D5: Rename -s to -sc for --max-supercluster-size

[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.

Part of #47. A breaking CLI change, kept separate so it is reviewable and release-notable on its own.

Change

--max-supercluster-size moves from -s to -sc (src/globals.cpp:326, usage line at :486), so
the mnemonic short form is available for the stratification flag that #47 adds.

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

-sc matches the existing multi-character convention already used by -sv, -mq, -ct, -md, and
-ci.

No -s alias is retained

This is the point of the change. A silent alias would let an existing -s 15000 invocation be
reinterpreted as a file path once -s means stratification, producing a confusing failure at best
and a wrong run at worst. Rejecting bare -s outright makes an old command line fail loudly.

Blast radius

No in-repo caller passes vcfdist's -s. The three 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, since only the short form changes.

Testing

• The existing parse-args-supercluster-ok and parse-args-supercluster-too-small-errors cases
  retargeted to -sc.
• A new case pinning bare -s as rejected, so the no-alias decision cannot be silently undone.
• Integration: -sc accepted, bare -s rejected.

Release notes

Breaking and user-facing.

Depends on

Nothing. Can start immediately, and must precede the stratification flag — the short form cannot mean
two things at once.