Jon Skinner in latest Dev build seems to be working on Indexing, and a myriad of annoying issues that can crop up. I am not game to attempt the latest Beta. It is enough to Run ST3 2016 public release Build 3114, on a desktop bulging with Internet of Things. Apple has a capable system-wide reset that can fix public release isses when they arise. Clean up behaviors similar to what is described in this blog:
Sublime Text 3 File Indexing
SMC Reset
Reset the System Management Controller (SMC) on your Mac
Shut down with ‘reopen apps’ unchecked.
Power cord, unplug for 15 seconds, then plug in.
Turn power on and press Shift-Control-Option ⇧⌃⌥-⌽.
Hold Shift-Control-Option ⇧⌃⌥ until login appears.
This can repair garbled fonts, App indexing, and many other performance issues.
Honestly, my Projects always get messy, even disappear when they are GB’s in size: SMC Reset will make Build 3114 Projects run smoothly.