How can I reset all menu data as a fresh install?

These three are the ones that would be modified by any changes in MenuLibre or Alacarte.

~/config/menus
~/.local/share/desktop-directories
~/.local/share/applications

Deleting files in these directories means that the system versions (in the other directories you found) will be used. If those are modified, the new versions will be in the above directories.

If you're using Ubuntu, be sure to have the latest version installed (Trusty has not yet been updated with the latest release). You can do so by installing from the Stable PPA.

sudo add-apt-repository ppa:menulibre-dev/devel
sudo apt-get update
sudo apt-get install menulibre

~/config/menus doesn't exist. try
~/.config/menus

There are more:
/etc/xdg/menus/gnome-applications.menu
/etc/xdg/menus/gnome-flashback-applications.menu
/etc/xdg/menus/kde4-applications.menu
/etc/xdg/menus/xfce-applications.menu
/etc/xdg/xdg-xubuntu/menus/xfce-applications.menu
/usr/share/app-install/desktop/applications.menu

Haven't figured out yet how to restore the menu that was there after initial Xubuntu Desktop installation, but I have determined that:
1. Not everything but most things installed with synaptic or sudo apt-get install are added to the Application Menu somewhere.
2. Uninstalling with synaptic or sudo apt-get (auto)remove can leave items on the Application Menu that are not visible in MenuLibre or Alacarte and that therefore cannot be removed with them (what started me messing with this in the first place).
3. It is not clear what file(s) MenuLibre or Alacarte modify when an added or modified menu item is saved, but strange things sometimes happen (added mugshot and got 2 copies in various places). Until I can figure out how to make the wierd things that are happening occur consistently, I can only suspect it would take me many more hours to fix my Application Menu using either MenuLibre or Alacarte than it will take to create panel launchers for the same applications.

Kent Lion (klsu) said:

Until I can figure out how to make the wierd things that are happening occur consistently, I can only suspect it would take me many more hours to fix my Application Menu using either MenuLibre or Alacarte than it will take to create panel launchers for the same applications.
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Kent, yes, this is where I was when I was trying to get my menus the way I want them. It just seems to me (and take this with a grain of salt, as I am ignorant of the inner-workings here) that this is far more complex than needed. I got lost among all these various folders and inter-actions. I suspect that the complexity comes from attempting to automatically assign a category to anything added through synaptic or a sudo apt-get install?

I'm a 'keep it simple' kind of guy, and my preference would be for new applications to simply be dropped into a 'recent additions' category, and then let me move them where I want, with full flexibility. I envision a simple folder hierarchy, with launchers placed in folders that the user can create, name, re-name, and use sub-folders if desired. There could be one folder for the user, and one system-wide (if an admin wants to make some common applications available to all users). The menu program would simply be a GUI that would reflect this folder structure (merging the system and user folders).

Again, maybe due to my ignorance I am missing something, but wouldn't this be far simpler, robust, flexible and user-friendly?

Maybe this isn't the right place to discuss design structure, but I would like to provide this input to the designers?

-KenC