These paths can be detected via pkg-config, which is already used in
the build. There is no point in installing them under PREFIX like the
other files.

Tested on Debian 8.

Additional changes:

* Use "shell" function instead of backticks to call pkg-config - this
  way, the already expanded compiler flags are shown in the build
  output.

* Dont delete empty dirs in "make uninstall" - we might not have
  created them after all.