Added fractional position output when particle is found outside box
Update quick start guide
rearrange doc pages in index
Update command line options docs
Update units docs
Update periodic boundary conditions description.
Update xml file format docs
Update MPI docs
Rename file format conversion page
Rename credits and license to dox
Update organization of concepts page

Also add autotuner documentation (not that autotuner control is functional yet).
Add MPI GPU selection to docs
Fix compile errors on ubuntu12.10
Error out if running on nyx without --mode
Add plumbing to control Autotuner

refs #291
Enabled caching of pair force arguments in constant memory
Added tune_kernels option to tune.r_buff

& enabled tune.r_buff <-> autotuner interop
Fix autotuner<->tune.r_buff() interop

The tuning period wasn't set correctly upon initialization
Removed unnecessary statement
Really fix tune.r_buff() now