Honor configure options better

[evanlinde]

I encountered a problem building from source and using a non-standard path. (Specifically, this was building on an HPC system without root/sudo.) The build would fail because the makefile was ignoring $LDFLAGS from the environment and failing to find nlopt and adolc.

Additionally, the makefile was setting the install prefix staticly rather than accepting the value from ./configure --prefix=something.

The proposed changes use the prefix value provided by ./configure (and use it more like standard unix/linux conventions) and also include the $LDFLAGS value from the environment.