(I also don't think it's true that the attacker has a "small window of time"—as soon as they get a single RCE, it's over, if they're running on a normal dev machine then they can daemonize into the background, add persistence, and snoop events over time. CI systems are obviously less vulnerable to this by nature.)
If you know your computer was compromised. Shut down and reinstall from a backup, you don’t try and clean it.
Edit: I’m assuming the attacker would be replacing a dependency with an empty repo since they don’t know the actual source code. If they know the interface the dependency is supposed to provide, it could spread across the entire organization before anyone noticed.
> I would hope most SSH keys are password-encrypted
TBH, these are probably weak passwords for convenience.