Issue Type: Bug

I keep all my dotfiles and settings in a repo, and my settings.json is symlinked into that repo. Whenever I open Preferences > Settings, my repo is added to the source control sidebar.

Steps to reproduce on Mac:

0. Quit VSCode
1. mv "$HOME/Library/Application Support/Code/User" "$HOME/mysyncedusersettings"
2. cd mysyncedusersettings; git init
3. ln -ns "../../../mysyncedusersettings" "$HOME/Library/Application Support/Code/User"
4. Open VSCode. The app can be in any state (a project may or may not be open).
5. Cmd-,

The settings UI opens -- I would expect opening my settings panel to do only that. What actually happens is that in mysyncedusersettings gets added to the source code panel in the sidebar. Sometimes it doesn't appear immediately, but it will always appear after a window reload.

I understand that this can be desirable behavior (and it sometimes is for me actually), but I feel like there should be an option to turn it off, or to open Preferences in a new window so that it doesn't affect the state of the existing window's Git sidebar.

VS Code version: Code 1.21.1 (79b44aa, 2018-03-14T14:39:09.335Z)
OS version: Darwin x64 17.4.0

System Info

Item	Value
CPUs	Intel(R) Core(TM) i7-4980HQ CPU @ 2.80GHz (8 x 2800)
Load (avg)	3, 3, 4
Memory (System)	16.00GB (2.07GB free)
Process Argv	/Applications/Visual Studio Code.app/Contents/MacOS/Electron -psn_0_50491428
Screen Reader	no
VM	0%

Extensions: none Reproduces without extensions