I'm confused about how to get Araxis Merge to make changes to the files in my repo. When I launch the application (in my case, from Tower, which is configured to use it) I see the expected comparisons, and can select which changes to move between the compared files. But in all cases the files I'm working on are (deeply buried) 'temp' files that are not part of my source tree. I see no way to save the selected changes into my repo.
How do I cause changes I've made to the temporary files I work on in Araxis Merge to apply to the corresponding files in my repo?
In the official Tower Help there's a dedicated section for Solving Merge Conflicts which explains the process with pictures.
Every diff tool gets it's files for comparison directly from Git itself. To work with them the diff tool needs to save them at some arbitrary place. As usual for temporary files most tools use the temp folder.
Tower waits for the mergetool to return a file-copy to use. Therefore everything you should need to do is save the resolved file at the place your tool suggests (CMD+S or CTRL+S as keyboard shortcut) and quit it afterwards.
Now the interface of Tower should show you your resolved file and end the merge conflict wizard.
The questioner made sure the command line utilities for Araxis Merge are set up correctly by symlink them using Homebrew.
The questioner disabled perform directory diff in the preferences screen of Tower.
Edit incorporates steps from the questioners comment