bundle: Fix for overwriting data file keys

This corrects an issue where data.json (or yaml) files in a bundle
would overwrite data if the file was at the root of the bundle
directory and was loaded after other data files.

This also helps avoid any issues with merging data files that
could have overlapped without any problems.

Fixes: #1763
Signed-off-by: Patrick East <east.patrick@gmail.com>