The canonicalization does not change the signed xml document. C14N happens during calculating digests or signatures and the result is never written back. Thus canonicalization could not make this change ---> \x0D\x0A.
The only idea I have for you is that you have problems with saving
the file (i.e. when you calculate the digest, it is calculated against
but when you save it, the entities are converted to \x0d\x0a).
Please try to sign your file with xmlsec command line utility. Try "--print-references"
(for 0.0.15) or "--store-references" (for 1.x) option and check *what*
was signed by xmlsec1. Also it might depend on libxml2 version
used. Try the latest version.
Aleksey
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