I've forked the Kibana codebase and messed with colors.less and a couple other less files around that one to create a custom theme.
Obviously that carries with it a bunch of things like merging when versions update. I'm exploring the ability to create a simple plugin that overrides the variables in the less files. You can also use the plugin simply override styles (much like you do with bootstrap).
"this" being creating a plugin that overrides styles?
I just figured that the css that spits out of a plugin is added to the global css file (like all css) and being there you could literally change anything as long as you select specific enough or use the dreaded !important flag.
I haven't tried it yet, but in theory it's possible? Actually would be a cool public plugin for people, where they can customize the look via the plugin and keep their hands out of kibana core '
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