By default, the text editor, Atom will follow your VCS’ ignore rules. For example if you’re ignoring some things in a .gitignore because Git is your VCS of choice, than Atom will exclude them in its tree view.
A thoughtful default I admit, but I found it annoying. This is because not all files listed in my ignore file should be hidden when I’m working in a project. For example, a lot of my projects have environment variables listed in a file. It is ignored from Git since I don’t want to version it. This is especially important if I’m sharing the code in a public repo.
When I’m working in a project, I’ll sometimes look at files like the one holding my environment variables or even my .git folder to see things like my config set up for remote repos. For this reason, I like to be able to view my VCS ignored files in Atom.
Toggle through Settings
You can make Atom reveal your VCS ignored files through the settings. To do this select Atom > Preferences. When your settings show up, click on Packages in the left hand column. Search for the installed package, tree-view. Once it comes up, click on Settings and then uncheck the option Hide VCS Ignored Files.
Toggle through Tree view
If you do prefer to hide your VCS files from time to time, a quicker way to toggle your ignored files is to first click into your Tree view pane on the left and tap the i key. This will immediately toggle the hidden files.