I am trying to manually code some changes into my SharePoint Site Template. I can get the stp/cab file open and have added a new Element to the manifest.xml file, but when I repackage the stp and load it onto the server - the new site that I create using the updated .stp does not reflect the new link that I have added to the manifest.xml
I realize this isn't the proper way to add a link to the sidebar but am interested to make it work this way, for other reasons.
I've never been able to get modifications of STP files to work correctly. The combination of complexity in the STP file and that the solution is very unlikely to be supported by Microsoft means this is going to be a tough road.
You really should look at using a feature-based approach to do this (just web search 'sharepoint feature' for more info). This will give the benefit of not having to hack STP files and being 100% supported by MS and the rest of the SharePoint community.
Perhaps you could update your question with the other reasons you'd like to do this?