Pass options to transformers

This PR exposes the options sent to `module-deps` to the transformers. It does so by assigning the `module-deps` options to a `_flags` property on the transformer options. 

The motivation for this PR is to make the bahaviour of transformers configured via `package.json` similar to that of transformers configured via CLI or scripts: in the `browserify` toolchain the later two methods of specifying a transformer (CLI and scripts)  will attach the `_flags` property to the transformer options ([here](https://github.com/substack/node-browserify/blob/adacea35f76d0a8645cc001752472c98fcdb6c60/index.js#L261)), but transformers specified in the `package.json` do not.