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Since the official Atom repository has been deprecated and thus support suspended, you can no longer expect such functionality to be supported.
I imagine the certificates used to encrypt the download/verify the legitimacy of the remote packages repository have been since revoked.
I'm personally unsure if there is a local workaround, but you do have forks of the Atom project available if you wish to continue to use Atom with these functionalities intact.
Among others, one such fork is Pulsar.
After installing atom, I can't install any packages. It shows "certificate has expired".
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