ALTHOUGH.
There are more complex cases than simple standalone
Java app debugging. You can run a ".BAT" file as an External Tool. It's how I
have to print from Eclipse under Java, since the Eclipse people refuse to build Linux printing into Eclipse itself.
If, within that ".BAT" file, you have a java app(s) that need debugging, just set up the java command line with remote debugging enabled, then have Eclipse attach as a remote debugger.
Mind you, this is the kind of nasty evil stuff
I like to do, and isn't appropriate for most situations.
The secret of how to be miserable is to constantly expect things are going to happen the way that they are "supposed" to happen.
You can have faith, which carries the understanding that you may be disappointed. Then there's being a willfully-blind idiot, which virtually guarantees it.