chain-spec-builder: Add support for `codeSubstitutes` (#4685)

While working on https://github.com/paritytech/polkadot-sdk/pull/4600 I
found that it would be nice if `chain-spec-builder` supported
`codeSubstitutes`. After this PR is merged you can do:

```
chain-spec-builder add-code-substitute chain_spec.json my_runtime.compact.compressed.wasm 1234
```

In addition, the `chain-spec-builder` was silently removing
`relay_chain` and `para_id` fields when used on parachain chain-specs.
This is now fixed by providing a custom chain-spec extension that has
these fields marked as optional.