normalize lacks in place modification & destroys line wrapping

Many projects have a requirement for line wrapping at 79/80 characters whenever possible.

Personally I find that it improves readability.

Would be great if `planemo normalize` didn't undo that.

Start at the `planemo normalize` CLI entry point and reproduce the reported behavior with an input containing lines wrapped near 79–80 characters. Done means normalization supports in-place modification as intended and preserves existing line wrapping whenever possible.

Written by the indexing model from the issue text.