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We discovered that the "missing ID issue" is also related to the circular references. Cleaning the entries removes the "sys" part of existing entries, which causes original entries to exist without ID. So, solving the issue mentioned above will lead to the error about the missing ID, eventually.
We solved it for now by deleting the circular references from the data before anything else happens, using a function in the config. We cannot use manipulateSingle for this, since the clean function gets invoked before that one fires. So, we introduced a new function: manipulateEntries. See our PR.
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