Opening / clone a configuration with different main XML

Apparently "Configuration.xml" is not always the default file but can be configured within the framework.
This makes it impossible for some projects to be opened in the flow.
Git projects also handle projects a little differently which is now broken by the same "Configuration.xml" requirement.

2 issues have already been made to work on each issue, this epic is meant to do a little more research into the matter before we assume fixes for the issues.