GNOME is not one program. It is a set of programs. GNOME Shell is one of them: GNOME's user interface. Trisquel is a set of programs too. Some of them are GNOME programs (e.g., the GNOME System Monitor) and some of them are not (e.g., LibreOffice).

Individual programs are "packaged" so that they are easily installable/removable through a package manager. A program usually needs other packages to work: other programs that it executes, libraries (pieces of software needed by several programs), fonts, etc. Those are called dependencies. If you install, from the package manager, a program that depends on other packages, they will be automatically installed as well (otherwise the program you want would not work). If you remove, from the package manager, a package that is a dependency of some programs, those programs will be automatically removed as well (since they would not work anymore). In both cases, the package manager first lists the whole list of packages it will install/remove and asks for a confirmation.

Sets of programs such as "GNOME" or "Trisquel" also relate to packages ("gnome" and "trisquel"). They are called "meta-packages" because they do not install anything by themselves. They only depend on other packages: all the programs in the set (the whole GNOME desktop environment and Trisquel's default system), which therefore becomes easily installable at once.

If my last two paragraphs were clear enough, you should now understand that removing a program in Trisquel's default install automatically triggers the removal of the "trisquel" package. It is no big deal because "trisquel" (or "gnome" or "trisquel-recommended" or ...) is a meta-package: by itself, the "trisquel" package does not install anything. Removing "trisquel" only means you will not have the whole Trisquel's default install anymore. Notice however that it also means that, upgrading to Trisquel 8, you will not get the new applications added to the default install, i.e., added as dependencies of the "trisquel" package.

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