Thanks all for the unanimous answer to the checkin question, and to Larry Rowland for the following comment.
In terms of tracking the production system used, we use a versioned production system (based on Ant build files and some extensive customizations of the standard DocBook transforms) and embed an HTML comment in each HTML result file that identifies the version of the transform tree used. The transform tree is in a separate Subversion repository, so it can easily be rolled back to any specific version if questions about the production environment come up.
If you have any specific questions about this, feel free to contact me directly.
Very helpful!
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