This is my exact issue! That's what keeps me coming back to Atom even though Sublime is much, much faster. The last package I saw tackle this required you to make a project -- which I just never do in Sublime.
Creating a projectname.sublime-project is usually my first step when I start a new development project. In fact, I do it so much I have a text expander shortcut for it.
The benefit seems to be that it _isn't_ synced with my .gitignore so I never have to worry about accidentally committing a .env or similar. I can toggle files and folders on and off as I need to.
Then I have a short bash alias `lime` that takes the place of `subl`: https://gist.github.com/imjared/db14e2c92df864ae048e1d2a94d0...
The benefit seems to be that it _isn't_ synced with my .gitignore so I never have to worry about accidentally committing a .env or similar. I can toggle files and folders on and off as I need to.