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I am using Windchill PDMLink Release 11.0 and Datecode with CPS M030-CPS11
1.API to create reference doc for on doc ojbect.
2.API to get reference doc by doc version.
2.1 get all version for one doc.
2.2 get referenc doc for each version doc.
Is there a specific question here? For your install, please see Java API
Windchill/wt/clients/library/api/index.html
All your points are searchable on the PTC Knowledge Base and are answered. Try to search it.
https://www.ptc.com/en/support
PetrH