Change from unsigned to signed values for Strip

We use -1 as the default value for strip numbers, so we can't use unsigned ints.

It took me a bajillion commits and everything to get it this clean, since I was accidentally tracking a bunch of extraneous files, but the diff looks good now so I think it is fine to auto-merge.

I can verify this compiles but I have a seg fault on making an analysis tree right now.  Not sure if this is due to my changes (it is entirely possible I left a value somewhere as unsigned) or if it is deeper.