[common] Refactor Protected Files, part 7

This commit refactors PF code without changing functionality (part 7 in
a series of commits). In particular, this commit renames:
- "key_id" to a more correct "nonce"
- "encrypted_part_plain" to "metadata_decrypted" (i.e. decrypted conents
  of the encrypted part of the metadata node)
- "file" to a more specific "host_file_handle"
- "file_metadata" to a more correct "metadata_node"
- "root_mht" to a more specific "root_mht_node"

Signed-off-by: Dmitrii Kuvaiskii <[email protected]>