The common package does not itself contain any software, only dependencies. Your only problem ist, that by removing the common package (which you apparently have to do, if you want to get rid of amazon) tghe package manager sees no need anymore to keep all other applications. Because it considered them just a nasty dependency of common in the first place.

You can safely mark the commons package for removal and mark all packages you want to keep for installation. Depending on the package manager you use, you can do this in one step, before executing the change, so the packaging system will not remove, redownload and reinstall any software. It will just keep everything you marked for ... keeping.