gh-39466: remove some deprecations in groups
    
found using the scripts in #39262

### 📝 Checklist

- [x] The title is concise and informative.
- [x] The description explains in detail what this PR is about.
    
URL: #39466
Reported by: Frédéric Chapoton
Reviewer(s): David Coudert

Author: Release Manager

src/doc/en/reference/groups/index.rst

@@ -78,8 +78,6 @@ Matrix and Affine Groups
    sage/groups/matrix_gps/group_element_gap
    sage/groups/matrix_gps/finitely_generated
    sage/groups/matrix_gps/finitely_generated_gap
-   sage/groups/matrix_gps/morphism
-   sage/groups/matrix_gps/homset
    sage/groups/matrix_gps/binary_dihedral
    sage/groups/matrix_gps/coxeter_group
    sage/groups/matrix_gps/linear

src/sage/groups/matrix_gps/homset.py

@@ -9,13 +9,11 @@ py.install_sources(
   'group_element.pxd',
   'group_element_gap.pxd',
   'heisenberg.py',
-  'homset.py',
   'isometries.py',
   'linear.py',
   'linear_gap.py',
   'matrix_group.py',
   'matrix_group_gap.py',
-  'morphism.py',
   'named_group.py',
   'named_group_gap.py',
   'orthogonal.py',

src/sage/groups/matrix_gps/meson.build

@@ -380,13 +380,12 @@ def PermutationGroup(gens=None, *args, **kwds):
         ...
         TypeError: gens must be a tuple, list, or GapElement
 
-    This will raise an error after the deprecation period::
+    This now raises an error (:issue:`31510`)::
 
         sage: G = PermutationGroup([(1,2,3,4)], [(1,7,3,5)])
-        doctest:warning
+        Traceback (most recent call last):
         ...
-        DeprecationWarning: gap_group, domain, canonicalize, category will become keyword only
-        See https://github.com/sagemath/sage/issues/31510 for details.
+        ValueError: please use keywords gap_group=, domain=, canonicalize=, category= in the input
     """
     if not isinstance(gens, ExpectElement) and hasattr(gens, '_permgroup_'):
         return gens._permgroup_()
@@ -402,18 +401,7 @@ def PermutationGroup(gens=None, *args, **kwds):
             raise ValueError("you must specify the domain for an action")
         return PermutationGroup_action(gens, action, domain, gap_group=gap_group)
     if args:
-        from sage.misc.superseded import deprecation
-        deprecation(31510, "gap_group, domain, canonicalize, category will become keyword only")
-        if len(args) > 4:
-            raise ValueError("invalid input")
-        args = list(args)
-        gap_group = args.pop(0)
-        if args:
-            domain = args.pop(0)
-            if args:
-                canonicalize = args.pop(0)
-                if args:
-                    category = args.pop(0)
+        raise ValueError("please use keywords gap_group=, domain=, canonicalize=, category= in the input")
     return PermutationGroup_generic(gens=gens, gap_group=gap_group, domain=domain,
                                     canonicalize=canonicalize, category=category)
 
@@ -1068,7 +1056,7 @@ def list(self):
         """
         return list(self)
 
-    def __contains__(self, item):
+    def __contains__(self, item) -> bool:
         """
         Return whether ``item`` is an element of this group.
 
@@ -1105,33 +1093,6 @@ def __contains__(self, item):
             return False
         return True
 
-    def has_element(self, item):
-        """
-        Return whether ``item`` is an element of this group -
-        however *ignores* parentage.
-
-        EXAMPLES::
-
-            sage: G = CyclicPermutationGroup(4)
-            sage: gens = G.gens()
-            sage: H = DihedralGroup(4)
-            sage: g = G([(1,2,3,4)]); g
-            (1,2,3,4)
-            sage: G.has_element(g)
-            doctest:warning
-            ...
-            DeprecationWarning: G.has_element(g) is deprecated; use :meth:`__contains__`, i.e., `g in G` instead
-            See https://github.com/sagemath/sage/issues/33831 for details.
-            True
-            sage: h = H([(1,2),(3,4)]); h
-            (1,2)(3,4)
-            sage: G.has_element(h)
-            False
-        """
-        from sage.misc.superseded import deprecation
-        deprecation(33831, "G.has_element(g) is deprecated; use :meth:`__contains__`, i.e., `g in G` instead")
-        return item in self
-
     def __iter__(self):
         r"""
         Return an iterator going through all elements in ``self``.
@@ -1161,9 +1122,9 @@ def __iter__(self):
         """
         if len(self._gens) == 1:
             return self._iteration_monogen()
-        else:
-            # TODO: this is too slow for moderatly small permutation groups
-            return self.iteration(algorithm='SGS')
+
+        # TODO: this is too slow for moderately small permutation groups
+        return self.iteration(algorithm='SGS')
 
     def _iteration_monogen(self):
         r"""