cannot clear tags from search filter

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I did the pip upgrade so as far as I know everything is exactly as from upstream, except for our theme which didn't change.

hmm, I see, but theme in askbot did change, javascript changed and some stuff in the templates, that is why I recommended using git if you intend to customize the skin. Also - do you have staging environment? - A very good idea, because it allows you to roll back easily in the case something does not work out, staging database is also very handy. I know, not very simple business... but you need to take precautions with an active public site.

Have you done changes in the template files or it is only css?