Hey Wendigo, I will try to offer some advice though my experience here is limited too. First, it doesn't surprise me Java would be an issue. But that's ok, if you want to use the command line you don't need Java now, that's just if you want to edit and run the game with LGM. Because I have been busy trying to focus on RGM, we haven't quite documented how to use the new command line as much, but it's pretty simple.
The process is well documented for Windows:https://enigma-dev.org/forums/index.php?topic=2939.msg27287#new
You just need a few additional packages such as protobuf, pugixml, yaml-cpp, and rapidjson. The best place to find the packages that you need for your Linux distribution is probably the Travis CI yaml file in our repo since the CI we run on every pull request builds the command line.https://github.com/enigma-dev/enigma-dev/blob/128d62949f988ef747f6926111fb11ae841558ad/.travis.yml#L17
You'll probably want to do a clean build, so I'd run [snip]make clean[/snip] first. Then you'll just want to run [snip]make emake[/snip] to build the C++ CLI. Once you've successfully built emake, instructions for running it can be found on the wiki.https://enigma-dev.org/docs/Wiki/Command_line_interface
In the future we can look at building a new debian package for emake. Right now my priority is getting an RGM beta out to start replacing LGM with it. RGM is not just a different IDE but builds your game using the same underlying tools as emake. In this way, an IDE like LGM or RGM is considered supplementary or optional.