BinaryDist: Use Pbzip2 if it exists

This makes the product of bzip2 tarballs faster if we have multiple
cores.
build.py: Added --add-ld-library-path as an option

This is for setting the LD_LIBRARY_PATH env option inside our
sanitized build sessions. This option gives the user the power to
destroy the build environment. Unfortunately it must be added for the
super computer environment where they have libstdc++ in a non standard
location.
deploy-base: There can be dirs between BaseSystem* and install

The previous regular expression was too strict. We can have
directories between BaseSystem* and install when the user uses the
option --build-root in the cases where they don't have write
permissions to /tmp.
packages: Upgrade flann, geos, qt
packages: Fix incompatibilities with new automake

There are a few command renames that have progressed from warnings to
errors. There is also a shipped bug where top_srcdir can be used
inside the TESTS variable. The only option is to not use it.
deploy-base.py: Fix replacement for Macs.

When I build BB in the a temporary folder, "-Tmp-" is used as a folder
name. This commit add - as a replace character.
Updates for geoid
deploy-base.py: Force superlu to show up after blas when linking
Modifications for local environment
shean_BB: tweaks
shean_bb: add notes
shean_BB: old changes from Pleiades build