There are many differences in the projectfile(s ?) between the branch and trunk.
It seems some of the merges did not really succeed.
Neither the windows nor the linux core-project-file should be compilable (linux is definitely not [LexModula.cxx is missing from cbp-file]), and the prefix-extension-stuff is quite different between both versions.
I did not check other parts for inconsistencies, but I think this should be fixed first.