Staging is buggy when working on repository subfolder

[jjwhitney]

Issue Type: Bug

1. Open any subfolder of a repository using "File -> Open Folder..."
2. Open any file in the folder and make changes to two different lines.
3. Open the "Working Tree" diff view of the file by clicking on it in "Source Control".
4. Click on one of the changed lines and use "Stage Selected Ranges".

The line is correctly staged, but the view is not updated to reflect this. Now if you try to stage the second changed line, the first line will be unstaged (!), and the view is still not updated.

Because of this bug, I've needed to manually reload the view after every staging command to ensure that it won't be undone later.

VS Code version: Code 1.25.0 (0f080e5, 2018-07-05T13:11:58.697Z)
OS version: Windows_NT x64 10.0.17134

System Info

Item	Value
CPUs	Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz (8 x 2394)
GPU Status	2d_canvas: enabled flash_3d: enabled flash_stage3d: enabled flash_stage3d_baseline: enabled gpu_compositing: enabled multiple_raster_threads: enabled_on native_gpu_memory_buffers: disabled_software rasterization: disabled_software video_decode: enabled video_encode: enabled vpx_decode: unavailable_software webgl: enabled webgl2: enabled
Memory (System)	15.91GB (6.92GB free)
Process Argv	C:\Program Files\Microsoft VS Code\Code.exe C:\Users\jjw\Desktop\VSCode_test2
Screen Reader	no
VM	67%

Extensions (3)

Extension	Author (truncated)	Version
githistory	don	0.4.1
gitlens	eam	8.4.1
python	ms-	2018.6.0

[vscodebot]

(Experimental duplicate detection)
Thanks for submitting this issue. Please also check if it is already covered by an existing one, like:

• Stage selected lines works in source control view only (#42909)
• When I stage a selected range, VSCode commits the entire file (staged AND unstaged parts) (#52367)
• Stage selected lines stages only big chunks for line deletions (#9475)
• Consider changing the focus after staging a file (#15112)
• Command to stage entire change aka hunk (#48965)

[joaomoreno]

/duplicate #3025