John's fixes to documentation
Jason's fixes to documentation
Added discussion of loading CHARMM files
Edits to documentation based on Jason's comments
AMBER example script uses periodic box vectors from inpcrd
Prevent sphinx from adding an index to PDF file
Marked GBVIForce as deprecated and removed it from the manual
Deleted obsolete documentation files
Very minor fix in developer guide
Merge pull request #580 from peastman/docs

Updates to documentation for 6.1