Update normalization code to enable normalization of sequences with more than two indels

[fnothaft]

Currently, the indel left normalization utility that we have can only left normalize and trim sequences with a single indel. However, it is ideal to be able to left normalize and trim more complex sequences; sequences of interest would include reads with combined insertion/deletions, and reads with multiple indels.

[fnothaft]

Closing as won't fix. We will probably EOL the indel realigner post 1.0.0.