One should not copy repository files while magnolia is running, at least not via the file system, since magnolia might be writing to the repository while you copy it; which would lead to an inconsistent copy of the repository.
To make a backup at runtime you should export the repository contents. Note that currently only the most recent version of your data gets imported.
You can import and export data using the context-menu in the
navigation tree or you can use the import/export servlets which are used by the tree as well:
/.magnolia/mgnl-export
and
/.magnolia/mgnl-import
