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fedy varies where it gets software from, so you can't have one answer.

For brackets.io, the operation happens in https://github.com/satya164/fedy/blob/master/plugins/soft/adobe_brackets.sh . It's unpacking a .deb package (which is unusual, because it could just as easily get a tarball instead of a package for a different distribution...)

There is a function there that looks like it will remove brackets. If you remove and reinstall it, you might get a newer version. You don't get the benefits of using the native package manager for updates when using software provided this way.