Remove obsolete and long-broken "SimpleAlignment" pipeline.

Leave a hollow model class so existing instances can be instantiated.
Remove outdated reference from error message.
Remove broken/obsolete `gmt hmp-shotgun align-metagenomes`.
Remove old "parallel command runner".
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
Remove obsolete database query tools.

These rely on the old Oracle tables and we don't store dbSNP data like
this anymore.
Remove obsolete comments.
Remove obsolete processing profile report that queries Oracle.
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
Merge branch 'master' into gms-pub
Merge branch 'gms-pub' of ssh://git/srv/git/genome into gms-pub