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I liked the ideas of /conf and /user/asau. In addition /sys/info for list of devices and /sys/conf (I don't like it to be in /proc). I also think we should kill all that /usr/bin /usr/local/bin /usr/local/local/bin etc. Should be one /bin and one /apps or /app or /opt (though "/opt" should not be). In addition, it would be good to become able to create temporary symlinks in root directory like "/my" (-> /user/asau), "my0" ( -> /asau/TeX/src ) etc. One abbreviation of "~" is not enough (but Midnight Commander must die, for not to come into dreams at midnight, brrr). OTOH, I don't think there is necessity to separate /logs from /var. Are you going to look at logs so often? On your desktop computer?
If your program wants a library, it should have a place (in /conf/APPNAME/libs, /var/APPNAME/conf, /app/APPNAME/libs or somewhere else) to write associations like "libc --> /lib/glibc-X.XX.X.so" or save its libs in /app/APPNAME/lib/ . If you run out of space you can replace real /app/APPNAME/lib/libc with symlink to /lib/glibc-X.XX.X.so Nothing is more simple. If you don't want to package libc, place a hook: "Notification: Replace /app/APPNAME/lib/libc with symlink to glibc-X.XX.X or compatible. Application stopped." And don't forget to make link from /app or /desk (like a shortcut):
----
About installation and package managing... KILL ALL "DEB"-s and "RPM"-s! Why you need yet another packaging and compressing format?! All installation should be done the right way: mkdir /app/APPNAME; cd /app/APPNAME; tar xvfz /tmp/APPNAME-X.XX.X.tar.gz THAT's all. "TAR is all you need!"
cat >/app/start/APPNAME <<END
#!/app/APPNAME/EXECFILE
END
chmod a+x /app/start/APPNAME (Or even simpler: make a (sym)link!)
Just KISS. Nothing can be so simple. You get rid of all those dependencies in one moment.
BTW, Plan9 has nice feature to mount some different directories to one point (something may overlap, but this can be resolved).