What is the missing-dependencies.jar file and how is it made?

My gradle build keeps looking for it, cannot find any documentation on this.

Never heard of it.
I don’t think this is coming from Gradle itself.
Maybe from your build, or from some plugin you apply.

It could help if you would tell the concrete error message you get.
Especially with the output from --stacktrace, and maybe also --info.
Optimally, you could supply a build --scan.