If it's running it's working. Complex files will take more time to process than simple ones. Just let it run until it completes. Some users have been known to have days processing highly complex files.
Any linked files will be included when generating a zip. The links in the file will be followed and I believe links in those files will be followed as well. So just adding the Singleton.html file will could cause the entire manual to be included in the archive.
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