diff --git a/Dockerfile b/Dockerfile
index 1911865..d64a6fd 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -12,6 +12,10 @@ RUN apt update && apt install --no-install-recommends --no-install-suggests -y \
 
 WORKDIR /app
 
+COPY pyproject.toml uv.lock README.md .
+
+RUN uv sync --locked --no-dev --no-install-project --no-cache
+
 COPY . .
 
 RUN uv sync --locked --no-dev --no-editable --no-cache
diff --git a/alembic.ini b/alembic.ini
new file mode 100644
index 0000000..e030b90
--- /dev/null
+++ b/alembic.ini
@@ -0,0 +1,90 @@
+# Alembic configuration file for nextcloud-mcp-server
+
+[alembic]
+# Path to migration scripts
+script_location = alembic
+
+# Template used to generate migration file names
+# Default: %%(rev)s_%%(slug)s
+file_template = %%(year)d%%(month).2d%%(day).2d_%%(hour).2d%%(minute).2d_%%(rev)s_%%(slug)s
+
+# Timezone for migration timestamps
+# Default: utc
+timezone = utc
+
+# Max length of characters to apply to the "slug" field
+# Default: 40
+# truncate_slug_length = 40
+
+# Set to 'true' to run the environment during the 'revision' command
+# Default: false
+# revision_environment = false
+
+# Set to 'true' to allow .pyc and .pyo files without a source .py file
+# Default: false
+# sourceless = false
+
+# Version location specification
+# Supports single or multiple directories
+version_locations = alembic/versions
+
+# Path separator for version locations (required to suppress deprecation warning)
+# Use os (for cross-platform compatibility)
+path_separator = os
+
+# Set to 'true' to search source files recursively in each "version_locations" directory
+# Default: false
+# recursive_version_locations = false
+
+# Output encoding used when revision files are written
+# Default: utf-8
+# output_encoding = utf-8
+
+# Database URL - can be overridden by:
+# 1. Passing -x database_url=... to alembic commands
+# 2. Setting in environment via get_database_url() in env.py
+# Default: sqlite:///app/data/tokens.db
+sqlalchemy.url = sqlite+aiosqlite:////app/data/tokens.db
+
+[post_write_hooks]
+# Post-write hooks allow you to run scripts after generating migration files
+# Example: format migrations with ruff
+# hooks = ruff
+# ruff.type = exec
+# ruff.executable = ruff
+# ruff.options = format REVISION_SCRIPT_FILENAME
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S
diff --git a/alembic/README b/alembic/README
new file mode 100644
index 0000000..27072cf
--- /dev/null
+++ b/alembic/README
@@ -0,0 +1,71 @@
+Database Migrations for nextcloud-mcp-server
+============================================
+
+This directory contains Alembic database migrations for the token storage database.
+
+Structure
+---------
+- env.py: Alembic environment configuration
+- script.py.mako: Template for generating new migration files
+- versions/: Directory containing migration scripts
+
+Usage
+-----
+Migrations are managed via the CLI:
+
+    # Upgrade database to latest version
+    uv run nextcloud-mcp-server db upgrade
+
+    # Show current database version
+    uv run nextcloud-mcp-server db current
+
+    # Show migration history
+    uv run nextcloud-mcp-server db history
+
+    # Create a new migration (developers only)
+    uv run nextcloud-mcp-server db migrate "description of changes"
+
+    # Downgrade database by one version (emergency use only)
+    uv run nextcloud-mcp-server db downgrade
+
+Direct Alembic Usage
+--------------------
+You can also use Alembic commands directly:
+
+    # Specify database URL via -x flag
+    uv run alembic -x database_url=sqlite+aiosqlite:////path/to/tokens.db upgrade head
+
+    # Or set in alembic.ini and run
+    uv run alembic upgrade head
+    uv run alembic current
+    uv run alembic history
+
+Writing Migrations
+------------------
+Since we don't use SQLAlchemy models, migrations are written with raw SQL:
+
+    def upgrade() -> None:
+        op.execute("""
+            ALTER TABLE refresh_tokens
+            ADD COLUMN new_field TEXT
+        """)
+
+    def downgrade() -> None:
+        # SQLite doesn't support DROP COLUMN, use table recreation
+        op.execute("""
+            CREATE TABLE refresh_tokens_new AS
+            SELECT user_id, encrypted_token, ... FROM refresh_tokens
+        """)
+        op.execute("DROP TABLE refresh_tokens")
+        op.execute("ALTER TABLE refresh_tokens_new RENAME TO refresh_tokens")
+
+Migration File Naming
+---------------------
+Format: YYYYMMDD_HHMM_<revision>_<slug>.py
+Example: 20251217_2200_001_initial_schema.py
+
+Notes
+-----
+- Migrations run automatically when RefreshTokenStorage.initialize() is called
+- Existing databases are automatically stamped with the initial version
+- SQLite has limited ALTER TABLE support - complex changes require table recreation
diff --git a/alembic/env.py b/alembic/env.py
new file mode 100644
index 0000000..4a3fadb
--- /dev/null
+++ b/alembic/env.py
@@ -0,0 +1,128 @@
+"""Alembic environment configuration for nextcloud-mcp-server.
+
+This module configures how Alembic runs database migrations for the
+token storage database. It supports both online and offline migration modes.
+
+Uses anyio for async operations, consistent with the project's async patterns.
+"""
+
+import logging
+from pathlib import Path
+
+import anyio
+from sqlalchemy import pool
+from sqlalchemy.engine import Connection
+from sqlalchemy.ext.asyncio import async_engine_from_config
+
+from alembic import context
+
+# Configure logging
+logger = logging.getLogger("alembic.env")
+
+# This is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# We don't use SQLAlchemy models, so target_metadata is None
+# Migrations will be written manually using op.execute() for raw SQL
+target_metadata = None
+
+
+def get_database_url() -> str:
+    """
+    Get the database URL from Alembic config or environment.
+
+    The URL can be set in alembic.ini or passed via -x database_url=...
+    when running Alembic commands.
+
+    Returns:
+        Database URL (SQLite URL format)
+    """
+    # Check if URL is passed via -x database_url=...
+    url = context.get_x_argument(as_dictionary=True).get("database_url")
+
+    if not url:
+        # Fall back to alembic.ini configuration
+        url = config.get_main_option("sqlalchemy.url")
+
+    if not url:
+        # Default to /app/data/tokens.db for Docker deployments
+        db_path = Path("/app/data/tokens.db")
+        url = f"sqlite+aiosqlite:///{db_path}"
+        logger.warning(
+            f"No database URL configured, using default: {url}. "
+            "Set sqlalchemy.url in alembic.ini or pass -x database_url=..."
+        )
+
+    return url
+
+
+def run_migrations_offline() -> None:
+    """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.
+
+    This mode is useful for generating SQL scripts without database access.
+    """
+    url = get_database_url()
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def do_run_migrations(connection: Connection) -> None:
+    """Execute migrations within a database connection."""
+    context.configure(connection=connection, target_metadata=target_metadata)
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_async_migrations() -> None:
+    """Run migrations in 'online' mode with async support.
+
+    In this scenario we create an async Engine and associate
+    a connection with the context.
+    """
+    # Get database URL and update config
+    url = get_database_url()
+    config.set_main_option("sqlalchemy.url", url)
+
+    # Create async engine
+    connectable = async_engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,  # Don't pool connections for migrations
+    )
+
+    async with connectable.connect() as connection:
+        await connection.run_sync(do_run_migrations)
+
+    await connectable.dispose()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode.
+
+    This function is called from storage.py's initialize() method via
+    anyio.to_thread.run_sync(), so it always runs in a worker thread
+    with its own event loop. We can safely use anyio.run() here.
+    """
+    anyio.run(run_async_migrations)
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()
diff --git a/alembic/script.py.mako b/alembic/script.py.mako
new file mode 100644
index 0000000..3525c5f
--- /dev/null
+++ b/alembic/script.py.mako
@@ -0,0 +1,26 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    """Apply migration changes to upgrade the database schema."""
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    """Revert migration changes to downgrade the database schema."""
+    ${downgrades if downgrades else "pass"}
diff --git a/alembic/versions/20251217_2200_001_initial_schema.py b/alembic/versions/20251217_2200_001_initial_schema.py
new file mode 100644
index 0000000..3f1110c
--- /dev/null
+++ b/alembic/versions/20251217_2200_001_initial_schema.py
@@ -0,0 +1,185 @@
+"""Initial schema for token storage database
+
+This migration creates the initial database schema including:
+- refresh_tokens: OAuth refresh tokens and user profiles
+- audit_logs: Audit trail for security events
+- oauth_clients: OAuth client credentials (DCR)
+- oauth_sessions: OAuth flow session state (ADR-004 Progressive Consent)
+- registered_webhooks: Webhook registration tracking (both OAuth and BasicAuth)
+- schema_version: Legacy schema version tracking (deprecated, use alembic_version)
+
+Revision ID: 001
+Revises:
+Create Date: 2025-12-17 22:00:00.000000
+
+"""
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "001"
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    """Create initial database schema."""
+
+    # Refresh tokens table (OAuth mode only, for background jobs)
+    op.execute(
+        """
+        CREATE TABLE IF NOT EXISTS refresh_tokens (
+            user_id TEXT PRIMARY KEY,
+            encrypted_token BLOB NOT NULL,
+            expires_at INTEGER,
+            created_at INTEGER NOT NULL,
+            updated_at INTEGER NOT NULL,
+            -- ADR-004 Progressive Consent fields
+            flow_type TEXT DEFAULT 'hybrid',
+            token_audience TEXT DEFAULT 'nextcloud',
+            provisioned_at INTEGER,
+            provisioning_client_id TEXT,
+            scopes TEXT,
+            -- Browser session profile cache
+            user_profile TEXT,
+            profile_cached_at INTEGER
+        )
+        """
+    )
+
+    # Audit logs table (both OAuth and BasicAuth modes)
+    op.execute(
+        """
+        CREATE TABLE IF NOT EXISTS audit_logs (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            timestamp INTEGER NOT NULL,
+            event TEXT NOT NULL,
+            user_id TEXT NOT NULL,
+            resource_type TEXT,
+            resource_id TEXT,
+            auth_method TEXT,
+            hostname TEXT
+        )
+        """
+    )
+
+    # Index on audit logs for efficient queries
+    op.execute(
+        """
+        CREATE INDEX IF NOT EXISTS idx_audit_user_timestamp
+        ON audit_logs(user_id, timestamp)
+        """
+    )
+
+    # OAuth client credentials storage (OAuth mode only)
+    op.execute(
+        """
+        CREATE TABLE IF NOT EXISTS oauth_clients (
+            id INTEGER PRIMARY KEY,
+            client_id TEXT UNIQUE NOT NULL,
+            encrypted_client_secret BLOB NOT NULL,
+            client_id_issued_at INTEGER NOT NULL,
+            client_secret_expires_at INTEGER NOT NULL,
+            redirect_uris TEXT NOT NULL,
+            encrypted_registration_access_token BLOB,
+            registration_client_uri TEXT,
+            created_at INTEGER NOT NULL,
+            updated_at INTEGER NOT NULL
+        )
+        """
+    )
+
+    # OAuth flow sessions (ADR-004 Progressive Consent)
+    op.execute(
+        """
+        CREATE TABLE IF NOT EXISTS oauth_sessions (
+            session_id TEXT PRIMARY KEY,
+            client_id TEXT,
+            client_redirect_uri TEXT NOT NULL,
+            state TEXT,
+            code_challenge TEXT,
+            code_challenge_method TEXT,
+            mcp_authorization_code TEXT UNIQUE,
+            idp_access_token TEXT,
+            idp_refresh_token TEXT,
+            user_id TEXT,
+            created_at INTEGER NOT NULL,
+            expires_at INTEGER NOT NULL,
+            -- ADR-004 Progressive Consent fields
+            flow_type TEXT DEFAULT 'hybrid',
+            requested_scopes TEXT,
+            granted_scopes TEXT,
+            is_provisioning BOOLEAN DEFAULT FALSE
+        )
+        """
+    )
+
+    # Index for MCP authorization code lookups
+    op.execute(
+        """
+        CREATE INDEX IF NOT EXISTS idx_oauth_sessions_mcp_code
+        ON oauth_sessions(mcp_authorization_code)
+        """
+    )
+
+    # Legacy schema version tracking table
+    # NOTE: This is deprecated in favor of Alembic's alembic_version table
+    # Kept for backward compatibility with pre-Alembic databases
+    op.execute(
+        """
+        CREATE TABLE IF NOT EXISTS schema_version (
+            version INTEGER PRIMARY KEY,
+            applied_at REAL NOT NULL
+        )
+        """
+    )
+
+    # Registered webhooks tracking (both BasicAuth and OAuth modes)
+    op.execute(
+        """
+        CREATE TABLE IF NOT EXISTS registered_webhooks (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            webhook_id INTEGER NOT NULL UNIQUE,
+            preset_id TEXT NOT NULL,
+            created_at REAL NOT NULL
+        )
+        """
+    )
+
+    # Indexes for efficient webhook queries
+    op.execute(
+        """
+        CREATE INDEX IF NOT EXISTS idx_webhooks_preset
+        ON registered_webhooks(preset_id)
+        """
+    )
+
+    op.execute(
+        """
+        CREATE INDEX IF NOT EXISTS idx_webhooks_created
+        ON registered_webhooks(created_at)
+        """
+    )
+
+
+def downgrade() -> None:
+    """Drop all tables and indexes.
+
+    WARNING: This will destroy all data in the database!
+    Use with extreme caution.
+    """
+
+    # Drop indexes first
+    op.execute("DROP INDEX IF EXISTS idx_webhooks_created")
+    op.execute("DROP INDEX IF EXISTS idx_webhooks_preset")
+    op.execute("DROP INDEX IF EXISTS idx_oauth_sessions_mcp_code")
+    op.execute("DROP INDEX IF EXISTS idx_audit_user_timestamp")
+
+    # Drop tables
+    op.execute("DROP TABLE IF EXISTS registered_webhooks")
+    op.execute("DROP TABLE IF EXISTS schema_version")
+    op.execute("DROP TABLE IF EXISTS oauth_sessions")
+    op.execute("DROP TABLE IF EXISTS oauth_clients")
+    op.execute("DROP TABLE IF EXISTS audit_logs")
+    op.execute("DROP TABLE IF EXISTS refresh_tokens")
diff --git a/docs/database-migrations.md b/docs/database-migrations.md
new file mode 100644
index 0000000..dead454
--- /dev/null
+++ b/docs/database-migrations.md
@@ -0,0 +1,301 @@
+# Database Migrations
+
+This document describes the database migration system for nextcloud-mcp-server's token storage database.
+
+## Overview
+
+The token storage database uses [Alembic](https://alembic.sqlalchemy.org/) for schema versioning and migrations. Alembic provides:
+
+- **Version Control**: Track schema changes in Git
+- **Rollback Support**: Safely downgrade schema if needed
+- **Audit Trail**: Migration files serve as schema changelog
+- **Automated Upgrades**: Database schema updates automatically on startup
+
+## Architecture
+
+### Migration Strategy
+
+The system handles three scenarios:
+
+1. **New Database**: Runs migrations from scratch to create all tables
+2. **Pre-Alembic Database**: Stamps existing database with initial revision (no changes)
+3. **Alembic-Managed Database**: Upgrades to latest version automatically
+
+### Directory Structure
+
+```
+nextcloud-mcp-server/
+├── alembic/                              # Alembic migrations
+│   ├── versions/                         # Migration scripts
+│   │   └── 20251217_2200_001_initial_schema.py
+│   ├── env.py                            # Alembic environment
+│   ├── script.py.mako                    # Migration template
+│   └── README                            # Migration usage guide
+├── alembic.ini                           # Alembic configuration
+└── nextcloud_mcp_server/
+    ├── auth/storage.py                   # Uses migrations on init
+    └── migrations.py                     # Migration utilities
+```
+
+## Usage
+
+### Automatic Migration on Startup
+
+Migrations run automatically when the server starts:
+
+```bash
+uv run nextcloud-mcp-server
+```
+
+The `RefreshTokenStorage.initialize()` method:
+1. Checks if database is Alembic-managed
+2. Stamps pre-Alembic databases with initial revision
+3. Upgrades to latest version
+
+### Manual Migration Commands
+
+```bash
+# Show current database version
+uv run nextcloud-mcp-server db current
+
+# Upgrade database to latest version
+uv run nextcloud-mcp-server db upgrade
+
+# Show migration history
+uv run nextcloud-mcp-server db history
+
+# Downgrade by one version (emergency use only)
+uv run nextcloud-mcp-server db downgrade
+
+# Specify custom database path
+uv run nextcloud-mcp-server db current -d /path/to/tokens.db
+```
+
+### Environment Variables
+
+- `TOKEN_STORAGE_DB`: Path to database file (default: `/app/data/tokens.db`)
+
+## Creating Migrations (Developers)
+
+### Step 1: Create Migration File
+
+```bash
+uv run nextcloud-mcp-server db migrate "add user preferences table"
+```
+
+This creates a new migration file in `alembic/versions/` with empty `upgrade()` and `downgrade()` functions.
+
+### Step 2: Write Migration SQL
+
+Since we don't use SQLAlchemy models, write raw SQL:
+
+```python
+def upgrade() -> None:
+    """Add user preferences table."""
+    op.execute("""
+        CREATE TABLE user_preferences (
+            user_id TEXT PRIMARY KEY,
+            theme TEXT DEFAULT 'light',
+            language TEXT DEFAULT 'en',
+            created_at INTEGER NOT NULL
+        )
+    """)
+
+    op.execute("""
+        CREATE INDEX idx_user_preferences_user_id
+        ON user_preferences(user_id)
+    """)
+
+
+def downgrade() -> None:
+    """Remove user preferences table."""
+    op.execute("DROP INDEX IF EXISTS idx_user_preferences_user_id")
+    op.execute("DROP TABLE IF EXISTS user_preferences")
+```
+
+### Step 3: Test Migration
+
+```bash
+# Test upgrade
+uv run nextcloud-mcp-server db upgrade -d /tmp/test.db
+
+# Verify schema
+sqlite3 /tmp/test.db ".schema"
+
+# Test downgrade
+uv run nextcloud-mcp-server db downgrade -d /tmp/test.db
+
+# Verify removal
+sqlite3 /tmp/test.db ".schema"
+```
+
+### Step 4: Commit Migration
+
+```bash
+git add alembic/versions/YYYYMMDD_HHMM_XXX_description.py
+git commit -m "feat: add user preferences table migration"
+```
+
+## SQLite Limitations
+
+SQLite has limited `ALTER TABLE` support:
+
+### Supported Operations
+
+- ✅ Add columns: `ALTER TABLE table ADD COLUMN ...`
+- ✅ Rename table: `ALTER TABLE old RENAME TO new`
+- ✅ Rename column: `ALTER TABLE table RENAME COLUMN old TO new` (SQLite 3.25+)
+
+### Unsupported Operations (Requires Table Recreation)
+
+- ❌ Drop column
+- ❌ Change column type
+- ❌ Add constraints to existing columns
+
+### Table Recreation Pattern
+
+For complex schema changes:
+
+```python
+def upgrade() -> None:
+    # Create new table with desired schema
+    op.execute("""
+        CREATE TABLE refresh_tokens_new (
+            user_id TEXT PRIMARY KEY,
+            encrypted_token BLOB NOT NULL,
+            new_field TEXT,  -- New column
+            expires_at INTEGER,
+            created_at INTEGER NOT NULL
+        )
+    """)
+
+    # Copy data from old table
+    op.execute("""
+        INSERT INTO refresh_tokens_new
+        (user_id, encrypted_token, expires_at, created_at)
+        SELECT user_id, encrypted_token, expires_at, created_at
+        FROM refresh_tokens
+    """)
+
+    # Drop old table and rename new table
+    op.execute("DROP TABLE refresh_tokens")
+    op.execute("ALTER TABLE refresh_tokens_new RENAME TO refresh_tokens")
+
+    # Recreate indexes
+    op.execute("CREATE INDEX idx_user_id ON refresh_tokens(user_id)")
+```
+
+## Best Practices
+
+### Naming Conventions
+
+- **Migrations**: `YYYYMMDD_HHMM_XXX_description.py`
+- **Revision IDs**: Sequential numbers (`001`, `002`, `003`)
+- **Descriptions**: Imperative mood ("add table", "remove column")
+
+### Migration Guidelines
+
+1. **Test Thoroughly**: Test both upgrade and downgrade paths
+2. **Preserve Data**: Ensure data migration logic is correct
+3. **Document Changes**: Add comments explaining complex operations
+4. **Small Changes**: One logical change per migration
+5. **No Breaking Changes**: Maintain backward compatibility when possible
+
+### Downgrade Considerations
+
+- **Data Loss**: Downgrade may lose data (dropped columns, tables)
+- **Confirmation**: Downgrade command requires explicit confirmation
+- **Testing**: Always test downgrade path before deploying
+- **Emergency Only**: Use downgrades only for critical rollbacks
+
+## Backward Compatibility
+
+### Pre-Alembic Databases
+
+Existing databases created before Alembic integration are automatically detected and stamped with revision `001`:
+
+1. Server detects no `alembic_version` table
+2. Checks if `refresh_tokens` table exists
+3. If yes, stamps database with `001` (no schema changes)
+4. Future updates use normal migration path
+
+### Migration Path
+
+```
+Pre-Alembic DB → Stamp(001) → Upgrade(002) → Upgrade(003) → ...
+New DB → Migrate(001) → Upgrade(002) → Upgrade(003) → ...
+```
+
+## Troubleshooting
+
+### Migration Fails
+
+```bash
+# Check current state
+uv run nextcloud-mcp-server db current -d /path/to/tokens.db
+
+# View migration history
+uv run nextcloud-mcp-server db history -d /path/to/tokens.db
+
+# Manually inspect database
+sqlite3 /path/to/tokens.db ".schema"
+```
+
+### Reset to Initial State
+
+**WARNING: This destroys all data!**
+
+```bash
+# Downgrade to base (empty database)
+uv run nextcloud-mcp-server db downgrade -d /path/to/tokens.db --revision base
+
+# Upgrade to latest
+uv run nextcloud-mcp-server db upgrade -d /path/to/tokens.db
+```
+
+### Corrupted Migration State
+
+If `alembic_version` table is corrupted:
+
+```bash
+# Manually fix via SQL
+sqlite3 /path/to/tokens.db
+> DELETE FROM alembic_version;
+> INSERT INTO alembic_version (version_num) VALUES ('001');
+> .quit
+
+# Verify and upgrade
+uv run nextcloud-mcp-server db current -d /path/to/tokens.db
+uv run nextcloud-mcp-server db upgrade -d /path/to/tokens.db
+```
+
+## CI/CD Integration
+
+### Pre-Deployment
+
+```bash
+# Run migrations in test environment
+export TOKEN_STORAGE_DB=/app/data/tokens.db
+uv run nextcloud-mcp-server db upgrade
+
+# Verify current version
+uv run nextcloud-mcp-server db current
+```
+
+### Docker Deployment
+
+Migrations run automatically on container startup via `RefreshTokenStorage.initialize()`.
+
+### Rollback Plan
+
+1. Stop application
+2. Backup database: `cp tokens.db tokens.db.backup`
+3. Downgrade: `uv run nextcloud-mcp-server db downgrade --revision XXX`
+4. Deploy previous application version
+5. Restart application
+
+## References
+
+- [Alembic Documentation](https://alembic.sqlalchemy.org/)
+- [SQLite ALTER TABLE Limitations](https://www.sqlite.org/lang_altertable.html)
+- [ADR-004: Progressive Consent](./ADR-004-progressive-consent.md) (migration 001)
diff --git a/nextcloud_mcp_server/api/management.py b/nextcloud_mcp_server/api/management.py
index 4329229..00ba141 100644
--- a/nextcloud_mcp_server/api/management.py
+++ b/nextcloud_mcp_server/api/management.py
@@ -873,6 +873,12 @@ async def unified_search(request: Request) -> JSONResponse:
             result_data["chunk_index"] = result.chunk_index
             result_data["total_chunks"] = result.total_chunks
 
+            # Add chunk offsets for modal navigation
+            if result.chunk_start_offset is not None:
+                result_data["chunk_start_offset"] = result.chunk_start_offset
+            if result.chunk_end_offset is not None:
+                result_data["chunk_end_offset"] = result.chunk_end_offset
+
             formatted_results.append(result_data)
 
         response_data: dict[str, Any] = {
diff --git a/nextcloud_mcp_server/auth/browser_oauth_routes.py b/nextcloud_mcp_server/auth/browser_oauth_routes.py
index a86673e..8f939be 100644
--- a/nextcloud_mcp_server/auth/browser_oauth_routes.py
+++ b/nextcloud_mcp_server/auth/browser_oauth_routes.py
@@ -376,16 +376,35 @@ async def oauth_login_callback(request: Request) -> RedirectResponse | HTMLRespo
         user_id = f"user-{secrets.token_hex(8)}"
         username = "unknown"
 
+    # Calculate refresh token expiration from token response
+    refresh_expires_in = token_data.get("refresh_expires_in")
+    refresh_expires_at = None
+    if refresh_expires_in:
+        import time
+
+        refresh_expires_at = int(time.time()) + refresh_expires_in
+        logger.info(
+            f"Refresh token expires in {refresh_expires_in}s (at timestamp {refresh_expires_at})"
+        )
+
+    # Extract granted scopes
+    granted_scopes = (
+        token_data.get("scope", "").split() if token_data.get("scope") else None
+    )
+
     # Store refresh token (for background jobs ONLY)
     if refresh_token:
         logger.info(f"Storing refresh token for user_id: {user_id}")
         logger.info(f"  State parameter (provisioning_client_id): {state[:16]}...")
+        logger.info(f"  Granted scopes: {granted_scopes}")
+        logger.info(f"  Expires at: {refresh_expires_at}")
         await storage.store_refresh_token(
             user_id=user_id,
             refresh_token=refresh_token,
-            expires_at=None,
+            expires_at=refresh_expires_at,
             flow_type="browser",  # Browser-based login flow
             provisioning_client_id=state,  # Store state for unified session lookup
+            scopes=granted_scopes,
         )
         logger.info(f"✓ Refresh token stored successfully for user_id: {user_id}")
         logger.info(
diff --git a/nextcloud_mcp_server/auth/oauth_routes.py b/nextcloud_mcp_server/auth/oauth_routes.py
index 35ae823..5499aca 100644
--- a/nextcloud_mcp_server/auth/oauth_routes.py
+++ b/nextcloud_mcp_server/auth/oauth_routes.py
@@ -517,12 +517,23 @@ async def oauth_callback_nextcloud(request: Request):
             token_data.get("scope", "").split() if token_data.get("scope") else None
         )
 
+        # Calculate refresh token expiration from token response
+        refresh_expires_in = token_data.get("refresh_expires_in")
+        refresh_expires_at = None
+        if refresh_expires_in:
+            import time
+
+            refresh_expires_at = int(time.time()) + refresh_expires_in
+            logger.info(f"  refresh_expires_in: {refresh_expires_in}s")
+            logger.info(f"  refresh_expires_at: {refresh_expires_at}")
+
         logger.info("Storing refresh token:")
         logger.info(f"  user_id: {user_id}")
         logger.info("  flow_type: flow2")
         logger.info("  token_audience: nextcloud")
         logger.info(f"  provisioning_client_id: {state[:16]}...")
         logger.info(f"  scopes: {granted_scopes}")
+        logger.info(f"  expires_at: {refresh_expires_at}")
 
         await storage.store_refresh_token(
             user_id=user_id,
@@ -531,7 +542,7 @@ async def oauth_callback_nextcloud(request: Request):
             token_audience="nextcloud",
             provisioning_client_id=state,  # Store which client initiated provisioning
             scopes=granted_scopes,
-            expires_at=None,  # Refresh tokens typically don't expire
+            expires_at=refresh_expires_at,
         )
         logger.info(f"✓ Stored Flow 2 master refresh token for user {user_id}")
         logger.info("=" * 60)
diff --git a/nextcloud_mcp_server/auth/storage.py b/nextcloud_mcp_server/auth/storage.py
index 9f4c1ff..b8bc898 100644
--- a/nextcloud_mcp_server/auth/storage.py
+++ b/nextcloud_mcp_server/auth/storage.py
@@ -117,7 +117,14 @@ class RefreshTokenStorage:
         return cls(db_path=db_path, encryption_key=encryption_key)
 
     async def initialize(self) -> None:
-        """Initialize database schema"""
+        """
+        Initialize database schema using Alembic migrations.
+
+        This method handles three scenarios:
+        1. New database: Run migrations from scratch
+        2. Pre-Alembic database: Stamp with initial revision (no changes)
+        3. Alembic-managed database: Upgrade to latest version
+        """
         if self._initialized:
             return
 
@@ -125,137 +132,59 @@ class RefreshTokenStorage:
         db_dir = Path(self.db_path).parent
         db_dir.mkdir(parents=True, exist_ok=True)
 
-        # Set restrictive permissions on database file
+        # Set restrictive permissions on database file if it exists
         if Path(self.db_path).exists():
             os.chmod(self.db_path, 0o600)
 
+        # Check database state and run appropriate migration strategy
         async with aiosqlite.connect(self.db_path) as db:
-            await db.execute(
-                """
-                CREATE TABLE IF NOT EXISTS refresh_tokens (
-                    user_id TEXT PRIMARY KEY,
-                    encrypted_token BLOB NOT NULL,
-                    expires_at INTEGER,
-                    created_at INTEGER NOT NULL,
-                    updated_at INTEGER NOT NULL,
-                    -- ADR-004 Progressive Consent fields
-                    flow_type TEXT DEFAULT 'hybrid',  -- 'hybrid', 'flow1', 'flow2'
-                    token_audience TEXT DEFAULT 'nextcloud',  -- 'mcp-server' or 'nextcloud'
-                    provisioned_at INTEGER,  -- When Flow 2 was completed
-                    provisioning_client_id TEXT,  -- Which MCP client initiated Flow 1
-                    scopes TEXT,  -- JSON array of granted scopes
-                    -- Browser session profile cache
-                    user_profile TEXT,  -- JSON cache of IdP user profile (for browser UI only)
-                    profile_cached_at INTEGER  -- When profile was last cached
+            # Check if database is managed by Alembic
+            cursor = await db.execute(
+                "SELECT name FROM sqlite_master WHERE type='table' AND name='alembic_version'"
+            )
+            has_alembic = await cursor.fetchone() is not None
+
+            if not has_alembic:
+                # Check if this is a pre-Alembic database with existing schema
+                cursor = await db.execute(
+                    "SELECT name FROM sqlite_master WHERE type='table' AND name='refresh_tokens'"
                 )
-                """
-            )
+                has_schema = await cursor.fetchone() is not None
 
-            await db.execute(
-                """
-                CREATE TABLE IF NOT EXISTS audit_logs (
-                    id INTEGER PRIMARY KEY AUTOINCREMENT,
-                    timestamp INTEGER NOT NULL,
-                    event TEXT NOT NULL,
-                    user_id TEXT NOT NULL,
-                    resource_type TEXT,
-                    resource_id TEXT,
-                    auth_method TEXT,
-                    hostname TEXT
+                if has_schema:
+                    logger.info(
+                        f"Detected pre-Alembic database at {self.db_path}, "
+                        "stamping with initial revision"
+                    )
+                else:
+                    logger.info(
+                        f"Initializing new database at {self.db_path} with migrations"
+                    )
+
+        # Run migrations in a worker thread using anyio.to_thread
+        # This allows Alembic to run its own async operations in a separate context
+        from anyio import to_thread
+
+        from nextcloud_mcp_server.migrations import stamp_database, upgrade_database
+
+        if not has_alembic:
+            if has_schema:
+                # Stamp existing database without running migrations
+                await to_thread.run_sync(stamp_database, self.db_path, "001")
+                logger.info(
+                    "Pre-Alembic database stamped successfully. "
+                    "Future schema changes will use migrations."
                 )
-                """
-            )
+            else:
+                # New database - run migrations
+                await to_thread.run_sync(upgrade_database, self.db_path, "head")
+                logger.info("Database initialized with migrations")
+        else:
+            # Alembic-managed database - upgrade to latest
+            await to_thread.run_sync(upgrade_database, self.db_path, "head")
+            logger.info("Database upgraded to latest version")
 
-            # Create index on audit logs for efficient queries
-            await db.execute(
-                "CREATE INDEX IF NOT EXISTS idx_audit_user_timestamp "
-                "ON audit_logs(user_id, timestamp)"
-            )
-
-            # OAuth client credentials storage
-            await db.execute(
-                """
-                CREATE TABLE IF NOT EXISTS oauth_clients (
-                    id INTEGER PRIMARY KEY,
-                    client_id TEXT UNIQUE NOT NULL,
-                    encrypted_client_secret BLOB NOT NULL,
-                    client_id_issued_at INTEGER NOT NULL,
-                    client_secret_expires_at INTEGER NOT NULL,
-                    redirect_uris TEXT NOT NULL,
-                    encrypted_registration_access_token BLOB,
-                    registration_client_uri TEXT,
-                    created_at INTEGER NOT NULL,
-                    updated_at INTEGER NOT NULL
-                )
-                """
-            )
-
-            # OAuth flow sessions (ADR-004 Progressive Consent)
-            await db.execute(
-                """
-                CREATE TABLE IF NOT EXISTS oauth_sessions (
-                    session_id TEXT PRIMARY KEY,
-                    client_id TEXT,
-                    client_redirect_uri TEXT NOT NULL,
-                    state TEXT,
-                    code_challenge TEXT,
-                    code_challenge_method TEXT,
-                    mcp_authorization_code TEXT UNIQUE,
-                    idp_access_token TEXT,
-                    idp_refresh_token TEXT,
-                    user_id TEXT,
-                    created_at INTEGER NOT NULL,
-                    expires_at INTEGER NOT NULL,
-                    -- ADR-004 Progressive Consent fields
-                    flow_type TEXT DEFAULT 'hybrid',  -- 'hybrid', 'flow1', 'flow2'
-                    requested_scopes TEXT,  -- JSON array of requested scopes
-                    granted_scopes TEXT,  -- JSON array of granted scopes
-                    is_provisioning BOOLEAN DEFAULT FALSE  -- True if this is a Flow 2 provisioning session
-                )
-                """
-            )
-
-            # Create index for MCP authorization code lookups
-            await db.execute(
-                "CREATE INDEX IF NOT EXISTS idx_oauth_sessions_mcp_code "
-                "ON oauth_sessions(mcp_authorization_code)"
-            )
-
-            # Schema version tracking
-            await db.execute(
-                """
-                CREATE TABLE IF NOT EXISTS schema_version (
-                    version INTEGER PRIMARY KEY,
-                    applied_at REAL NOT NULL
-                )
-                """
-            )
-
-            # Registered webhooks tracking (both BasicAuth and OAuth modes)
-            await db.execute(
-                """
-                CREATE TABLE IF NOT EXISTS registered_webhooks (
-                    id INTEGER PRIMARY KEY AUTOINCREMENT,
-                    webhook_id INTEGER NOT NULL UNIQUE,
-                    preset_id TEXT NOT NULL,
-                    created_at REAL NOT NULL
-                )
-                """
-            )
-
-            # Create indexes for efficient webhook queries
-            await db.execute(
-                "CREATE INDEX IF NOT EXISTS idx_webhooks_preset "
-                "ON registered_webhooks(preset_id)"
-            )
-            await db.execute(
-                "CREATE INDEX IF NOT EXISTS idx_webhooks_created "
-                "ON registered_webhooks(created_at)"
-            )
-
-            await db.commit()
-
-        # Set restrictive permissions after creation
+        # Set restrictive permissions after initialization
         os.chmod(self.db_path, 0o600)
 
         self._initialized = True
diff --git a/nextcloud_mcp_server/cli.py b/nextcloud_mcp_server/cli.py
index a7b9d06..94ce3db 100644
--- a/nextcloud_mcp_server/cli.py
+++ b/nextcloud_mcp_server/cli.py
@@ -253,5 +253,195 @@ def run(
     )
 
 
+@click.group()
+def db():
+    """Database migration management commands."""
+    pass
+
+
+@db.command()
+@click.option(
+    "--database-path",
+    "-d",
+    envvar="TOKEN_STORAGE_DB",
+    default="/app/data/tokens.db",
+    show_default=True,
+    help="Path to token storage database (can also use TOKEN_STORAGE_DB env var)",
+)
+@click.option(
+    "--revision",
+    "-r",
+    default="head",
+    show_default=True,
+    help="Target revision (default: head for latest)",
+)
+def upgrade(database_path: str, revision: str):
+    """Upgrade database to a specific revision.
+
+    \b
+    Examples:
+      # Upgrade to latest version
+      $ nextcloud-mcp-server db upgrade
+
+      # Upgrade to specific revision
+      $ nextcloud-mcp-server db upgrade --revision 001
+
+      # Use custom database path
+      $ nextcloud-mcp-server db upgrade -d /path/to/tokens.db
+    """
+    from nextcloud_mcp_server.migrations import upgrade_database
+
+    try:
+        click.echo(f"Upgrading database to revision: {revision}")
+        upgrade_database(database_path, revision)
+        click.echo(click.style("✓ Database upgraded successfully", fg="green"))
+    except Exception as e:
+        click.echo(click.style(f"✗ Upgrade failed: {e}", fg="red"), err=True)
+        raise click.ClickException(str(e))
+
+
+@db.command()
+@click.option(
+    "--database-path",
+    "-d",
+    envvar="TOKEN_STORAGE_DB",
+    default="/app/data/tokens.db",
+    show_default=True,
+    help="Path to token storage database",
+)
+@click.option(
+    "--revision",
+    "-r",
+    default="-1",
+    show_default=True,
+    help="Target revision (default: -1 for previous version)",
+)
+@click.confirmation_option(
+    prompt="Are you sure you want to downgrade the database? This may result in data loss."
+)
+def downgrade(database_path: str, revision: str):
+    """Downgrade database to a specific revision.
+
+    WARNING: This may result in data loss! Use with caution.
+
+    \b
+    Examples:
+      # Downgrade by one version
+      $ nextcloud-mcp-server db downgrade
+
+      # Downgrade to specific revision
+      $ nextcloud-mcp-server db downgrade --revision 001
+
+      # Downgrade to base (empty database)
+      $ nextcloud-mcp-server db downgrade --revision base
+    """
+    from nextcloud_mcp_server.migrations import downgrade_database
+
+    try:
+        click.echo(f"Downgrading database to revision: {revision}")
+        downgrade_database(database_path, revision)
+        click.echo(click.style("✓ Database downgraded successfully", fg="green"))
+    except Exception as e:
+        click.echo(click.style(f"✗ Downgrade failed: {e}", fg="red"), err=True)
+        raise click.ClickException(str(e))
+
+
+@db.command()
+@click.option(
+    "--database-path",
+    "-d",
+    envvar="TOKEN_STORAGE_DB",
+    default="/app/data/tokens.db",
+    show_default=True,
+    help="Path to token storage database",
+)
+def current(database_path: str):
+    """Show current database revision.
+
+    \b
+    Example:
+      $ nextcloud-mcp-server db current
+    """
+    from nextcloud_mcp_server.migrations import get_current_revision
+
+    try:
+        revision = get_current_revision(database_path)
+        if revision:
+            click.echo(f"Current revision: {click.style(revision, fg='cyan')}")
+        else:
+            click.echo(
+                click.style(
+                    "Database is not versioned (no alembic_version table)", fg="yellow"
+                )
+            )
+    except Exception as e:
+        click.echo(
+            click.style(f"✗ Failed to get current revision: {e}", fg="red"), err=True
+        )
+        raise click.ClickException(str(e))
+
+
+@db.command()
+@click.option(
+    "--database-path",
+    "-d",
+    envvar="TOKEN_STORAGE_DB",
+    default="/app/data/tokens.db",
+    show_default=True,
+    help="Path to token storage database",
+)
+def history(database_path: str):
+    """Show migration history.
+
+    \b
+    Example:
+      $ nextcloud-mcp-server db history
+    """
+    from nextcloud_mcp_server.migrations import show_migration_history
+
+    try:
+        click.echo("Migration history:")
+        show_migration_history(database_path)
+    except Exception as e:
+        click.echo(click.style(f"✗ Failed to show history: {e}", fg="red"), err=True)
+        raise click.ClickException(str(e))
+
+
+@db.command()
+@click.argument("message")
+def migrate(message: str):
+    """Create a new migration script (developers only).
+
+    The MESSAGE argument describes the changes in this migration.
+
+    \b
+    Examples:
+      $ nextcloud-mcp-server db migrate "add user preferences table"
+      $ nextcloud-mcp-server db migrate "add index on refresh_tokens.user_id"
+
+    Note: You must manually edit the generated migration file to add SQL statements.
+    """
+    from nextcloud_mcp_server.migrations import create_migration
+
+    try:
+        click.echo(f"Creating new migration: {message}")
+        create_migration(message)
+        click.echo(click.style("✓ Migration created successfully", fg="green"))
+        click.echo(
+            "Edit the migration file in alembic/versions/ to add upgrade/downgrade SQL."
+        )
+    except Exception as e:
+        click.echo(
+            click.style(f"✗ Failed to create migration: {e}", fg="red"), err=True
+        )
+        raise click.ClickException(str(e))
+
+
+# Create CLI group with subcommands
+cli = click.Group()
+cli.add_command(run)
+cli.add_command(db)
+
+
 if __name__ == "__main__":
-    run()
+    cli()
diff --git a/nextcloud_mcp_server/migrations.py b/nextcloud_mcp_server/migrations.py
new file mode 100644
index 0000000..bbff578
--- /dev/null
+++ b/nextcloud_mcp_server/migrations.py
@@ -0,0 +1,186 @@
+"""Database migration utilities for nextcloud-mcp-server.
+
+This module provides helper functions for managing Alembic database migrations
+programmatically. It enables automatic migration on application startup and
+provides CLI integration.
+"""
+
+import logging
+from pathlib import Path
+
+from alembic.config import Config
+
+from alembic import command
+
+logger = logging.getLogger(__name__)
+
+
+def get_alembic_config(database_path: str | Path | None = None) -> Config:
+    """
+    Get Alembic configuration for programmatic use.
+
+    Args:
+        database_path: Path to SQLite database file. If None, uses default
+                      from alembic.ini (/app/data/tokens.db)
+
+    Returns:
+        Alembic Config object configured for the specified database
+    """
+    # Get path to alembic.ini (in project root)
+    project_root = Path(__file__).parent.parent
+    alembic_ini_path = project_root / "alembic.ini"
+
+    if not alembic_ini_path.exists():
+        raise FileNotFoundError(
+            f"alembic.ini not found at {alembic_ini_path}. "
+            "Ensure Alembic is properly initialized."
+        )
+
+    # Create Alembic config
+    config = Config(str(alembic_ini_path))
+
+    # Override database URL if provided
+    if database_path:
+        db_path = Path(database_path).resolve()
+        # Use sqlite+aiosqlite:// for async support
+        url = f"sqlite+aiosqlite:///{db_path}"
+        config.set_main_option("sqlalchemy.url", url)
+        logger.debug(f"Alembic configured with database: {db_path}")
+
+    return config
+
+
+def upgrade_database(
+    database_path: str | Path | None = None, revision: str = "head"
+) -> None:
+    """
+    Upgrade database to a specific revision.
+
+    Args:
+        database_path: Path to SQLite database file
+        revision: Target revision (default: "head" for latest)
+    """
+    config = get_alembic_config(database_path)
+    logger.info(f"Upgrading database to revision: {revision}")
+    command.upgrade(config, revision)
+    logger.info("Database upgrade completed successfully")
+
+
+def downgrade_database(
+    database_path: str | Path | None = None, revision: str = "-1"
+) -> None:
+    """
+    Downgrade database to a specific revision.
+
+    Args:
+        database_path: Path to SQLite database file
+        revision: Target revision (default: "-1" for previous version)
+    """
+    config = get_alembic_config(database_path)
+    logger.warning(f"Downgrading database to revision: {revision}")
+    command.downgrade(config, revision)
+    logger.info("Database downgrade completed successfully")
+
+
+def get_current_revision(database_path: str | Path | None = None) -> str | None:
+    """
+    Get the current database revision by directly querying the alembic_version table.
+
+    Args:
+        database_path: Path to SQLite database file
+
+    Returns:
+        Current revision ID or None if not versioned
+    """
+    import sqlite3
+
+    if database_path is None:
+        database_path = "/app/data/tokens.db"
+
+    db_path = Path(database_path).resolve()
+
+    if not db_path.exists():
+        logger.debug(f"Database does not exist: {db_path}")
+        return None
+
+    try:
+        # Query alembic_version table directly
+        conn = sqlite3.connect(str(db_path))
+        cursor = conn.cursor()
+
+        # Check if alembic_version table exists
+        cursor.execute(
+            "SELECT name FROM sqlite_master WHERE type='table' AND name='alembic_version'"
+        )
+        has_table = cursor.fetchone() is not None
+
+        if not has_table:
+            conn.close()
+            return None
+
+        # Get current version
+        cursor.execute("SELECT version_num FROM alembic_version")
+        row = cursor.fetchone()
+        conn.close()
+
+        return row[0] if row else None
+
+    except Exception as e:
+        logger.error(f"Failed to get current revision: {e}")
+        return None
+
+
+def stamp_database(
+    database_path: str | Path | None = None, revision: str = "head"
+) -> None:
+    """
+    Stamp database with a specific revision without running migrations.
+
+    This is useful for marking existing databases that were created before
+    Alembic was introduced. It tells Alembic "this database is at revision X"
+    without actually running the migration.
+
+    Args:
+        database_path: Path to SQLite database file
+        revision: Revision to stamp (default: "head" for latest)
+    """
+    config = get_alembic_config(database_path)
+    logger.info(f"Stamping database with revision: {revision}")
+    command.stamp(config, revision)
+    logger.info("Database stamped successfully")
+
+
+def show_migration_history(database_path: str | Path | None = None) -> None:
+    """
+    Display migration history.
+
+    Args:
+        database_path: Path to SQLite database file
+    """
+    config = get_alembic_config(database_path)
+    command.history(config, verbose=True)
+
+
+def create_migration(message: str, autogenerate: bool = False) -> None:
+    """
+    Create a new migration script.
+
+    Args:
+        message: Description of the migration
+        autogenerate: Whether to attempt auto-generation (requires SQLAlchemy models)
+
+    Note:
+        Since we don't use SQLAlchemy models, autogenerate will be disabled
+        and migrations must be written manually.
+    """
+    config = get_alembic_config()
+    logger.info(f"Creating new migration: {message}")
+
+    if autogenerate:
+        logger.warning(
+            "Auto-generation is not supported (no SQLAlchemy models). "
+            "Migration will be created with empty upgrade/downgrade functions."
+        )
+
+    command.revision(config, message=message, autogenerate=False)
+    logger.info("Migration created successfully. Edit the file to add SQL statements.")
diff --git a/pyproject.toml b/pyproject.toml
index 8823ce8..0e403f4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,6 +20,7 @@ dependencies = [
     "caldav",
     "pyjwt[crypto]>=2.8.0",
     "aiosqlite>=0.20.0", # Async SQLite for refresh token storage
+    "alembic>=1.14.0", # Database migrations
     "authlib>=1.6.5",
     "qdrant-client>=1.7.0",
     "fastembed>=0.7.3", # BM25 sparse vector embeddings for hybrid search
@@ -128,7 +129,7 @@ dev = [
 ]
 
 [project.scripts]
-nextcloud-mcp-server = "nextcloud_mcp_server.cli:run"
+nextcloud-mcp-server = "nextcloud_mcp_server.cli:cli"
 smithery-main = "nextcloud_mcp_server.smithery_main:main"
 
 [[tool.uv.index]]
diff --git a/third_party/astrolabe/lib/Search/SemanticSearchProvider.php b/third_party/astrolabe/lib/Search/SemanticSearchProvider.php
index e4f5d45..8da0cb4 100644
--- a/third_party/astrolabe/lib/Search/SemanticSearchProvider.php
+++ b/third_party/astrolabe/lib/Search/SemanticSearchProvider.php
@@ -223,39 +223,51 @@ class SemanticSearchProvider implements IProvider {
 	}
 
 	/**
-	 * Build URL to navigate to the original document.
+	 * Build URL to navigate to Astrolabe with chunk viewer.
 	 *
-	 * URL formats match App.vue's getDocumentUrl() implementation for consistency.
+	 * Links to Astrolabe app with query parameters that trigger the chunk modal,
+	 * allowing users to preview the chunk before navigating to the full document.
 	 */
 	private function buildResourceUrl(array $result): string {
+		// Build base URL to Astrolabe app
+		$baseUrl = $this->urlGenerator->linkToRoute(Application::APP_ID . '.page.index');
+
+		// Extract chunk parameters
 		$docType = $result['doc_type'] ?? 'unknown';
 		$id = $result['id'] ?? null;
-		$path = $result['path'] ?? null;
+		$chunkStart = $result['chunk_start_offset'] ?? null;
+		$chunkEnd = $result['chunk_end_offset'] ?? null;
 
-		return match ($docType) {
-			'note' => $id
-				? $this->urlGenerator->linkToRoute('notes.page.index') . '/#/note/' . $id
-				: $this->urlGenerator->linkToRoute('notes.page.index'),
+		// If we have chunk information, build URL with parameters
+		if ($id !== null && $chunkStart !== null && $chunkEnd !== null) {
+			$params = [
+				'doc_type' => $docType,
+				'doc_id' => $id,
+				'chunk_start' => $chunkStart,
+				'chunk_end' => $chunkEnd,
+			];
 
-			'file' => $id
-				? $this->urlGenerator->linkToRouteAbsolute('files.view.index') . 'files/' . $id . '?dir=/&editing=false&openfile=true'
-				: $this->urlGenerator->linkToRouteAbsolute('files.view.index'),
+			// Add optional metadata
+			if (isset($result['title'])) {
+				$params['title'] = $result['title'];
+			}
+			if (isset($result['path'])) {
+				$params['path'] = $result['path'];
+			}
+			if (isset($result['page_number'])) {
+				$params['page_number'] = $result['page_number'];
+			}
+			if (isset($result['board_id'])) {
+				$params['board_id'] = $result['board_id'];
+			}
 
-			'deck_card' => isset($result['board_id']) && $id
-				? $this->urlGenerator->linkToRoute('deck.page.index')
-				  . "board/{$result['board_id']}/card/{$id}"
-				: $this->urlGenerator->linkToRoute('deck.page.index'),
+			// Encode parameters for URL
+			$queryString = http_build_query($params);
+			return $baseUrl . '?' . $queryString;
+		}
 
-			'calendar', 'calendar_event' => $this->urlGenerator->linkToRoute('calendar.view.index'),
-
-			'news_item' => $id
-				? $this->urlGenerator->linkToRoute('news.page.index') . 'item/' . $id
-				: $this->urlGenerator->linkToRoute('news.page.index'),
-
-			'contact' => $this->urlGenerator->linkToRoute('contacts.page.index'),
-
-			default => $this->urlGenerator->linkToRoute(Application::APP_ID . '.page.index'),
-		};
+		// Fallback to base URL if no chunk information
+		return $baseUrl;
 	}
 
 	/**
diff --git a/third_party/astrolabe/src/App.vue b/third_party/astrolabe/src/App.vue
index 3ecf271..0958225 100644
--- a/third_party/astrolabe/src/App.vue
+++ b/third_party/astrolabe/src/App.vue
@@ -501,6 +501,10 @@ export default {
 			return this.results.filter(r => (r.score || 0) >= threshold)
 		},
 	},
+	mounted() {
+		// Check for URL parameters to open chunk viewer
+		this.handleUrlParameters()
+	},
 	beforeDestroy() {
 		// Clean up Plotly event handlers to prevent memory leaks
 		const plotDiv = document.getElementById('viz-plot')
@@ -509,6 +513,51 @@ export default {
 		}
 	},
 	methods: {
+		handleUrlParameters() {
+			// Parse URL parameters
+			const urlParams = new URLSearchParams(window.location.search)
+			const docType = urlParams.get('doc_type')
+			const docId = urlParams.get('doc_id')
+			const chunkStart = urlParams.get('chunk_start')
+			const chunkEnd = urlParams.get('chunk_end')
+
+			// If we have chunk parameters, open the viewer
+			if (docType && docId && chunkStart !== null && chunkEnd !== null) {
+				// Construct a minimal result object
+				const result = {
+					doc_type: docType,
+					id: parseInt(docId, 10),
+					chunk_start_offset: parseInt(chunkStart, 10),
+					chunk_end_offset: parseInt(chunkEnd, 10),
+					title: urlParams.get('title') || this.t('astrolabe', 'Chunk Viewer'),
+					metadata: {},
+				}
+
+				// Add optional metadata
+				const path = urlParams.get('path')
+				if (path) {
+					result.metadata.path = path
+				}
+				const pageNumber = urlParams.get('page_number')
+				if (pageNumber) {
+					result.page_number = parseInt(pageNumber, 10)
+				}
+				const boardId = urlParams.get('board_id')
+				if (boardId) {
+					result.metadata.board_id = boardId
+				}
+
+				// Open the chunk viewer
+				this.$nextTick(() => {
+					this.viewChunk(result)
+				})
+
+				// Clear URL parameters to avoid reopening on navigation
+				const newUrl = window.location.pathname
+				window.history.replaceState({}, '', newUrl)
+			}
+		},
+
 		toggleDocType(docTypeId, checked) {
 			if (checked && !this.selectedDocTypes.includes(docTypeId)) {
 				this.selectedDocTypes.push(docTypeId)
@@ -616,6 +665,12 @@ export default {
 			case 'note':
 				return generateUrl(`/apps/notes/#/note/${id}`)
 			case 'file':
+				// For PDFs with page numbers, use the PDF viewer with page anchor
+				if (result.page_number && metadata.path) {
+					const pageParam = `#page=${result.page_number}`
+					return generateUrl(`/apps/files_pdfviewer/?file=${encodeURIComponent(metadata.path)}${pageParam}`)
+				}
+				// For other files, use the standard file viewer
 				if (id) {
 					return generateUrl(`/apps/files/files/${id}?dir=/&editing=false&openfile=true`)
 				}
diff --git a/uv.lock b/uv.lock
index 5b4eca1..c5c2ef5 100644
--- a/uv.lock
+++ b/uv.lock
@@ -144,6 +144,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/f5/10/6c25ed6de94c49f88a91fa5018cb4c0f3625f31d5be9f771ebe5cc7cd506/aiosqlite-0.21.0-py3-none-any.whl", hash = "sha256:2549cf4057f95f53dcba16f2b64e8e2791d7e1adedb13197dd8ed77bb226d7d0", size = 15792, upload-time = "2025-02-03T07:30:13.6Z" },
 ]
 
+[[package]]
+name = "alembic"
+version = "1.17.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "mako" },
+    { name = "sqlalchemy" },
+    { name = "typing-extensions" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/02/a6/74c8cadc2882977d80ad756a13857857dbcf9bd405bc80b662eb10651282/alembic-1.17.2.tar.gz", hash = "sha256:bbe9751705c5e0f14877f02d46c53d10885e377e3d90eda810a016f9baa19e8e", size = 1988064, upload-time = "2025-11-14T20:35:04.057Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ba/88/6237e97e3385b57b5f1528647addea5cc03d4d65d5979ab24327d41fb00d/alembic-1.17.2-py3-none-any.whl", hash = "sha256:f483dd1fe93f6c5d49217055e4d15b905b425b6af906746abb35b69c1996c4e6", size = 248554, upload-time = "2025-11-14T20:35:05.699Z" },
+]
+
 [[package]]
 name = "annotated-types"
 version = "0.7.0"
@@ -1558,6 +1572,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/6c/77/d7f491cbc05303ac6801651aabeb262d43f319288c1ea96c66b1d2692ff3/lxml-6.0.2-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:27220da5be049e936c3aca06f174e8827ca6445a4353a1995584311487fc4e3e", size = 3518768, upload-time = "2025-09-22T04:04:57.097Z" },
 ]
 
+[[package]]
+name = "mako"
+version = "1.3.10"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "markupsafe" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/9e/38/bd5b78a920a64d708fe6bc8e0a2c075e1389d53bef8413725c63ba041535/mako-1.3.10.tar.gz", hash = "sha256:99579a6f39583fa7e5630a28c3c1f440e4e97a414b80372649c0ce338da2ea28", size = 392474, upload-time = "2025-04-10T12:44:31.16Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/87/fb/99f81ac72ae23375f22b7afdb7642aba97c00a713c217124420147681a2f/mako-1.3.10-py3-none-any.whl", hash = "sha256:baef24a52fc4fc514a0887ac600f9f1cff3d82c61d4d700a1fa84d597b88db59", size = 78509, upload-time = "2025-04-10T12:50:53.297Z" },
+]
+
 [[package]]
 name = "markdown-it-py"
 version = "4.0.0"
@@ -1966,6 +1992,7 @@ version = "0.52.1"
 source = { editable = "." }
 dependencies = [
     { name = "aiosqlite" },
+    { name = "alembic" },
     { name = "anthropic" },
     { name = "authlib" },
     { name = "boto3" },
@@ -2016,6 +2043,7 @@ dev = [
 [package.metadata]
 requires-dist = [
     { name = "aiosqlite", specifier = ">=0.20.0" },
+    { name = "alembic", specifier = ">=1.14.0" },
     { name = "anthropic", specifier = ">=0.42.0" },
     { name = "authlib", specifier = ">=1.6.5" },
     { name = "boto3", specifier = ">=1.35.0" },
@@ -3617,6 +3645,48 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/14/a0/bb38d3b76b8cae341dad93a2dd83ab7462e6dbcdd84d43f54ee60a8dc167/soupsieve-2.8-py3-none-any.whl", hash = "sha256:0cc76456a30e20f5d7f2e14a98a4ae2ee4e5abdc7c5ea0aafe795f344bc7984c", size = 36679, upload-time = "2025-08-27T15:39:50.179Z" },
 ]
 
+[[package]]
+name = "sqlalchemy"
+version = "2.0.45"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "greenlet", marker = "platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'" },
+    { name = "typing-extensions" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/be/f9/5e4491e5ccf42f5d9cfc663741d261b3e6e1683ae7812114e7636409fcc6/sqlalchemy-2.0.45.tar.gz", hash = "sha256:1632a4bda8d2d25703fdad6363058d882541bdaaee0e5e3ddfa0cd3229efce88", size = 9869912, upload-time = "2025-12-09T21:05:16.737Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/a2/1c/769552a9d840065137272ebe86ffbb0bc92b0f1e0a68ee5266a225f8cd7b/sqlalchemy-2.0.45-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:2e90a344c644a4fa871eb01809c32096487928bd2038bf10f3e4515cb688cc56", size = 2153860, upload-time = "2025-12-10T20:03:23.843Z" },
+    { url = "https://files.pythonhosted.org/packages/f3/f8/9be54ff620e5b796ca7b44670ef58bc678095d51b0e89d6e3102ea468216/sqlalchemy-2.0.45-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:b8c8b41b97fba5f62349aa285654230296829672fc9939cd7f35aab246d1c08b", size = 3309379, upload-time = "2025-12-09T22:06:07.461Z" },
+    { url = "https://files.pythonhosted.org/packages/f6/2b/60ce3ee7a5ae172bfcd419ce23259bb874d2cddd44f67c5df3760a1e22f9/sqlalchemy-2.0.45-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:12c694ed6468333a090d2f60950e4250b928f457e4962389553d6ba5fe9951ac", size = 3309948, upload-time = "2025-12-09T22:09:57.643Z" },
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