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The shortcut of Npp is complete customizable by GUI or XML, but there are some problem:
If change/add/remove shortcut by editing the XML file, one of the problem is that it's hard to findout the corresponding id or internalId, and changing key code directly is somewhat inconvenient than editing key character or its alias.
If change/add/remove shortcut by editing from the config menu, you'll find this one is rather weak, it can't search by command name, can't search by shortcut, can't even tell wether you newly set shortcut is conflict with others or not. You know that only after you pressing the shortcut and something you didn't expected happened.
You can at least search https://sourceforge.net/apps/mediawiki/notepad-plus/index.php?title=IdeaTorrent_Summary#Main_section for one of the multiple ideas concerning the Shortcut mapper, and vote for it.
You can even provide a patch to implement the much needed enhancements.
Cool, I hope one of them can be implement soon