add status column for allocations
Modified rfam ace file so rfam score and rfam_product are added
Also added a filter so less than 50 score rfam genes do not enter into
the ace file
Rfam ace file changes for egap

Merge branch 'master' of ssh://git/srv/git/genome
remove concept of preserved allocations
Updated class browser cache.
Updated `genome` tab completion.
join the outout for R into a single string before calling status_message()

response to UR's change where the *_message functions work like sprintf with
a format string and list
add is_optional to output_vcf because otheriwse it breaks for some reason I dont understand.
set archive_after_time automatically on allocation creation
updated ur submodule to d4ddfbb
DV2 Filter False Indels: init stats
remove do-not-archive globally in favor of delay archiving
updated ur submodule to 99babd9