storage: Handle multi-bundle data with overlapping roots

If the bundles being activated share a manifest root prefix, it
would result in overwriting the bundle data based on the activation
order. This happened since the truncate call writes data to the
store based on the top-level keys in the data. When multiple
bundles with overlapping bundle root prefixes are being activated
as part of the same txn, adding data to the store by iterating
over the top-level keys in the data object would result in an unintended
overwrite. The truncate call would be able to properly write
data if it had knowledge of the bundle roots. This commit passes
the bundle roots to the truncate call to assist in writing data
to the store.

Fixes: #4998

Signed-off-by: Ashutosh Narkar <anarkar4387@gmail.com>