They are located in "tests/ref/".
I've had to change the Makefile target names for some tests, which also changes the filenames of the generated files.
Therefore, the reference files can't simply by updated by "make fate GEN=1", have to be renamed as well.
In order to stay git patch compatible, here's what you do:
Remove the old reference files:
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$ git rm tests/ref/previous_ref_filenames
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$ make fate GEN=1
$ git add tests/ref/*