Keep soft deletes in sync with on-disk DocValues

Today we pass on the doc values update to the PendingDeletes
when it's applied. This might cause issues with a rentention policy
merge policy that will see a deleted document but not it's value on
disk.
This change moves back the PendingDeletes callback to flush time
in order to be consistent with what is actually updated on disk.

This change also makes sure we write values to disk on flush that
are in the reader pool as well as extra best effort checks to drop
fully deleted segments on flush, commit and getReader.