Hi Rodney,
I agree, it's a pain trying to get all the stuff from websites - it's impossible to get a consistent set of progs. I recommend buying the Schatztruhe 3xCD set of "The Amiga Unix Compendium". It has everything on it, although some apps are a little out of date, but you can get later versions from GNU.org and compile them.
Although AmigaOS doesn't support some Linux stuff, it just ignores it and doesn't screw it up either. So if folder permissions are wrong, you can easily change them with "chmod -R 755 xyz". I don't remember getting that error when ratting (that's the opposite of tarring).
As far as symlinks go, the GG distro creates a few - not as many as kaffe or some big progs like that. They appear to AmigaDOS as a directory that doesn't work - can't be opened. Latest AOS apps (like 3.9 stuff) either ignore them or do the right thing, I'm not sure which. Earlier apps (like DirOpus 4) show them as dirs that can't be opened, and screw up when you try to copy them. I haven't found any Amiga-side apps that can correctly copy *nix-style symlinks. So you can't make a copy of the GG: directory tree with AmigaDOS, or a backup, etc. It has to be done with "cp" under GG:
GG is not a fun system. Also, it's an emulator, so you've got AmigaOS running an emulated version of BSD running your program. It's slow. It's easier to install m68k Linux on its own partition, and use that. At least it runs 3-5 times faster (on my 060/50, anyway).
tony