bundle: Add support for merging and other improvements

This commit does a few things:

* Extend the low-level file loader and callers to ensure ModuleFile
objects have a URL field. This means we can tell if two ModuleFile
objects refer to the same source file. Previously we had to keep track
of bundle names to do this. This commit does not touch the bundle
activation logic which does this already--we can revisit that in the
future.

* Update the bundle writer to use the URL field by default. This
allows us to write merged bundles correctly.

* Add a merge function that will be used by the new build command to
combine multiple bundles.

* Add a helper function for checking if roots contain a path. In the
process refactor the overlap helper to use the same logic. Also add a
helper function to ensure roots exist in the bundle manifest.

* Add a deepcopy function for bundles. This is useful if mutating
  bundles and there is a need to revert.

* Format bundle contents on write by default. Callers of the old
Write function will not be affected (it disables formatting.)

* Format the overlap error to quote roots in case they are empty.

Signed-off-by: Torin Sandall <torinsandall@gmail.com>