EXTERMINATEs core packages installed in ~/.atom/packages
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When people install core Atom packages as if they are community packages, it can cause many problems that are very hard to diagnose. This package is intended to notify people when they are in this precarious position so they can take corrective action.
apm uninstall [package-name]
Please feel free to ask on the official Atom message board.
Good catch. Let us know what about this package looks wrong to you, and we'll investigate right away.