refactor: reorganized exports and removed obsolete helper branches

- Removed export leakage by demoting many helper and const symbols to module-local scope.
- Renamed underscore-prefixed internals and cache fields, then updated related references and `satisfies never` checks.
- Deleted obsolete logic branches and helpers, including harmony-stream interruption flow and unused benchmark runtime helpers.
- Updated Biome config and manifests by broadening lint coverage and removing an unused `@napi-rs/cli` dev dependency.
- Adjusted tests and utilities to use renamed test helpers and remove redundant private test-only helpers/locals.

packages/coding-agent/examples/extensions/plan-mode.ts

@@ -334,7 +334,6 @@ export default function planModeExtension(pi: ExtensionAPI) {
 		}
 
 		// Remove any previous plan-mode-context messages
-		const _beforeCount = event.messages.length;
 		const filtered = event.messages.filter(m => {
 			if (m.role === "user" && Array.isArray(m.content)) {
 				const hasOldContext = m.content.some(