Initial version from Aaron
Remove Emacs swap files
Work from the last week or so

Just now starting to use git with this project..
Temporary fix for fork+MPI issue
Remove compressfasta during clean
Add directory structure, add my version of stdiowrap
Remove stdiowrap binaries
Add first pass of documentation
Add top-level Makefile
Add basic example job
Use signal for unlocking fork section
Prefix output directory with job name
Awful work-around for fork+free issues on Newton
Remove broken static-argv manipulation

Doesn't seem to be needed with the newer fork/free fixes.
New out-dirs, remove blkseq throttle, Timing printfs
Failed input compression removal
Don't even attempt to remove input compression for now

The whole program relies on the file being processed
into blocks first.  Might as well still do this from
compressfasta.
`cc` instead of `mpicc` on Kraken
Add TIMING log level and move timing code there
First version of "Flush yo junk"

Slaves now flush when the time is running out.  Unfortunately,
this is thanks to a timer on each slave instead of by a command
from master.  Cannot do arbitrary Master->Slave comm since
MPI_THEAD_MULTIPLE is not supported.  Instead:  Restructure slave
to only have one communicator thread; dove-tails into the whole
remove worker threads issue.