I have Gist installed which has defined in it’s keymap file

{ "keys": "ctrl+k", "ctrl+l"], "command": "gist_private" },

Obviously, this overrides ST2 lowercase shortcut (Ctrl+k, Ctrl+l). I’m trying to understand how to best prevent this from happening. If I simply comment out the line in Gist’s keymap file, then that works until I do and Upgrade/Overwrite All Packages, which then overwrites the Gist default keymap file. If instead, I assign new definition in my Key Bindings - User file, the lowercase command still doesn’t work.

What is the proper way to handle these scenarios?

You can add lower case binding to your Key Bindings - User settings:

{ "keys": "ctrl+k", "ctrl+l"], "command": "lower_case" }

I’ve tried and it works fine. As I remember, when I start this plugin binding “ctrl+k”, “ctrl+l” was free.