So you are on linux 
That is same …
You have to check structure of ET
your game folder must contain mp_bin.pk3 (for example /xxx/zzz/Enemy territory/etmain
/stilomod
/pb (punkbuster folder
then check parameter , must be +set fs_game stilomod (beware Linux is case sensitive)
try to rename mp_bin.pk3 to zzz_mp_bin.pk3
Make sure that .so files are not in another directory (pk3 must not have any other directory , for example there must not be /stilomod/xxx.so , but just xxx.so)
your problem is simple , you don´t have to pack your mod , it must be another folder (etmain is pure ET , so you will make new folder , it must be next to the etmain , in enemy territory directory , but it can´t be in etmain directory .)
you can try download mod and see how it works…