Addressed comments by Sebastiaan.

In particular, the most important changes include:
- now the auto-group flag is called `--auto-group`, is
  a flag and is False by default
- only kept `--include` and `--exclude` options, checking
  typestrings and allowing to end with `%`. One benefit
  is that while reimplementing I replaced some `isinstance`
  with string comparisons, with potential further benefits.
- `--include` and `--exclude` are now mutually exclusive
- improved documentation of the main point of the issue

aiida/cmdline/commands/cmd_run.py

@@ -40,12 +40,12 @@ def update_environment(argv):
         sys.path = _path
 
 
-def validate_entrypoint_string_or_all(ctx, param, value, allow_all=True):  # pylint: disable=unused-argument,invalid-name
-    """Validate that `value` is a valid entrypoint string or the string 'all'."""
+def validate_entrypoint_string(ctx, param, value):  # pylint: disable=unused-argument,invalid-name
+    """Validate that `value` is a valid entrypoint string."""
     from aiida.orm import autogroup
 
     try:
-        autogroup.Autogroup.validate(value, allow_all=allow_all)
+        autogroup.Autogroup.validate(value)
     except Exception as exc:
         raise click.BadParameter(str(exc) + ' ({})'.format(value))
 
@@ -55,58 +55,41 @@ def validate_entrypoint_string_or_all(ctx, param, value, allow_all=True):  # pyl
 @verdi.command('run', context_settings=dict(ignore_unknown_options=True,))
 @click.argument('scriptname', type=click.STRING)
 @click.argument('varargs', nargs=-1, type=click.UNPROCESSED)
-@click.option('--group/--no-group', default=True, show_default=True, help='Enables the autogrouping')
+@click.option('--auto-group', is_flag=True, help='Enables the autogrouping')
 @click.option(
     '-l',
-    '--group-label-prefix',
+    '--auto-group-label-prefix',
     type=click.STRING,
     required=False,
     help='Specify the prefix of the label of the auto group (numbers might be automatically '
-    'appended to generate unique names per run)'
+    'appended to generate unique names per run).'
 )
 @click.option(
     '-n',
     '--group-name',
     type=click.STRING,
     required=False,
-    help='Specify the name of the auto group [DEPRECATED, USE --group-label-prefix instead]'
+    help='Specify the name of the auto group [DEPRECATED, USE --auto-group-label-prefix instead]. '
+    'This also enables auto-grouping.'
 )
 @click.option(
     '-e',
     '--exclude',
     cls=MultipleValueOption,
-    default=lambda: [],
-    help='Exclude these classes from auto grouping (use full entrypoint strings)',
-    callback=functools.partial(validate_entrypoint_string_or_all, allow_all=False)
+    default=None,
+    help='Exclude these classes from auto grouping (use full entrypoint strings).',
+    callback=functools.partial(validate_entrypoint_string)
 )
 @click.option(
     '-i',
     '--include',
     cls=MultipleValueOption,
-    default=lambda: ['all'],
-    help='Include these classes from auto grouping  (use full entrypoint strings or "all")',
-    callback=validate_entrypoint_string_or_all
-)
-@click.option(
-    '-E',
-    '--excludesubclasses',
-    cls=MultipleValueOption,
-    default=lambda: [],
-    help='Exclude these classes and their sub classes from auto grouping (use full entrypoint strings)',
-    callback=functools.partial(validate_entrypoint_string_or_all, allow_all=False)
-)
-@click.option(
-    '-I',
-    '--includesubclasses',
-    cls=MultipleValueOption,
-    default=lambda: [],
-    help='Include these classes and their sub classes from auto grouping (use full entrypoint strings)',
-    callback=functools.partial(validate_entrypoint_string_or_all, allow_all=False)
+    default=None,
+    help='Include these classes from auto grouping  (use full entrypoint strings or "all").',
+    callback=validate_entrypoint_string
 )
 @decorators.with_dbenv()
-def run(
-    scriptname, varargs, group, group_label_prefix, group_name, exclude, excludesubclasses, include, includesubclasses
-):
+def run(scriptname, varargs, auto_group, auto_group_label_prefix, group_name, exclude, include):
     # pylint: disable=too-many-arguments,exec-used
     """Execute scripts with preloaded AiiDA environment."""
     from aiida.cmdline.utils.shell import DEFAULT_MODULES_LIST
@@ -126,20 +109,22 @@ def run(
         globals_dict['{}'.format(alias)] = getattr(__import__(app_mod, {}, {}, model_name), model_name)
 
     if group_name:
-        warnings.warn('--group-name is deprecated, use `--group-label` instead', AiidaDeprecationWarning)  # pylint: disable=no-member
-        if group_label:
-            raise click.BadParameter('You cannot specify both --group-name and --group-label; use --group-label only')
-        group_label = group_name
-
-    if group:
+        warnings.warn('--group-name is deprecated, use `--auto-group-label-prefix` instead', AiidaDeprecationWarning)  # pylint: disable=no-member
+        if auto_group_label_prefix:
+            raise click.BadParameter(
+                'You cannot specify both --group-name and --auto-group-label-prefix; use --group-label only'
+            )
+        auto_group_label_prefix = group_name
+        # To have the old behavior, with auto-group enabled.
+        auto_group = True
+
+    if auto_group:
         aiida_verdilib_autogroup = autogroup.Autogroup()
-        # if group_label_prefix is None, use autogenerated name
-        if group_label_prefix is not None:
-            aiida_verdilib_autogroup.set_group_label_prefix(group_label_prefix)
+        # Set the ``group_label_prefix`` if defined, otherwise a default prefix will be used
+        if auto_group_label_prefix is not None:
+            aiida_verdilib_autogroup.set_group_label_prefix(auto_group_label_prefix)
         aiida_verdilib_autogroup.set_exclude(exclude)
         aiida_verdilib_autogroup.set_include(include)
-        aiida_verdilib_autogroup.set_exclude_with_subclasses(excludesubclasses)
-        aiida_verdilib_autogroup.set_include_with_subclasses(includesubclasses)
 
         # Note: this is also set in the exec environment! This is the intended behavior
         autogroup.CURRENT_AUTOGROUP = aiida_verdilib_autogroup