Hi,
thank you for your submission. The problem is in the way you declare arguments. Though your input would work on older dokka, new one is using kotlinx.cli for parameters parsing. Because kotlinx.cli is lacking mechanism allowing nested parameters, you have to provide all parameters with values as a single argument for -sourceSet. The only way to obtain that is to enclose your arguments in "", so for your case it would go -sourceSet "-moduleName Compiler -src C:\JMooreMACS\Teaching\Compiler\Projects\Compiler\src". Of course you can chain many source sets in the same manner e. g. -sourceSet "..." -sourceSet "..." .... I know it’s not clearly stated in README manual, we will fix it as soon as possible and sorry for your inconvenience.
However, your configuration is not exhaustive yet. New dokka decoupled default documentation templating etc from the engine, therefore you have to provide it manually yourself. All you need is dokka-base, which is published as dokka-base.jar. You can add it using -pluginsClasspath parameter. Note you have to provide all required classpath dependencies e. g. kotlinx.html in order to work.
Unfortunately, currently there is a problem with loading one of such dependencies classpath: kotlin-analysis.jar. You can subscribe to this issue to get notified about current state on that bug Cannot add kotlin analysis to classpath while using CLI · Issue #1364 · Kotlin/dokka · GitHub
If you have any further questions, feel free to ask