Sorry to "reopen" the post (I'm new at this) I have a similar issue - I am running everything locally on my machine and when I use "touch" or "rm" for remove from the command line, the Sublime Text 2 sidebar navigation is not updating instantaneously like it has in the past. I am running ST2 Version 2.0.2, 2221 on a Mac OS X 10.9.2. The only way to get the sidebar to update is to click Project > Refresh Folders (for which there is no shortcut key), which is not efficient at all.
This is extremely frustrating and I feel like I've done endless amounts of google searching on the web for answers that are more recent and this thread has been my best shot at similar information and recency.
Any word on possible updates? I have tried a few that are out there, but nothing seems to be working. I've uninstalled and reinstalled ST2, tried updating settings, etc.