feat(cli)!: rename -s to -sc for --max-supercluster-size (#233)

[TimD1-bot]

Note

Authorship: the content below was drafted by Claude Opus 5 (an AI coding agent) and
filed via gh under @TimD1-bot, a bot account operated by @TimD1. It reflects the
agent's analysis, not a statement authored by @TimD1.

Resolves #233. Part of #47.

Warning

Breaking, user-facing CLI change. Any existing command line passing -s to vcfdist now
fails; see below.

Targets dev directly — the branch is rebased onto dev and carries a single commit.

Change

--max-supercluster-size moves from the short form -s to -sc.

Before	After	Long form
-s	-sc	--max-supercluster-size

-sc matches the multi-character convention already used by -sv, -mq, -ct and -ci. The
point of the move is to free the mnemonic -s for the stratification flag added under #47 — a
short form cannot mean two things at once.

Only the short form changes, so the long form still works, and the prose references to
--max-supercluster-size in src/cluster.cpp:580,977,1010 and the validation message at
src/globals.cpp:409 all still read correctly and are untouched.

No -s alias is retained

Deliberately. A silent alias would let an existing -s 15000 invocation be reinterpreted as a
file path once -s means stratification — a confusing failure at best, a wrong run at worst.
Bare -s now falls through to Unexpected option '-s' and exits 1, so an old command line
fails loudly instead of being silently reinterpreted.

Testing

• ParseArgs.SuperclusterOk and ParseArgs.SuperclusterTooSmallErrors retargeted to -sc, as
  was the -l 200 -sc 100 case in ParseArgs.SuperclusterLtMaxSizePlus2Errors.
• New ParseArgs.SuperclusterBareSDashRejected pins bare -s as rejected, so the no-alias
  decision cannot be silently undone.
• New ParseArgs.SuperclusterLongFormOk pins the long form as unaffected by the rename.
• PrintUsage.ListsDocumentedFlags now requires the usage text to advertise
  -sc, --max-supercluster-size.
• Integration: test_max-supercluster-size_sc-short-form-accepted runs the swallowed_snps
  fixtures with -sc 20000 and pins counts identical to the default-flag run;
  test_max-supercluster-size_bare-s-rejected runs the same invocation with -s 20000 and
  requires exit 1 with Unexpected option '-s'.

Verified locally on a clean rebuild of the rebased tree: 777/777 unit tests pass, 124/124
pytest cases pass (122 before, plus the two new integration cases). -Wall -Wextra builds of
src/ and tests/unit/build/ produce no warnings, and doxygen src/Doxyfile reports none.

Blast radius

No in-repo caller passes vcfdist's -s; the only occurrences were the unit tests updated here.
No documentation under docs/ or README.md mentions the flag.