main.js was still carrying drift-prone mirrors of context, output, and scaffold helpers even after the earlier seam extraction. This cleanup switches the runtime onto the shared modules, removes dead stubs that were never wired into the command surface, and locks the concrete drift cases with focused tests.

Constraint: Keep setup/doctor/install behavior stable while deleting duplicate helper ownership
Rejected: Keep local mirrors in main.js | preserves help/gitignore/release drift across modules
Confidence: high
Scope-risk: moderate
Directive: Add future shared CLI helpers in extracted modules first, then import them into main.js instead of reintroducing local copies
Tested: node --check src/cli/main.js src/context.js src/output/index.js src/scaffold/index.js; node --test test/cli-args-dispatch.test.js; node --test test/cli-args-dispatch.test.js test/setup.test.js test/doctor.test.js test/install.test.js test/metadata.test.js; openspec validate agent-codex-dedupe-cli-main-context-output-scaffold-2026-04-22-14-29 --type change --strict; openspec validate --specs; npm test
Not-tested: gx branch finish / PR merge automation