Remove generated files from the repository, change build system to match

Remove generated files from the repository, change build system to match

A new shell script buildaux/regenerate-build-system.sh will regenerate
the build system from scratch, which is needed to run a repository
version. (The contents of distribution tarballs are unchanged.) Many
build system changes are needed to make everything work correctly,
including the integration of the pit and src makefiles (the pit
makefile needs to know where the pit actually /is/); make distcheck
now passes.