When reading a DiffX file using the DOM and then writing it back out,

the contents of the file would change. Since DiffX files are intended to

be a mutable format, we don't want to make any unwanted changes.
There were a few problems leading to this:
1) When reading into a file into a DiffX object, default options would

   be preserved. This is really a problem for the main encoding

   option, which would default to UTF-8 if missing in the DiffX file

   content, and would then be written back out. Now, options are cleared

   out before they're set.
2) Similarly, if an explicit main encoding value wasn't provided, the

   default in DiffXWriter would be used. We now explicitly pull out

   the encoding option, defaulting to None if not found in the file,

   and pass it in to DiffXWriter.
2) DiffXWriter was hard-coding the version being set, and the DOM

   therefore wasn't setting a version when writing. Now it will accept

   a provided version. While not important right now, this will be

   important for compatibility with future spec versions. It's up to

   the caller to ensure the version being provided is valid.
Unit tests were added to ensure that we now get byte-for-byte results.

Unit tests pass.