Temp. to PairHMM to avoid bad likelihoods

-- Simply caps PairHMM likelihoods from rising above 0 by taking the min of the likelihood and 0.  Will be properly fixed in GATK 2.5 with better PairHMM implementation.
Release scripts: small changes to reduce intermittent failures

-don't check exit status of wget in the trigger_pdfgen script;
 it was exiting with non-0 status even though the pdf generation
 was being triggered correctly

-introduce a delay after filtering the git history to allow HEAD
 to be properly reset

-re-enable sanity checks in filter_stable and source_release scripts
 that had temporarily been disabled while the new protected repository
 was being set up