File repository now filters by status=active in all query methods (FindByID, FindByUserID, FindByParentID, FindByNameAndParent).
Delete now performs soft-delete by setting status to 'user_deleted' instead of physical row deletion.
Add ListIncludeDeleted to UserRepository for admin views of all users.
Add tests: StatusFilter, SoftDelete, DeleteIdempotent, StatusFilterCount.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
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