refactor: generate tsconfig to .deno/tsconfig.json and reduce path mappings
Move generated tsconfig from `tsconfig.deno.json` to `.deno/tsconfig.json`.
Ensure root `tsconfig.json` exists and extends it. Only generate `npm:` and
`jsr:` prefixed path mappings -- bare aliases and glob variants are
unnecessary since TypeScript resolves them via node_modules with bundler
module resolution.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>