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Fix #394: in-frame stop-codon deletion with empty 3' UTR is a Deletion (#395)

* Fix #394: in-frame stop-codon deletion with empty 3' UTR is a Deletion

An in-frame deletion that removes the stop codon of a transcript with no
3' UTR sequence (e.g. MAPK3-006 / ENST00000395199, whose
three_prime_utr_sequence is "") raised:

    ValueError: If no amino acids added by StopLoss then it should be Silent

translate_in_frame_mutation sets using_three_prime_utr=True whenever the
mutation runs past the reference stop codon, even when there is no UTR
sequence to translate into. predict_in_frame_coding_effect then took the
StopLoss branch with an empty aa_alt, which the StopLoss constructor
rejects.

Only emit StopLoss when readthrough actually adds residues (n_aa_alt > 0);
otherwise fall through to the existing n_aa_alt == 0 branch, which reports
a C-terminal Deletion. This is the honest classification: with no UTR
sequence we cannot predict an extended protein.

The earlier #246 fix only covered transcripts with a non-empty 3' UTR.

Tests: the reported MAPK3 variant exercises both sides from one input —
ENST00000395199 (no UTR) -> Deletion, ENST00000403394 (804nt UTR) ->
StopLoss readthrough — plus a splice-free unit test of the branch.

Claude-Session: https://claude.ai/code/session_0149VWj5Rm1rYFf9azu4ry62

* Also fix protein_diff classifier + bump to 6.0.1

The default annotator (protein_diff -> classify_from_protein_diff)
independently mislabeled the same empty-3'UTR stop deletion as a
PrematureStop ("p.G355*") on a clean in-exon variant. That's wrong: the
mutant CDS contains no stop codon at all — the protein simply runs off
the end of the available sequence. A PrematureStop requires a stop codon
to exist.

Guard the PrematureStop branch so it only fires when the mutant
transcript actually terminated at a stop codon (i.e. translation did not
consume every available codon). When translation ran off the end, fall
through to the C-terminal Deletion classifica... (continued)
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