Initial version.  Works.
Added cff2qiime.pl.
Added cff2qiime.pl comments.
Added 2 more filters for files created by various editors.
My earlier change didn't seem to affect the git status of #* files.  This edit didn't seem to work either...
Escaped comment character to properly filter temporary files created by editors.
Major upgrade to --454-mode.  Now finds only homopolymer indels in a small fraction of the time it takes to find all indels.
Formalized the homopolymer mode code and added options to control it.  has not been tested with anything other than the default options.  Runs extremely fast compared to all other modes.  Engineered it so that muscle is not run at all in this mode.
Got rid of some obsolete code and removed the restriction on homopolymer length (because larger numbers than 94 work - you just can't print characters corresponding with them.  Added a warning about printing these characters in debug mode.
Updated documentation to reflect a change in support for 454 data analysis.
Deleted run_CFF_on_454_FastA.tcsh.