Have you deleted the any of the pk3 files?
Here is how I do it:
1. Create a folder called "mymod" next to "baseoa"
2. zip the vm folder in build/release*/baseq3/
3. copy the zip file to mymod and rename the file to mymod.pk3
4. start the engine with "+set fs_game mymod"
This is the exact command use for the elimination mod (paths needs to be changed):
make && cd build/release-linux-x86_64/baseq3 && rm vm/vm.d && zip -r /mnt/winG/games/openarena-0.8.1/elimination/elimination.pk3 vm && /mnt/winG/games/openarena-0.8.1/openarena.x86_64 +set fs_game elimination +set debug 1 +set sv_pure 0
Explanation:
make // Build the qvm files
cd build/release-linux-x86_64/baseq3 // Go to the location of the vm directory
rm vm/vm.d // Useless file created on some systems
zip -r /mnt/winG/games/openarena-0.8.1/elimination/elimination.pk3 vm // zip the vm directory and place it in the mod folder
/mnt/winG/games/openarena-0.8.1/openarena.x86_64 +set fs_game elimination +set debug 1 +set sv_pure 0 // Run the game. debug and sv_pure is optional but useful
I think the script is included in the modSDK as "supermake"