Question.

4 hours ago, IlIDestroyerIlI said:

so each skill has this section           "permissions": null 

is this a permission that is required or is it a permission that is granted when a player gets the skill ? 
can we edit this ? 

It gives permissions.

You can add an example to your config that shows you how to do it by typing addtestpermsnode into your server console. This will create a new skill under Cooking called "Test perms node" which will be disabled by default.