Added a configure check for clang and llvm-config. If llvm-config exists
then we check for the libraries in the libdir returned by llvm-config.
All of these must be present for configure to pass.
refs #130
So I found that I didn't write many of the autoconf rules correctly including
the one searching for motif. I also messed up the checks for bison, flex, and
perl. I added new rules to search for Xwindows headers and libraries. The
motif rule is only executed if we find fermi-ware where it is used.
refs #119
Added AX_PTHREAD to the configure.ac script. This change forces us to
have install-sh, config.sub and some other autoconf files. Created
an autoconf directory to hold these files. Changed the makefiles to
use the PTHREAD variables coming out of configure.
refs #69
