ipfs file ls is the same as ipfs ls.
ipfs ls works on IPFS paths.
An IPFS path is a CID that resolves to a DAG that represents a directory (e.g. /ipfs/Qmfoo) or a subdirectory (e.g. /ipfs/Qmfoo/subdir)
IPFS paths are not MFS paths.
MFS paths are used by the ipfs files ... commands and look like traditional Unix paths but apply to a DAG in your repo.
Please see the IPFS primer for more information: https://dweb-primer.ipfs.io and the docs https://docs-beta.ipfs.io