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I have spent about 30 minutes now looking through the docs and searching plugins about theming and changing the CSS. I can't believe that there isn't a plugin that covers this task.
I saw ' A Quick-Start Guide to Creating Themes for Vanilla' and get the principals behind it and making into your own theme and editing a custom CSS. but it occurred to me that that creating a whole new custom theme seems a long way round for some one who just wants to tweak a theme for some basic color changes to blend in with site branding. Background colors, Header text color, text color, link colors etc.
I haven't the skill set to create one myself but it seems there is an opening there for someone who does?