feat(cli): skip public-API generation for hand-written contracts

[Chase J (chajac)]

Overview of Changes

The public-API command generator mints one CLI command per contract in @qawolf/api-contracts. The flow.list contract (new in 0.2.0) is already served by the hand-written qawolf flows list --remote, so generating it would create a duplicate command surface for the same endpoint.

This adds a skip mechanism: buildCommandSpecs accepts a skipContractNames set, and the composite root declares handWrittenContractNames (currently flow.list) in src/commands/publicApi/index.ts. Skipping happens before spec building, so a hand-written contract never needs to be expressible as generated flags, and no empty namespace group command is created. AGENTS.md and the domain structure rule doc now document the skip list as the mechanism behind "never register the same endpoint both ways".

Testing

bun run typecheck
bun run lint
bun run format:check
bun run knip
bun run test
bun run build

New coverage: commandSpecs.test.ts proves a skipped contract produces no spec (using an intentionally flag-unmappable input to pin the skip-before-build behavior), and commands/publicApi/index.test.ts proves a flow.list contract in the tree registers no flow command while siblings still register.

Checklist

• Changes follow the code style of this project
• Self-review completed
• Tests added/updated (or not applicable)
• No breaking changes (or described below)

[coderabbitai]

🚥 Pre-merge checks | ✅ 4

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title follows Conventional Commits, uses an allowed type and scope, and clearly describes the skip behavior change.
Description check	✅ Passed	The description matches the template with overview, testing commands, and a completed checklist; the optional issue link is the only missing piece.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch generator-skip-list

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