Fix incorrect behavior when deduplicating meta-Diff Files

As a result of a recent prod regression, some incorrect code was exposed as a result of testing an untested code path.

We have almost all of the pieces necessary to add a unique ID for all diff files:

• A consistent commit for each diff
• A way to generate a unique ID for diff files (reverted)

To fix this incorrect test and prepare for a more reliable Diffs app, we should re-add the Unique ID and use it to correctly deduplicate files going through prepareDiffFiles.