I tried the utility method provided by luaj to call a lua file with command line args (this one http://lua-users.org/wiki/SourceCodeFormatter)
Globals globals = JsePlatform.standardGlobals();
String script ="src/codeformatter.lua";
File f = new File(script);
LuaValue chunk = globals.loadfile(f.getCanonicalPath());
List<String> argList = Arrays.asList("--file","test.lua");
JsePlatform.luaMain(chunk, argList.toArray(new String[argList.size()]));
However i always get attempt to call nil where the code tries to access the arg table ( while i < table.getn(arg) do) - i tried other examples and they all result in the same error - luaj does not seem to set the "arg" table correctly - even a simply print arg[1] will not work.
LuaJ does not support table.getn anymore because it got removed in lua 5.1 - replace every occurances of table.getn with #varname - and init the args array with ocal args={...} at the top made it work.
Still, the code formatter does not really do what i expected it todo