Add check to make sure that all subdirs and source files are used

This is meant to prevent that a subdirectory is added to a project, but not declared in the top level CMakeLists.txt.

The idea is that cases like that described in Analysis!839 (merged) can be detected as warnings in the ci-test builds.

I also added a check that subdirectories that contain source files effectively use all of them (*.cpp and *.cxx).

Closes #161 (closed).

Requires: Rec!2626 (merged) and Analysis!839 (merged) (to avoid warnings)