Customizing the names list and whitelist used by the Auto Rename System is fairly simple. This article will show you how.
I will note here in the beginning for the TL;DR crowd. If you modify this file during a live game, you will need to rebuild the data arrays using the Advanced menu of the settings holotape, craftable at the chemistry station under utility. Once the Auto Rename System has grabbed and processed an NPC, it is never processed again. (technical: a faction is applied so our alias fill condition ignores them) If you add whitelist names and want this mod to recheck previously checked actors, there is an 'Ignore previously checked actors' toggle in the Advanced menu of the settings holotape. I recommend turning this setting off as soon as you think the added whitlisted NPCs have been renamed as it is wasting processing time grabbing and checking all actors loaded in the area.
First, everything is in an xmlx file, so you will need a program that can edit xmlx files. Excel and Google Docs can do this. Sadly, xmlx is not supported by Open Office.
After installing Rename Anything Enhnaced, you should find `MS Name Data.xmlx` located in `\Steam\steamapps\common\Fallout 4\Data\F4SE\Plugins\MS Auto Rename`
There are 4 sheets. Whitelist, BOS, Gunner and Names.
Names Sheet:
The Names sheet contains the names used by the Auto Rename System. The first row of all sheets will be deleted on import, so ignore it. The names are divided between male and female, normal and raider. I separated them so someone has the ability to create a unique list of raider names. I wasted much time flexing my google-fu and didn't find a list of names that would be appropriate, so the list is populated with weird and uncommon names. The common names was distilled from US Census data of common names used between 1920 and 1959.
Be aware that all names added will count towards the 64MS Script Property Data Limit. See Baka Scrap Heap for more information. (I wouldn't go much beyond 2000 rows)

Whitelist Sheet:
This sheet contains names used in the game we want to allow the Auto Rename System to rename. The position of a name within a column doesn't matter but performance will improve slightly if the most common names are moved toward the top. Any name from any mod can be added without dependency. This is imported as a string array and grabbed NPCs have their current name checked against it, so adding names that are not ever used wouldn't matter. (other than having an extra entry to search)
Normal Column:
A 'Normal' whitelisted name will be renamed using the 'Male' and 'Female' names from the Names sheet.
Raider Column:
'Raider' whitelisted names will be renamed using 'Raider' names from the Names sheet.
Synth Column:
Whitelisted names in the 'Synth' column will have a randomly generated name applied. These will be in an 'A1-23' format. (prefix used are: A, B, F, H, K, X, Y and Z followed by 3 random 0-9 digits) This follows the naming of named synths found in the vanilla game files. This is hard coded in the script, so I would have to create a system to handle it if someone wanted a separate name list for synths.

BOS and Gunner Sheets:
I separated these out to give the renamed NPC a title like Knight Bob and Private Fred. You can add to these if you want to give a certain generic named NPC a title when automatically renamed. The whitelist name must be indexed to the title name for this to work. If you leave the title blank, no title will be added as if added to the Whitelist sheet.
Note: Due to a Papyrus array length limitation, do not have more than 128 rows in either of these sheets. Rows in excess will be ignored during the import.

The Gunner Sheet works the same way.
So, hopefully I have properly instructed as to how this works. I guess if I failed, leave a comment. ;)
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