1. Boxed `File` and `FileSystem` to allow more easily passing this
through the CLI code (as shown within this pr).
2. `StdFileResource` is now `FileResource`. `FileResource` now contains
an `Rc<dyn File>`.
1. Adds cli/standalone folder
2. Writes the bytes directly to the output file. When adding npm
packages this might get quite large, so let's not keep the final output
in memory just in case.
