I just posted in discuss.atom.io explaining in depth an ignoredNames inconsistency issue between tree-view, fuzzy-finder and find-and-replace.

https://discuss.atom.io/t/ignorednames-issue/13299

I summary, scandal file search indexing is inconsistent with fuzzy-finder because instead of matching full file paths it's using relative file paths.

https://github.com/atom/scandal/blob/master/src/path-filter.coffee#L79