To upgrade your Thunder module you should copy the .zip file (that you downloaded) from your local machine to your remote server (where is installed your Sitefinity project, that you want to upgrade). You should execute step 5 from the documentation in your remote server. You should extract the .zip inSitefinityWebApp folder (as described in step 5 from the documentation).
Do not hesitate to contact us if you have any additional questions.
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