fixed storage
Merge pull request #6 from jhprinz/master

Removed duplicate and unnecessary files
Updated README to include req'd packages.

Also, corrected my name in conf.py. :-P
Removed _build directory from docs/

This requires that the user build this, ensuring that it isn't out of date
compared to the source in the commit.
Added .gitignore for docs generated in _build.
Removed *pyc files and added them to gitignore.
Corrected URLs in docs/README.md.
Merge pull request #4 from dwhswenson/docs_iss3

Docs (Issue 3)
Merge pull request #8 from dwhswenson/master

python/docs cleanup
Merge branch 'dev_storage'

Conflicts:
	code/python/PySRMSTIS/OpenMM based SR-MS-TIS.md
	code/python/PySRMSTIS/src/Simulator.py
	code/python/PySRMSTIS/src/data/mdtraj.pdb
	code/python/PySRMSTIS/src/data/trajectory.nc
	code/python/PySRMSTIS/src/forkable_trajectory_storage.pyc
	code/python/PySRMSTIS/src/sandbox.py
	code/python/PySRMSTIS/src/simulator.pyc
	code/python/PySRMSTIS/src/snapshot.py
	code/python/PySRMSTIS/src/snapshot.pyc
	code/python/PySRMSTIS/src/trajectory.pyc
	code/python/PySRMSTIS/src/transition_interface_sampling.pyc
Merge branch 'master' of github.com:choderalab/msm-tis

Conflicts:
	code/python/PySRMSTIS/OpenMM based SR-MS-TIS.md
	code/python/PySRMSTIS/src/Simulator.py
	code/python/PySRMSTIS/src/data/mdtraj.pdb
	code/python/PySRMSTIS/src/data/trajectory.nc
	code/python/PySRMSTIS/src/forkable_trajectory_storage.pyc
	code/python/PySRMSTIS/src/sandbox.py
	code/python/PySRMSTIS/src/simulator.pyc
	code/python/PySRMSTIS/src/snapshot.py
	code/python/PySRMSTIS/src/snapshot.pyc
	code/python/PySRMSTIS/src/trajectory.pyc
	code/python/PySRMSTIS/src/transition_interface_sampling.pyc
Delete forkable_trajectory_storage.pyc
Delete simulator.pyc
Delete snapshot.pyc
Delete trajectory.pyc
Delete transition_interface_sampling.pyc
Delete trajectory.nc
Delete mdtraj_long.pdb
Merge branch 'master' of github.com:choderalab/msm-tis

Conflicts:
	code/python/PySRMSTIS/src/Simulator.py
	code/python/PySRMSTIS/src/data/mdtraj.pdb
	code/python/PySRMSTIS/src/sandbox.py
	code/python/PySRMSTIS/src/snapshot.py