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Reproduce with this:
<?xml version="1.0" encoding="UTF-8"?>
<p:declare-step xmlns:p="http://www.w3.org/ns/xproc" version="1.0">
<p:store href="file:/tmp/tmp.xml" method="html" version="5.0">
The doctype in the output is <!DOCTYPE HTML>. It should be <!DOCTYPE html>.
I believe this is a bug in Saxon. I've reported it: http://saxon.markmail.org/search/?q=list%3Asaxon-help#query:list%3Asaxon-help+page:1+mid:tg55l3ptubcysmdc+state:results
As replied in the saxon-help list, this is not strictly-speaking a bug: the HTML5 doctype is case-insensitive
Ultimately, the serialization is performed by Saxon so I'm going to close this without prejudice.