Fix --with-compiler / --with-hc inconsistency in ./configure flags

setup configure takes a --with-compiler option, but used to change 
that into a --with-hc option when calling ./configure.
Now that we've added autoconfUserHooks and deprecated defaultUserHooks we
can fix this without breaking any existing scripts. The autoconfUserHooks
now passes --with-compiler to ./configure and defaultUserHooks is unchanged.
Fixes ticket #114.