For those of us working on the audit, this tool+format might be of use to you. It defines a quick and dirty format for notes files on the code files. This can later easily be converted into the official doc system, if we need it. It also contains ljsummary.pl, which you can use on your notes files to generate summaries (in plain text, or ghetto HTML) to send to Brad, or to look over yourself. There's also an example file of what the format looks like.
All of the features I wanted into the format are there, except for the use of CALL:: (see the FORMAT file for info on that). All of the features I wanted into the ljsummary.pl file are there except for --dir=./path/to/place, which would run screaming through the directory, generating summary files (or one big summary file, haven't decided yet) on all of the notes. Also, a trace command for use with CALL:: (which I still might not do.)
Comment if you care, it's a crappy tool, but it helps. If anyone wants to compare notes, e-mail me with some proof that you have the source code ;) I don't have too much yet (just one pass through ljlib.pl) but I'll be cranking out the note starting today (starting yesterday, actually... ljlib.pl is huge.)
[Update: Fixed a small bug that just gave you crappy perl errors if you didn't bother specifying a file to parse for some reason. Re-download if you feel you need that feature to work:)]