Modified install script to clean in-between each use. Also enabled the PFB correlator plugin creation in Makefile.am

Modified pfb correlator thread to match PFB thread. Also added conditional path setting to install script and CUDA path setting

working on adding pfb thread into hashpipe. Have a include cuda error trying to have automake include it

Updated codes to work with new libtool and automake versions; created install script that compiles and installs everything needed to use FLAG