The in-tree ML-KEM-768 was round-3 CRYSTALS-Kyber mislabelled "FIPS 203" and
was NOT interoperable with a compliant ML-KEM. Discovered and fixed by
validating against OpenSSL 3.5's FIPS 203 ML-KEM-768 as an oracle.
Three deviations, all fixed in src/zupt_mlkem.c:
1. Matrix  transpose convention. FIPS 203 K-PKE.KeyGen samples
Â[i][j] = SampleNTT(XOF(ρ, j, i)) and K-PKE.Encrypt uses (ρ, i, j); the
code had both index orders swapped. It was self-consistent (encaps/decaps
round-tripped) but transposed vs the standard — which is exactly why a
self-consistency-only round-trip test never caught it. With the same seed,
keygen now produces a byte-identical ek to OpenSSL.
2. Shared-secret KDF. FIPS 203 returns K = G(m‖H(ek))[0:32] directly; removed
the round-3 final K = KDF(K̄‖H(c)) step (encaps + decaps success key).
3. Implicit rejection. Now K̄ = J(z‖c) = SHAKE256(z ‖ full-ciphertext) instead
of the round-3 KDF(z‖H(c)).
Validation (tests/test_mlkem_fips203.sh + mlkem_fips203_harness.c, wired into
make check): against OpenSSL 3.5 ML-KEM-768 —
- deterministic keygen (same d‖z seed) -> byte-identical ek
- our encaps -> OpenSSL decap: shared secret matches
- OpenSSL encap -> our decaps: shared secret matches
The harness feeds a fixed random stream (MLKEM_RAND) so the FIPS 203 seed is
reproducible; the test skips gracefully without an ML-KEM-capable openssl.
BREAKING: --pq / --pq-only keys and archives from <= 4.2.1 no longer decrypt
(the KEM math changed). Regenerate keys and re-encrypt. Password mode and plain
compression are unaffected; wire format stays v1.6. make check 16/16.
