Starting from Puppy 2.14 we use the XDG menu system to manage the menus for most window managers.
If you want to edit the menu directly
Templates for each window manager are stored in /etc/xdg/templates
For example, the template file for JWM is /etc/xdg/templates/_root_.jwmrc and from that generates /root/.jwmrc. Therefore, if you want to manually edit the JWM config file, edit the template file, because if you edit /root/.jwmrc it will be overwritten the next time the menus are updated using the fixmenus command (/usr/sbin/fixmenus)
the menu files are in etc/xdg/menus/
menu lists ".directory" are in /usr/share/desktop-directories/
individual menu item ".desktop" files are in /usr/share/applications/ though apparently other places work too
The category each desktop file is placed in is defined by etc/xdg/menus/hierarchy
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Here's how it works.
When you run fixmenus, either explicitly, or as a result of installing something, it rebuilds the ~/.jwmrc file.
It gets the info needed using /etc/xdg/templates/_root_.jwmrc
as a template and scanning /etc/xdg/menus/jwm.menu
which lists the main menu entries between <name></name> tags:
Desktop
System
Setup
Utility
Filesystem
Graphic
Document
Calculate
Personal
Network
Internet
Multimedia
Fun
Console
Shutdown
Each menu item also has a "xxxxx.directory" between <Directory></Directory> tags.
They are inserted at those points by reading them from /usr/share/desktop-directories/
They seem to serve mostly to give the icon for the menu item.
The actual items in the submenu are sorted from the xxxx.desktop files in /usr/share/desktop-directories/
These do the real work. They give the name of the item, its icon, a comment (currently unused), the program to be executed, whether it runs in a terminal or not, and the category.
This last, the category, is how the item is grouped onto which submenu. How the categories relate is listed by /etc/xdg/menus/hierarchy
