Remove some dependencies on bootstrapping.conf from libraries/Makefile

Remove some dependencies on bootstrapping.conf from libraries/Makefile
They were causing some unnecessary work:
Running make in a built tree reregisters the GHC package in
bootstrapping.conf, and the build system thought that this updated
timestamp meant that the configure stamps were out of date. This is
particularly bad for the libraries with configure scripts, as those
take a while to run.

The bootstrapping.conf is built in an earlier phase ("make boot") so
one shouldn't rely on the dependencies anyway.