The intention of the original implementation was that all installed apps appear unless the user intentionally turns off the icons in some menu editor. Why would I ever install something unless I wanted to run it. Any other behavior is a critical bug in my opinion.
Picking "main categories" was exactly what the menu spec was supposed to avoid. That is, you should pick the CORRECT categories, not miscategorize your application just in order for it to appear in some currently badly designed menu. The set of category keywords was supposed to be independent of the menu structure!
Example of total miscategorization: Science/Mathematics apps. There's quite a bit of them, but they will never appear in a proper category, so they are all miscategorized just so that they appear. Properly, something like Octave or Maxima should include Application;Science;Math; and should appear in "Other" or in "Science" or "Science & Math" submenu. As it is, Maxima for example, appears in "Education" in fedora.
In any case the situation is no better (and it may in fact be worse) than it was before the vfolder menu spec. Stupid arbitrary submenus are pretty much enforced and you MUST categorize your application within these in order for your app to appear. So even if a good implementation came along, it wouldn't correctly categorize your menus since the .desktop files have bogus (or not enough) information in them. At least in the way things were done before all apps were at least displayed.
Anyway, I just felt like ranting.
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