Continue restructuring project management related files.

 * project.vala | project_file    | package_managment | buildsystem/base
    ------------|-------------------------------------|-----------
                |                 | package_exists   <|------
                |                 | package_flags    <|------
         -------|-----------------|>VersionRelation   |
         -------|>VLP_VERSION_MIN |                   |
         -------|>LoadingError    |                   |