fate: use do_md5sum instead of the md5 protocol for most md5 fate tests

fate: use do_md5sum instead of the md5 protocol for most md5 fate tests

The md5 protocol has no seek support, but some tests use seeks. This changes
the fate tests to actually create the output files and calculate the md5 on the
written files, which also makes the tests independent of the size of the output
buffers and output buffering in general.

A new md5pipe fate test method is also introduced to keep the old functionality
for tests where using a non-seekable output was intentional, and matroska md5
tests are changed to use that.

Signed-off-by: Marton Balint <cus@passwd.hu>