Unstaged changes view goes weird after staging a hunk #2550

Prerequisites

• Put an X between the brackets on this line if you have done all of the following:
  • Reproduced the problem in Safe Mode: https://flight-manual.atom.io/hacking-atom/sections/debugging/#using-safe-mode
  • Followed all applicable steps in the debugging guide: https://flight-manual.atom.io/hacking-atom/sections/debugging/
  • Checked the FAQs on the message board for common solutions: https://discuss.atom.io/c/faq
  • Checked that your issue isn't already filed: https://github.com/issues?utf8=✓&q=is%3Aissue+user%3Aatom
  • Checked that there is not already an Atom package that provides the described functionality: https://atom.io/packages

Description

When viewing unstaged changes for a file, sometimes when I click on "Stage Hunk", the view jumps down to a seemingly random place. When I scroll back up, the hunk that I just staged is still visible in the "Unstaged changes" view. If I go to the "Staged changes" view, the hunk that I just staged is shown. If I go back to "Unstaged changes" view, the hunk is no longer visible.

This only seems to happen in some files and not others...

Here is a video demonstrating the problem in safe mode, with factory default settings: https://youtu.be/-jeOiUgCPLg

Steps to Reproduce

1. Open "Unstaged changes" view
2. Click on "Stage hunk" for one of the unstaged hunks

Expected behavior:

After clikcing "Stage hunk", expect this hunk to disappear from "Unstaged changes" view, and that the next unstaged hunk moves up in the view.

Actual behavior:

Here is a video showing the actual behaviour:

https://youtu.be/-jeOiUgCPLg

After clicking "Stage hunk", the "Unstaged changes" view jumps down to a seemingly random unrelated hunk elsewhere. After scrolling back up to the hunk I had tried to stage, it is still visible in the "Unstaged changes" view, except the line numbers in the gutter no longer make sense (the hunk I just staged seems to now have the line numbers from the next unstaged hunk sitting in the gutter beside it). If I go to "Staged changes" view, I see that the hunk did in fact get staged. If I go back to "Unstaged changes" view, the hunk is no longer there.

Reproduces how often:

100% of the time.

Versions

C:\Users\Boompy>atom --version

Atom : 1.52.0
Electron: 6.1.12
Chrome : 76.0.3809.146
Node : 12.4.0

C:\Users\Boompy>apm --version
apm 2.5.2
npm 6.14.8
node 12.4.0 x64
atom 1.52.0
python 3.8.3
git 2.16.2.windows.1
visual studio 2015

Windows 10 Home (64 bit)

Additional Information

Here is the file that I was trying to stage/unstage hunks from:

CM_comm_protocol.zip

I tried moving the base file to a different repositoy, commit, then apply all the same changes. When trying to stage those changes, I get a totally different flavor of bug. It seems like this bug may have something to do with the fact that the file that I am trying to stage diff hunks from is considered by atom to have a "large diff", and therefore the diff does not auto-load? See #799

Maybe it will help diagnose the issue?

Actual behavior:

Here is a video showing the actual behaviour:

https://youtu.be/zox8HrWV-wM

After clicking "Stage hunk", the "Unstaged changes" view seems to bring back the "load diff" message. If I click "load diff", then the unstaged change view displays the correct unstaged changes, except with no diff highlighting. See https://youtu.be/-jeOiUgCPLg