CRAP: command input, interaction and system output branches

Purpose

Burn down part of the coverage-based CRAP list from #3414.

Function	CRAP	CC	Coverage
`src/commands/cli-grammar/common.ts:227` readJsonObject	30	5	0%
`src/commands/interaction/index.ts:619` run	35	8	25%
`src/commands/interaction/runtime/settle.ts:249` sessionBaseline	30	5	0%
`src/commands/system/output.ts:67` formatAppleAppState	42	6	0%
`src/commands/system/runtime/system.ts:448` normalizeAlertWaitResult	30	5	0%

settle.ts and system.ts were recently moved by the daemon-extraction work (#3394), so start from current main.

Every function above is absent from pnpm check:coverage-crap --all on the PR head (score < 30), or is exempted where this issue says so.
Tests go through the owning module's public entry point. No new production exports for tests and no test-only DI (docs/agents/testing.md).
Only the owned files, the tests that exercise them, and *.fixtures.ts helpers change. The PR stays under the 1,000-line gross budget, and pnpm check:affected --run passes on the pushed head.

Part of #3414.

test(commands): cover gesture, settle-baseline, appstate, alert-wait,…