new "rally" master/slave parallel search architecture

new "rally" master/slave parallel search architecture

greylag-rally is the master, organizing the search process and farming out
work chunks to greylag-chase processes running on various nodes.  Both make
use of the Python asyncore/asynchat modules.

the 'enable_pca_mods' parameter now defaults to "yes"

add new command 'greylag-shuffle-database', which generates shuffled or
reversed sequence databases

removed the unused 'decoy_locus_prefix' parameter

moved common code to greylag.py

zapped SIMR directory (there is no longer any SIMR-specific code)

whole run testing is disabled--need to rework how this is done, in light of
the architecture change

fixed greylag-validate mark
fixed greylag-validate determination of peptide trypticity
have greylag-validate --fdr use "effective" FDR

greylag-sqt omits DTASelect-incompatible lines unless '--enhanced-output'
specified

doc updates
other minor updates and fixes