Fix a bug that wrongly computed and specified the output file names:
a. Extract the tier inside the for loop.
b. Use the correct for loop variable (j instead of i) when specifying the output file name.
First pass at removing commented out code.
Second pass at removing commented out code.
Remove commented out code in WQ stats.
Remove the $rank variable which isn't used anywhere.
Remove commented out library imports.
Remove commented out code that directly access swig bindings.
Remove commented out stuff that have long been unused.
Remove commented out for killing maintain.pl.
Minor reorg of where we define the WQ port.
Merge the handling of 1 sequence per task with the handling of multiple
sequences per task.
Remove unused "failed" array.
Update the to-do list.
Remove $size variable which is used only once.
Always run maker_wq with WQ. And so remove the option to specify running with WQ.
Remove unused global variable - $RANK.
Update To-Do list.
Redo the checks for query size for each task.
Clean up the help string and remove maker related text in there.
Use the wq_specify_log() API to record the WQ stats.