Refactor ipautil.run

The ipautil.run function now returns an object with returncode and
output are accessible as attributes.

The stdout and stderr of all commands are logged (unless skip_output is given).

The stdout/stderr contents must be explicitly requested with a keyword
argument, otherwise they are None.
This is because in Python 3, the output needs to be decoded, and that can
fail if it's not decodable (human-readable) text.

The raw (bytes) output is always available from the result object,
as is "leniently" decoded output suitable for logging.

All calls are changed to reflect this.

A use of Popen in cainstance is changed to ipautil.run.

Reviewed-By: Jan Cholasta <jcholast@redhat.com>

ipaserver/install/replication.py

@@ -93,10 +93,10 @@ def replica_conn_check(master_host, host_name, realm, check_ca,
     if ca_cert_file:
         args.extend(["--ca-cert-file", ca_cert_file])
 
-    (stdin, stderr, returncode) = ipautil.run(
+    result = ipautil.run(
         args, raiseonerr=False, capture_output=False, nolog=nolog)
 
-    if returncode != 0:
+    if result.returncode != 0:
         sys.exit("Connection check failed!" +
                  "\nPlease fix your network settings according to error messages above." +
                  "\nIf the check results are not valid it can be skipped with --skip-conncheck parameter.")