Added processing of data from Starita, et al

Added an explicit section on dependencies to processing files
Did quite a few scattered changes
* changed processing (flattened aa matrices) to make it easier to use both square and triangle
* changed assess_study_power to use EX instead of EXS
* changed "Missense", "Nonsense", "Synonymous" values to lower-case
* added processing of study by Deng, et al
* renamed template_mut_report.Rmd to mut_report_template.Rmd so I can gitignore any *report.Rmd
A variety of minor improvements and bug fixes.
* fixed missing nts_changed data in bloom, deng, melamed, thyagarajan
* added Grantham test to assess study power
* added degraded conservative/radical distinctions to assess study power
* fixed aberrations in reports that presented incorrect results (on nt paths via ddply)
* incorporated EX (asymmetric) instead of EXS
* altered processing of triangle matrices to assign val to rows AA1AA2 and AA2AA1 instead of ordered(AA1,AA2)
* removed autogenerated report files that are *not* supposed to be tracked
Minor things
* cleaning up a bit from last commit
* removing autogenerated files that should not be tracked
* updating and adding gitignore files