This is why I have my own routine to install stuff...

• unzip to a "dump" folder with a fake runtime in it. I have one for V4, one for A3, etc... but that's only because that's how I arrange my runtimes.

• delete/dump any and all "readme" folders (save for those things that actually need one), dump any and all templates into their own universal subfolder.

• open my dump runtime on one side, my destination (real) runtime on the other.

• copy/merge in "Geometries" and "Textures" wholesale. Move any morph/inj folders over as needed.

• Open "libraries" on both sides. I'm usually lazy, so I copy/merge over "camera", "face", and "Lights" wholesale.

• I then go in and maunally sort out the "character", "pose" and "props" folders. 

Meanwhile, I make regular backups of my runtime folders (all of which are under a folder called "runtimes"), and can dump them in wholesale or in part from backup, to any machine I care to. I use rsync (kicked off manually) for my backups, so any changes that I make locally (adds, deletes, and moves), are automatically made on the backup copy. 

Doing this, I've managed to keep a coherent Runtime structure for literally a decade now. What I now call "old-runtime" was the original one, with files I installed just about 10 years ago. These original files have sat intact on Windows, Mac, and Linux boxes, and have been transferred back and forth quite a few times.

I think there was only one problem I had run across early on, which had arisen from a USB backup disk being squirrelly, but I was able to recover the files before the HDD had completely went splat. Otherwise, if I load Dork into my shiny new i7 laptop, it's the exact same file that I originally installed a decade ago on a Gen1 Pentium4 1.7MHz box w/64 MB of RAMBUS (puke).