This is already in your commit history, so why hardcode it into the source?
> FILENAME: functions.php
This is obvious because you just opened the file. So again, why even put it there? When the file gets renamed the documentation is no longer correct? These things are also hard to refactor.
> STATUS: ACTIVE
Every part of the code is always active...
> PURPOSE: All of the functions for this application (app name)
Okay, probably the most useful one here. But what if we're refactoring the code and the purpose changes? Or if someone adds a few functions and the documentation no longer covers the purpose?
> NOTES: There are several unused functions in this file that are commented out but once in production They can be deleted as we likely will not be needing them at all.
Very dangerous, again because the source might change while the documentation doesn't. But why even write "they can be deleted"? Why not just delete them? That's what version control is for.