%s refers to the test file in the source tree. This was accidentally added in
r351197 / 2b46d30 ("[OMPT] Second chunk of final OMPT 5.0 interface updates").
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LGTM, thanks for catching this!
The output is written to the build dir anyways:
runtime/test/lit.cfg:127
config.substitutions.append(("FileCheck", "tee %%t.out | %s" % config.test_filecheck))