Dear all,
These .all files are groups of header files, provided for convenience of the user (was an old request of a reviewer who complained that their was too many files to include!). Bio++ classes are sorted in directories, such as Bpp/Phyl/Model/Protein for instance, which contains all classes of phylogenetic models for protein sequences. It was kind of a trick to emulate "subpackages", as g++ did not allow to include a directory: #include <Bpp/Phyl/Model.all> would include all phylogenetic models, while #include <Bpp/Phyl/Model/Protein.all> would only include all protein models. As more libs were introduced, however, these .all files could not be pre-generated and had to be generated while installing, which led to several post-install and post-uninstall scripts. We had agreed however to remove them some time ago, and they will not be present in the next version of the libraries. In theory they can be removed from the current version I think, only some unit tests might not compile anymore...
I apologize that we're so delayed with the next release. For sure it will be much easier to maintain, and I'm including all your suggestions for easier packaging. As for gcc6, it should normally work: at least I could compile the latest code in a virtual machine and did not face any issue.
Best,
J.