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Comment by jbrooksuk | Hacker News Reader

AFAIK they only get excluded from indexing, if you don't want them to show in the sidebar, that's something else.

I may be wrong, so please let me know :)

It's part of Atom's own tree-view package. You can either edit the options [1] or add this to your config.cson (under the "*" key):

  "tree-view":
    hideIgnoredNames: true
    hideVcsIgnoredFiles: true