mlexample

I have a repo on GitHub that had a branch (handtracking) that I was doing some development on. In the mean time I had made a number of changes on master, and I wanted to merge them from master to handtracking, so that my dev branch would have the latest changes.

I used the Github Desktop client on Windows to do this, I did not use the command line. I performed the following steps (in Github Desktop unless otherwise noted):

1. Committed all changes, sync'd everything up to prepare.
2. Switch to master branch via the branch pulldown.
3. Created a pull request in the client and selected the destination branch; it clearly stated "from master into handtracking".
4. Submitted it, then opened it on the web site, where it also very clearly states master -> handtracking.
5. There were conflicts; so I chose to resolve them on the web site editor. For some reason when I did this, it committed the resolution to master, although I don't see an actual commit for this anywhere. This part is where I became confused.
6. I then clicked the merge button on the pull request on the web site, which still said it was going from master into handtracking.

But then, at this point, it created two commits. One from handtracking into master, which is where all the wrong way stuff happened; and then a second one from the updated master back into an apparently new handtracking branch ("apparently new" because the color changed on the Insights -> Network view).

The second commit is the one that referenced the pull request, and is the only one I expected to happen. The first seemed to have come out of nowhere, and merged all the handtracking changes into master, which is what I didn't want to happen.

The network graph now looks like this (the highlighted bit is what this whole process created):

But I had expected it to be like this:

My questions are:

1. What the heck happened? What was my mistake? I can't understand where that first handtracking -> master merge came from, especially because at every point there were descriptions stating clearly that the merge was going the other, correct direction.

2. How could I have avoided this while still using Github Desktop + the web site? Or is doing this only possible with the command line client?

I know (I think?) I've done this before with no issues, I can't figure out what was different this time.