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Some of this has been discussed over in the Extras forum:

Depending on what you're doing with the OmniFocus data, you may find it easier to work with the OmniFocus AppleScript library (which can also be accessed via bridges from Ruby, Python and Objective-C, I think) than to program to the file format directly. That way you can let OmniFocus deal with the nitty gritty details of transaction ids and whatnot, while you code to projects and contexts.

We offer tech support for our AppleScript libraries and try to keep them backwards compatible with previous versions as much as possible. We will also try to answer specific questions about our file format, but don't have any plans to document it, and reserve the right to change it completely without warning in a future version.