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For EOS, please re-read the specification. If you then still think it is not needed, read it again :-) The documentation in liblzma is irrelevant, only the PKWARE specification matters. Take particular notice of the phrase "implementers should include the EOS marker whenever possible"
For bzip: propose a patch that does just the bzip stuff, and any infrastructure changes needed for it. Having the LZMA patch depend on this is fine.
Re: extensible compressors. I don't think that's needed. There is only a finite set, and if somebody wants to support some compression method, they should submit a patch.
Re: allowZip64. This depends on whether you create or extract. Not using a feature on creation is fine - we don't *have* to use all supported features. On extraction, if a feature is used and we support it, it should get used regardless of any configuration (note: I didn't check what allowZip64 currently does).
Re: 7zip. What it does is irrelevant. The ZIP format is defined by PKWARE, so if you want to look at a reference implementation, use theirs. Else use the spec.