force `subprocess.run` to check return code is 0

In general, this should help to capture unintentional errors.

Where the change has created failures, they have been fixed. (Mostly because the git repository that was looked for was missing.)

mpsd-software-environment.py

@@ -54,9 +54,9 @@ class os_chdir:
 
 def run(*args, counter=[0], **kwargs):
     """
-    Call subprocess.run(*args, **kwargs) and print logging data.
+    Run a subprocess and log the call.
 
-    Conveniene function to call `subprocess.run` and provide some metadata
+    Convenience function to call `subprocess.run` and provide some metadata
     about the call.
 
     Parameters