Argh, I have seen the "ref not found" error before, hmm I think it has something to do with the entity.manifest

Did you replace the other ability or could you have forgotten to add the entity file to/change the entityNameCount in the manifest?

Well if you don't know what it is then you probably haven't added it and that is the problem, go to the install folder and then entrenchment, there should be a file named entity.manifest. When you add new entity files you need to edit this file or you will get this error. You won't have to convert it in order to open it, just use the program you normally use to edit txt files. It has to be placed in the mod folder where you have all the other folders. When you open it, it should be clear enough what you have to do.

The manifest file is basicly a register of all the files belonging to that manifest. So the entity.manifest is a register of the entity files and when you add new ones they have to be registeret in the file.

I am saying this from experience and not knowledge, so it might not be 100 % corect.

I've modified the manifest file, and placed it with my mod.  When I try to run it, it says that it can't find the files, and gives the same error message as before (in addition to the new error messages.)  Is there any particular format that the manifest has to be in?

EDIT:  Nevermind, I found the problem... I forgot to put .entity at the end of the file names.