Comment cleanups to improve generated docs

- added comments to fields which didn't have any.
- changed all `//` comments to the new format
- fixed indents/line lengths/style on lines I touched
Even if the majority of searches didn't have a reference sequence, setting this to 0 shouldn't do any harm - so sgtm. (I think this is a case of the comment just not matching the code - we've had this in other places too)