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If you are using Jive 6 or later, you can use the "basic theme” editor to change the favicon without customizing templates. Here are the high level steps.
Step 1: Click on Customize Your Site from your profile menu in the upper right. You must have administration rights to see the Manage links in this menu.
Step 2: Under Branding and Decoration, expand the Favicon option and upload your custom ICO file. Unfortunately, this approach only supports ICO at this time.
Step 3: Save your new basic theme and publish.
Bear in mind, since you are using a custom theme, you will get a warning about using both the basic theme and custom theme. Using both themes simultaneously is working for us as long as we avoid duplicating changes between themes.
Otherwise, there should be a template that you can add to your custom theme to replace the favicon. We did this prior to moving to Jive 6 and I can look into the name later when I get a chance.