The system is a Mac OS X El Capitan running Sublime Text 3.
I was perfectly able to run ST3 from the terminal, using the symbolic link by typing "subl". I have no idea what could have possibly changed.
Now everytime I try to start subl from the terminal in any given directory (by running "subl .") I get a "Permission Denied" window every 5 seconds.
[Sublime opens the specified directory, whichever it is, and then everytime I switch back to ST3, the window pops up "Permission Denied"]
The only message in ST's console is: "error: Permission denied".
When opening Sublime Text from the GUI (not CLI), this doesn't happen at all.
The only way I could find was disabling all the plugins altogether.
This stopped the error message. Now I'm enabling them back, one by one, so far so good.