How stop my IDE from showing hidden files on Sierra?
It's up to individual apps to decide whether to show hidden files and to provide options to change it.


The ‘AppleShowAllFiles’ key is written to ‘com.apple.Finder’, so it only applies in Finder. Finder's GUI option for changing this setting is ⇧⌘..
Other apps may have their own options, which you'll need to investigate on a per-app basis. For example, How do I hide certain files from the sidebar in Visual Studio Code?.