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Editing map data outside of Editor

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I have an alpha tile in my map, but as shown in this thread, (Alpha Tile for Dummies) The order of the tiles matters. Unfortunately when I edit my tileset, units/doodads are deleted and the triggers related to those objects are as well. Can I just sneakily edit the tile order without these issues? Or is my best bet to just redo some terrain?
 
I think it is possible, but I don't know how.

Back in the day when JNGP was the go-to editor it was the only way to add tiles, and it was always added at the very end. I'd bet a small amount of money they could have put it anywhere. So if you dig into the source code for that, maybe you can find out how.
 
There is no public github for it, I think.

There is still a download in the hive tool section, a lot of the code is in .lua files so you can open them no worries.
There was also the hosted project WEX which replaced JNGP for a while. Not sure if the author is still active.

Another possible solution, ugly but maybe?
What if you juggle the tiles.

If I have the tiles added to my map in the following order:
A B C D E

and I want to replace B with a new tile, X.

Add X:
A B C D E X

Remove B
A C D E X

Remove C D E
A X

Add C D E
A X C D E
 
Use a hex editor. The custom tileset data is listed near the front of the w3e file inside the map archive/folder. It is loaded in order of implicit cliff associated tile types followed by explicit tile types with duplicates removed. There is no limit to how many can be defined here, however only the first 16 tile types and first 2 cliff types can be used due to other limits. Each tile type is a 4 character code, and they could be swapped around as required.

Technically up to 16 cliff types can also be used, however another internal limit means that meshes for only the first 2 work correctly in game, with all others repeating those or appearing square.
 
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