FYI I decided to ask skynet about the change detection thing, particaularly in the project json file, and here's the advice it gave me.

More importantly, ieshelp.docs.json looks like Documentation Monster's project file. The app writes that itself when it saves project settings; you don't edit it in the Markdown editor. .NET JSON serializers on Windows usually write CRLF, so every time Documentation Monster saves the project, it likely writes CRLF again no matter what the editor is set to.

It recommended adding a line to the .gitattributes file that explicitly tells git to use CRLF for the project json file:

*.docs.json  text eol=crlf

It walked me through a few other steps to normalize the file and then verify. I am happy to say that the project file is no longer showing up in a status check as changed except when it should. 😃