Versions 1.0 and 1.1 are based on the same core, including the storage backend and most of the XQuery engine. However, 1.1 features a brand new indexing scheme at its heart, which represents a major technological switch and removes some limitations eXist had up to this point: in particular, the new indexing scheme drops the previous document size/complexity limits and offers faster node-level updates via XUpdate or XQuery update extensions.
XQuery standard conformance improved to about 92.7% according to the W3C's XQuery test suite. eXist now passes 13,569 out of 14,637 tests for the 1.1 release (XQTS 1.0.1).
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