remove commented out code
remove write instead of setting absolute permissions

Setting absolute permissions is often not the correct thing to do because it
doesn't account for other bits the file/directory might have, e.g. setgid, or
executable.  So, for example, instead of setting thing readonly by doing `chmod
444` one could instead do `chmod a-w`.
Added Tier 1 filter and related test.

The tier 1 consequence types list needs to be updated, this is just a
handful of valid types so far.
Added ProcessManualReview
small change
fixed mis-placed use statement
rename summarize-builds
Rename file in diff-ignore as well.
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
Added more tests
Updated tier 1 consequence types per cmiller.
remove unused function
remove set_file_permissions and set_directory_permissions

Remove set_file_permissions and set_directory_permissions to be replaced
with 'mode' and File::Find::Rule.
remove 'other' permission bits

This is only a half-measure to reflect the new policy that 'other'
shouldn't have access to Genome or its output.
updated jenkins submodule to da389bf
skip LIMS reports for now
update tests
update clinseq blessed