It would also be a good idea if the non-power user could see, from within Pd, a list of all the directories Pd will scan for externals and abstractions. Then the user could choose which one to use. The Pd I have here (Pd 0.46.6) has preferences->path which contains the single item /usr/lib/pd/extra, which is not user-writeable. I can't find any reference to the settings file. There is a 'save all settings' that may or may not actually do something, but I'd need to be a power user to figure out which file was changed.

As far as hidden directories they are (by design) hard to see...you have to list your directories in a terminal with ls -al, usually not possible with the double-click-on-an-icon approach which the non-power user tends to adopt.

For example the Arduino IDE has a settings dialog that lets you change some settings but also, in the same dialog, gives the path to the actual settings file so you can change other settings with a text editor.

Martin