Decided to kill the --fixBadPadding option, it was a poorly conceived, overcomplicated in how it was going to integrate and furthermore, wasn't yet implemented. It's gone now.
It was a solution to a rare problem. Instead I decided to make a new util called fixseqpadding to handle the rare times that this fix needs to happen in keeping with unix philosopy, make tools do simple things well and chain them together. Seems a far better approach.
Also, much better README.md now and better --help output. Some other logic cleanup in the util as well. Passes all regression tests.