You can decompile the class files with the option add line numbers as comments and you will be able to realign the code with JD-Eclipse, see: http://mchr3k.github.io/jdeclipse-realign/
You won't be able to decompile with line numbers if the class files are compiled with the flag -g:none
:
-g:none
Do not generate any debugging information.
Also see: Eclipse skipping lines while debugging