Implementation Notes: Issue 45 Packaged CLI Script Runtime

Summary

Added a shared runtime helper for generated JavaScript maintenance scripts so Bun-packaged CLI installs do not use the packaged CLI entrypoint as the child script runtime.

Changes

• apps/cli/src/runtime/scripts.ts exposes runJavaScriptFileSync.
• apps/cli/src/scaffold/output.ts uses the helper for generated .agents/scripts/sync-subagents.mjs.
• apps/cli/src/update/run.ts uses the helper for staged wiki scripts/sync-content.mjs.
• apps/cli/src/update/run.test.ts adds a regression test for packaged Bun CLI entrypoint behavior.
• docs/README.md, docs/runbooks/dp-cli-scaffolding.md, and routed debt/spec docs record the operator contract.

Validation Evidence

• RED: targeted host-runtime regression failed before the helper because process.execPath pointed at a fake CLI entrypoint.
• GREEN: bun run --cwd apps/cli test src/update/run.test.ts --testNamePattern "host runtime"
• GREEN: bun run --cwd apps/cli check-types
• GREEN: bun run --cwd apps/cli check
• GREEN: bun run --cwd apps/cli test src/update/run.test.ts
• GREEN: bun run apps/cli/src/index.ts update --check --baseline bundled --json
• GREEN: bun run --cwd apps/cli build
• GREEN: git diff --check
• GREEN: bun run --cwd apps/cli test src/update/run.test.ts src/scaffold/run.test.ts
• GREEN: bun run apps/cli/src/index.ts update --check --baseline stable --refresh-baseline --json reaches normal managed scaffold drift and includes react-doctor expected changes instead of throwing a missing baseline asset error.
• BLOCKED: built executable update checks still fail while executing generated sync-subagents.mjs.

Manual Review Checklist