Add ability to specify base directory on the repository level

This change is needed to support multiple repositories per S3 bucket
Update snapshot list when snapshot is deleted
try and extract store directory also if its wrapped in a compound dir
fix bloom filter posting format to get the fpp from the correct settings
Add repository information to docs

This adds the apt and yum repo information to the setup docs.
Use a List of shards per shard ID rather than a set.

The shards in the set are mutated after they are added to the
set such that the hashcode doesn't fit anymore. For this reason
this used an identity hashset before but the downside of this is
that the iteration order is not deterministic. We can just use a list
since shard removal is a very rare action and the size of the list is
very small such that iteration is fast.
Remove hard-coded "ok": true from REST responses

Fixes #4310