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Some of the linux specifics stem from the idTech 4 (aka D3) engine way of doing things and we couldn't change some of them w/o access to the source code. However, now that we have merged the D3 GPL source and our source, there where already number of improvements done for v1.08 (done by taaki, and Serpentine):
The installation now only needs one directory /home/username/.doom3/darkmod/ and all the FMs are only under /home/username/.doom3/darkmod/fms/ and no longer copied on "install". The mod itself also does no longer restart to install/uninstall a mission, it just reloads all the assets. This fixes issues with duplicate files and directory confusion.
Also, symlinks work just find, you can f.i. put everything into: /home/username/foo/darkmod/ or wherever you like, and put symlinks like these:
lrwxrwxrwx 1 xx xx 36 2012-08-14 23:11 pak005.pk4 -> /home/xx/games/doom3/base/pak005.pk4
I know this works, because I'm using it on my system
When TDM goes stand-alone, even these symlinks to the D3 PK4s will go and everything should be self-contained inside one darkmod/ directory, which you can place wherever you like.
=> I reported all this text from user "Tels" from DarkMod Forum. Tels it's a great contributor to the DarkMod project.