The mod system has changed a bit. User installed mods are not per game anymore. Install them in:
For windows builds and run_in_place linux version that is:
and for globally installed linux versions (create if needed):
The mods are enabled per world (disabled by default to not screw up already existing worlds). So, if you install a mod you need to go to the "Configure" window for the world in the singleplayer tab and enable it there, or, write this to world.mt:
This system will be used in 0.4.7, so if you update make sure to move all your mods from mods/<minetest, survival, build, whatever gameid>/ to mods/
Games are not affected by this change.