Extract files based on the manifest id

Renamed rhizome extract file to rhizome dump file
Added rhizome extract file [manifest] [filepath] [pins]
Modified tests to use the appropriate command, assuming that MeshMS payloads will be encrypted
Add offset to nonce instead of replacing byte values
Don't check for duplicates if an existing id has been supplied
Generate version id before reading the file contents
Tidy up rhizome secret handling to improve reusability
Only consider duplicate manifests that we can re-author