def run_migrations_offline() -> None:
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online() -> None:
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

alembic/versions/001_initial.py

@@ -0,0 +1,27 @@
+"""Initial schema
+
+Revision ID: 001
+Revises:
+Create Date: 2026-03-30
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+revision: str = '001'
+down_revision: Union[str, None] = None
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # All schema creation is handled in database.py init_db()
+    # This migration is a no-op since we use raw SQL for SQLite-specific features
+    pass
+
+
+def downgrade() -> None:
+    pass