I see that directory as "the application directory", i.e. it contains the actual program (the .pl file) and the things it needs. It works fine with the way I do things. If you think your program logs should be a level up, I don't see why you shouldn't do that.

What type of file structure within 'notes' and release?

The "notes" dir is free-form. It's too varied between projects to specify in any more detail. The release dir just contains scripts for making a release, and versioned zipped files or installers for each release. The "t" directory contains module tests obviously.

/J