dh_md5sums is a debhelper program that is responsible for generating a DEBIAN/md5sums file, which lists the md5sums of each file in the package.
All files in DEBIAN/ are omitted from the md5sums file, as are all conffiles (unless you use the --include-conffiles switch).
Include conffiles in the md5sums list. Note that this information is redundant since it is included elsewhere in debian packages.
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