Adds permissions for many of the commands that were previously missing them.

Argument: All commands should be at the discretion of the server operator to assign.

Adding these permissions adds some inconvenience to the server operator when assigning them (commands with sub-permissions must have the "main" permission for that command to work), but gives more control. For instance, this player has zero WorldEdit permissions, but sees this screen upon using /help: 
![we-pre](https://f.cloud.github.com/assets/931325/915367/7078bef8-fe68-11e2-965e-a11149d24a65.png)

Following this pull request, that same player sees this screen upon using /help:
![we-post](https://f.cloud.github.com/assets/931325/915372/861ecfa4-fe68-11e2-8cc6-7989b11cf093.png)