Some of the changes in this build augmented the existing options for filtering files and folders. In addition to completely removing node_modules, you can cause it to be ignored from Goto Anything by marking it as "binary", or exclude it from indexing if you don't want Goto Definition and Goto References to show for that. 3.1 also adds the ability to specify all of these filtering options per-folder. See https://www.sublimetext.com/docs/3/projects.html for the details.

My plan is to get .gitignore working natively in a future dev build. I have definitely heard the request from a number of users, and I can appreciate why people would want that option.