Atom, search in all the files

For MacOS:

Atom > Preferences > Settings > uncheck Exclude VCS Ignored Paths and now I have a full search and now, you can search through all the files.

This is probably due to the Exclude VCS Ignored Paths setting in Atom's Core settings. Please try the search again after unselecting the respective checkbox in the settings:

You can find this setting on the first page of the Atom Settings, a bit down under Core Settings.

The setting's description describes what is excluded from functionality like the fuzzy finder and the search and replace function. You're probably running into that at the moment...