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I've been having a similar issue with mkdocs which uses bootstrap by default. 

mkdocs is a static document generator that is based on markdown: 

I've been trying to setup a new github pages setup and I get the same conflict.

You can see it here:

Both the bibbase menus don't work and the bootstrap header is rendered incorrectly.

mkdocs allows theming. Switch to a 'material` theme and the problem goes away. I'm guessing it is some bootstrap related CSS issue.