markdown reference links in comments

In proto comments there are a lot of markdown reference-style links:

```markdown
// [Secret][google.cloud.secrets.v1.Secret]
```

They won't work in JSDoc, so I suggest that we replace them with JSDoc-style links:

```js
/**
 * {@link google.cloud.secrets.v1.Secret|Secret]
 */ 
```

These replacements should happen in the templates and not in the code.