I'd like it to have automatic cookie file find in this sense.
Open a source file in your folder subtree.
SourceCookifier goes up automatically in the tree to find a cookie file. It stops when it is found.This happens wothout specifying which cookie file to use.
That cookie file is the one applied to the project (subtree) where you're working on.
This is how it happens with a non official N++ plugin named OpenCtags. I use it since in SourceCookifier I have to specify which cookiefile and only applies to a session or so.
With OpenCtags I can jump immediately to the definition within my project subtree.
When there is no ctags file (equivalent to cookie file) I have to specify where to save it (usually in the root of my project subtree), after that when I need to regenerate since it was found automatically it uses that file.
Hope at least this to be an idea.