Properly handle triple slash reference paths directives in output

I tried importing:

```ts
import * as test from "https://esm.sh/stripe?target=deno";

console.log(test);
```

And got a bunch of type errors about declaration files not existing in stripe.d.ts:

```
npm/src/deps/esm_sh/stripe.d.ts:58:22 - error TS6053: File 'V:/stripe-test/npm/src/deps/esm_sh/Mandates.d.ts' not found.

58 ///
```

...it seems `/// ` directives are not handled? Need to investigate.

There are also some issues with node name collisions here. Also, in order to import I had to fix https://github.com/kitsonk/deno_cache/pull/2