Add note to CLI

Author: benjeffery

docs/cli.rst

@@ -4,6 +4,11 @@
 Command line interface
 ======================
 
+.. warning::
+
+    The command line interface only supports the deprecated SampleData format
+    used in tsinfer<0.4.0. 
+
 The command line interface in ``tsinfer`` is intended to provide a convenient
 interface to the high-level :ref:`API functionality <sec_api>`. There are two
 equivalent ways to invoke this program:
@@ -25,7 +30,7 @@ form is useful when multiple versions of Python are installed or if the
 The :command:`tsinfer` program has five subcommands: :command:`list` prints a
 summary of the data held in one of tsinfer's :ref:`file formats <sec_file_formats>`;
 :command:`infer` runs the complete :ref:`inference process <sec_inference>` for a given
-input VCF Zarr dataset; and
+input SampleData file; and
 :command:`generate-ancestors`, :command:`match-ancestors` and
 :command:`match-samples` run the three parts of this inference
 process as separate steps. Running the inference as separate steps like this