added option to save solution DOF after the time step
Merge pull request #37 from erdc-cm/save_dof

added option to save solution DOF after the time step
Improve Makefile (Cygwin Bootstrap, Doc Fixes)
hashstack2 -> hashstack
Merge pull request #40 from erdc-cm/ahmadia/restore_bootstrap

Improve Makefile (Cygwin Bootstrap, Doc Fixes)
Garnet Port

* added PetscMalloc calls to contruct arrays for partitioning adjacency matrices
* fixes from garnet including PetscMalloc's for partitioning weights
* put in some flags to prevent multiple re-writes of the polyfile and regenerating the mesh
a few more .gitignore entries
Harden Makefile
Improve Makefile.  Add proteus/proteus_env

Also, updated test Garnet script to use new scripts

proteus - Launch Python with the correct environment for using Proteus
or any of its dependencies

ex: ./darwin/bin/proteus test/test_meshParitionFromTetgenFiles.py

proteus_env - Setup environment for using Proteus or any of its
dependencies

ex: source ./darwin/bin/proteus_env.sh; \
mpirun -np 4 ${PROTEUS_PYTHON} test/test_meshParitionFromTetgenFiles.py
Merge branch 'garnet_port' of https://github.com/erdc-cm/proteus into garnet_port

Conflicts:
	Makefile
	test/test_meshPartitionFromTetgenFiles.py
	test/test_proteus_garnet.pbs
Upgrade hashdist usage in Makefile, Cygwin bugfix

1. updated to new hit syntax

As of https://github.com/hashdist/hashdist/commit/610985 we now have to
specify the profile file being used if we're going to use the `target`
positional argument.

2. Fixed Cygwin bootstrap "touch"

Tab/space error
BUG: fix ordering of hashdist tool
updated Makefile to new hit syntax
Makefile improvements

more version information in build steps
save version information to prefix/tool.version
include LD_LIBRARY_PATH in proteus and proteus_env.sh scripts
restore hashdist force builds (-f)
corrected hashdist/hashstack version swap
Merge remote-tracking branch 'origin/master' into garnet_port_final

Conflicts:
	Makefile
added optional shared library preloading
removed pass statement
Merge branch 'cekees/preload_config' into garnet_port

Conflicts:
	proteusConfig/config.py.garnet.gnu
	scripts/parun
fixed shell brackets to POSIX style
fixed import of config.py in parun and iproteus, removed ld preload from test_mesh...