Refactor manifest: specific setter functions

Replace generic rhizome_manifest_set() and rhizome_manifest_set_ll()
with per-field setter functions, eg, rhizome_manifest_set_filesize().

Struct rhizome_manifest elements for all known fields, to replace the
use of rhizome_manifest_get() and rhizome_manifest_get_ll() everywhere.

More use of unsigned int, size_t and uint64_t where appropriate.