The plugin was never designed with this intention. The perm based trees were designed for servers that wanted to restrict the tree based on external factors.
If you are wanting a progression system, you would be better off adding the skills to "Skill required to unlock node [Requires max level]".
Like this:
"Braided Line": {
"Permission required to show this node": null,
"Minimum prestige required to unlock this node": 0,
"Skill required to unlock node [Requires max level]": "Harvesting Tree",
"Skill that if unlocked, will prevent this node from unlocking": null,
"enabled": true,
"max_level": 5,
"tier": 1,
"value_per_buff": 0.07,
"buff_info": {
"Key": "Rod_Tension_Bonus",
"Value": "Percentage"
},
"icon_url": "https://www.dropbox.com/s/p3rkfmoay0tglpz/Warriorskill_38_nobg.v1.png?dl=1",
"skin": 3012306483,
"permissions": null
},