Merge pull request #68 from erdc-cm/ahmadia/garnet_fix

remove debugging code from dd37fa41c1ff6ec548c8c7f3c8fbbb35d45d6db3
Makefile: install --prefix=${PROTEUS_PREFIX} (helps host-python)
Merge pull request #69 from erdc-cm/jed/makefile-install-prefix

Makefile: install --prefix=${PROTEUS_PREFIX} (helps host-python)
[cygwin] fix bootstrap
Merge pull request #78 from erdc-cm/ahmadia/cygwin_fix_bootstrap

[cygwin] fix bootstrap
ignore cygwin_bootstrap.done file
Merge pull request #79 from erdc-cm/ignore_bootstrap

ignore cygwin_bootstrap.done file
add verbose flag
Merge pull request #87 from erdc-cm/ahmadia/add_verbose_flag

add verbose flag
Resolve real path of PROTEUS dir

This is helpful on HPC systems where the current working dir may
not be the absolute path, leading to hashdist launcher errors
Merge pull request #88 from erdc-cm/ahmadia/use_absolute_paths

Resolve real path of PROTEUS dir
Merge remote-tracking branch 'origin/stable/garnet' into garnet_stable