refactor(schema): use Zod transforms instead of manual mutation

Replace manual result mutation in safeParseConfig/safeParsePartialConfig
with proper Zod .transform() methods:

- Add budgetSchema transform for string-to-number conversion (e.g., '10ms' → ns)
- Add budgetsSchema transform for nested-to-flat structure conversion
- Extract baseConfigProperties to avoid duplication between runtime and
  JSON Schema generation schemas
- Export ModestBenchConfigInput type for consumers needing the input shape
- Export partialModestBenchConfigInputSchema for JSON Schema generation
  (transforms can't be represented in JSON Schema)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Author: boneskull

scripts/generate-schema.ts

@@ -12,15 +12,15 @@ import { dirname, resolve } from 'node:path';
 import { fileURLToPath } from 'node:url';
 import * as z from 'zod';
 
-import { partialModestBenchConfigSchema } from '../src/config/schema.js';
+import { partialModestBenchConfigInputSchema } from '../src/config/schema.js';
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = dirname(__filename);
 
 const generateSchema = async () => {
   try {
     // Convert Zod schema to JSON Schema using native Zod v4 functionality
-    const jsonSchema = z.toJSONSchema(partialModestBenchConfigSchema, {
+    const jsonSchema = z.toJSONSchema(partialModestBenchConfigInputSchema, {
       target: 'draft-2020-12',
     });