Right now what we have is a reverse engineered clone of the pathfind generation that is (at least assuming there are no bugs left) producing valid correct usable output that matches the output of the original Westwood code in all the places that matter. And we have the same thing for the vis generation but its full of bugs that we are still in the process of fixing and is 100% not usable as of right now (to the point where using it guaranteed to produce bad output assuming it doesn't crash first).
Note that pathfinding in Mammoth can't be canceled in the way it can with Leveledit so you will need enough pathfind blocking objects to ensure it is able to complete without running out of memory.
We haven't really made any improvements to the pathfinding or vis generation yet (well there is one improvement in that if you proxy in a ladder transition object, it will now get proper action portals and bots will use that ladder). What happens in terms of improvements to that stuff will depend on what Neijwiert (the genius who did most of the work around pathfinding) ends up implementing.
As for a UI that can edit the sky colors, that's not as easy as it sounds unfortunately. Maybe in the future I will look into it but right now the priority is to get all the things done that need to be done before we can completly drop LevelEdit for good.
In terms of dependencies, what you need to do is to open Mammoth (assuming the version you are using is new enough) then open your level and choose "edit-include files". Anything you add to the list in there will be included in the mix file automatically when you use "export to mix" or "run game" or whatever). The list itself is stored in the .lvl file.