autotools: update applications/ and libraries/ so that all the subcomponents
can be bootstrapped after being git cleaned.

The issue is that without an auxdir autoconf looks for the install-sh script
in . ../ and ../../ which usually succeeds in ../, sadly that directory will
never contain ltmain.sh for instance, so we need to make sure that all links
to install-sh etc. are local to the sub-component.