This has been an annoyance to me, too, because some of the code digs through the filesystem (when sourcing the Tcl library) while others ignore anything not in the .info file (as you point out)
At minimum things should be consistent, either the .info file significance should be dumped or everything should be driven by it.
I'd label this a triage issue, i.e. there's a fair amount of code to whack away at, and it's not near the top of my list of things to whack away at in the near future.
On the other hand I really appreciate all the improvements to the APM you're making. If folks agree with the idea of driving things from the filesystem depending on the standard file patterns and you're sufficiently annoyed by the current state of affairs that you'll go ahead and rewrite it ... sure!
