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I found this script that find all manually installed packages in Fedora (every argument that I passed yum install). Specifically, the script does not return dependencies that were automatically installed. Is there something similar for Ruby Gems?
Otherwise, does Ruby Gems keep a command history somewhere?
If YUM works like APT (which I assume it does based on your description), it recognizes a difference between explicitly installed packages (“manually” as you say) and implicitly installed ones (i.e. as a dependency).
Rubygems has no such distinction, and thus this is not possible. As mentioned in the comments, Bundler can do this, but that’s on a project level more than a system level.