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I have successfully created a user defined language file in Notepad++ and this file has formatting, highlighting, etc.

What I am hoping to do however is tie these into the main theme is. But it looks like each of these are defined separately (see \Notepad++\themes*.xml files).

Is there a good way to incorporate a custom language into these? Or is my only bet to write a script to merge the userDefineLang.xml with the themes?

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You can copy the style you want from the file stylers.xml and modify it into your own style. It is located in C:\Users\yourUserName\AppData\Roaming\Notepad++\stylers.xml

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