chore: standardized code quality and formatting for tooling scripts

- Added `scripts/**/*.ts` to the linter and formatter inclusion list in `biome.json`.
- Replaced manual array index searches with standard `indexOf` operations.
- Cleaned up unused variables, obsolete helpers, and command-line flags.
- Applied consistent formatting and code style across tooling scripts.

scripts/trace-loader.ts

@@ -10,20 +10,20 @@ Bun.plugin({
 	name: "trace-loader",
 	setup(build) {
 		// Trace module resolution (doesn't interfere with loading)
-		build.onResolve({ filter: /.*/ }, (args) => {
+		build.onResolve({ filter: /.*/ }, args => {
 			// Skip if already traced this path
 			if (resolved.has(args.path)) {
 				return undefined;
 			}
 			resolved.add(args.path);
-			
+
 			const elapsed = ((Bun.nanoseconds() - startTime) / 1e6).toFixed(1);
 			// Only trace local/project files, not node_modules
 			if (!args.path.includes("node_modules") && !args.path.startsWith("node:")) {
 				const shortPath = args.path.replace(process.cwd(), ".");
 				process.stderr.write(`[${elapsed}ms] resolve: ${shortPath}\n`);
 			}
-			
+
 			// Return undefined to let Bun handle resolution normally
 			return undefined;
 		});