Strange behavior while removing meteor package

I have been working lately in a meteor project, we want to clear not used packages, for example: removing minimongo but I have found that doing meteor remove minimongo returning in terminal minimongo is not a direct dependency in this project. removing it from .meteor/packages and .meteor/versions and also make sure package is removed from home/.meteor/packages on machine
but starting the server it get downloaded, I see on terminal: Changes to your project's package version selections: minimongo added, version 1.4.4

I suspect it’s because of in .meteor/package-metadata but I can’t understand how this happens, is it right? if right how is this done? if not right, so, how that happened?

however, I need to know the right way to remove a package from being in packages on my machine, and remove not used dependencies from .meteor/packages file

You can use meteor list --tree to find all dependants of minimongo.