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I think we can simply change the path to the assets and point it to the template/assets_ on the root folder - instead of {{root_path}}assets_/css/main.css we would use something like ../../template/assets_/css/main.css.
the ideal option would be to add new setting to mdoc to avoid copying the assets folder, but I can totally live with a non-optimal approach specially since mdoc source code is such a big mess... (I coded it in a few hours over a weekend and after that I only monkey-patched new features as needed).
this change will also require some sort of metadata on the HTML to set which version tag to use on the "source" and "specs" links (since the content of the files changes quite often) - I would probably add something to the body element like VERSION_TAG = $('body').data('versionTag') || 'master'
will be easier to make changes across all files.
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