Simple bat file that resets all your perks that you can get by leveling so you won't lose perks from magazines and such. And second bat file that you need to edit yourself for adding perks.

Installation:

• Unzip to game directory (eg. where Fallout4.exe resides)
• Edit addperks.txt as desired
• Execute "bat" commands in the game.
• ???
• Profit.
  

The file that gives you perks must be edited by yourself. The way I go about it is something like this :

• Check your current level and subtract one for number of perks available.
• Plan your special points remembering that you have 21 points to work with + 1 point from "You are Special!" + every bobblehead you got already.
• Delete ; before all perks that you want. To keep track of requirements I suggest you to use online planner (like this) to get them right but keep in mind your current  level because if you add additional special points it will show wrong level thinking you used perk points to increase them.
• Launch your game, load your save and run this two commands in console:
  

• bat resetperks
• bat addperks