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I created a "calculator" entry in main applications menu of Xubuntu, using Alacarte (gcalctool command - it seems to be a wrong one, as it can't find it).

BUT:

it is not shown in the list of Alacarte, so I cannot delete or hide it.

I suppose I have to edit a .desktop file. I found two of them and I tried "Hide only root entries" from here but none of them has "X-Xfce-Toplevel;" in it's categories.

Why does not Alacarte "control" some entries? How can I repair or delete these entries?

edit: I have found that there are also some entries of this type by default, not only in the root menu, but also in the submenus. Even after restoring the "system default" menu.

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When I tried to redo what you did, I got two new desktop files at:

~/.local/share/applications/alacarte-made.desktop
~/.local/share/applications/alacarte-made-1.desktop

Since they are top-level, they do not have any category, it seems.

Alacarte takes the system default from /usr/share/applications and adds from ~/.local/share/applications.

Repairing or deleting installed desktop files is not a commendable approach for a multi-user system, so each user can only modify his/her own view of what's installed.

In case you misconfigured your view, there's a nice Revert button next to Close.

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