gh-35366: Many more namespace packages – follow up
    
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### 📚 Description

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Follow-up from #35322.
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### ⌛ Dependencies

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URL: #35366
Reported by: Matthias Köppe
Reviewer(s): Gonzalo Tornaría

Author: Release Manager

src/doc/en/reference/combinat/module_list.rst

@@ -368,7 +368,7 @@ Comprehensive Module List
     sage/combinat/tutorial
     sage/combinat/vector_partition
     sage/combinat/words/abstract_word
-    sage/combinat/words
+    sage/combinat/words/all
     sage/combinat/words/alphabet
     sage/combinat/words/finite_word
     sage/combinat/words/infinite_word

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

@@ -29,7 +29,7 @@ Modules with basis
 .. toctree::
    :maxdepth: 1
 
-   sage/modules/with_basis/__init__
+   sage/modules/with_basis/all
    sage/modules/with_basis/cell_module
    sage/modules/with_basis/indexed_element
    sage/modules/with_basis/invariant

src/sage/combinat/all.py

@@ -26,7 +26,7 @@
 - :ref:`sage.combinat.species.all`
 - :ref:`sage.combinat.designs.all`
 - :ref:`sage.combinat.posets.all`
-- :ref:`sage.combinat.words`
+- :ref:`sage.combinat.words.all`
 - :ref:`sage.combinat.bijectionist`
 
 Utilities

src/sage/combinat/words/__init__.py

@@ -1,3 +1,48 @@
+r"""
+Combinatorics on words
+
+**Main modules and their methods:**
+
+- :ref:`sage.combinat.words.abstract_word`
+- :ref:`sage.combinat.words.finite_word`
+- :ref:`sage.combinat.words.infinite_word`
+- :ref:`sage.combinat.words.alphabet`
+- :ref:`sage.combinat.words.words`
+- :ref:`sage.combinat.words.paths`
+- :ref:`sage.combinat.words.morphism`
+- :ref:`sage.combinat.words.shuffle_product`
+- :ref:`sage.combinat.words.suffix_trees`
+
+Main classes and functions meant to be used by the user:
+
+    :func:`~sage.combinat.words.word.Word`,
+    :class:`~sage.combinat.words.words.FiniteWords`,
+    :class:`~sage.combinat.words.words.InfiniteWords`,
+    :func:`~sage.combinat.words.words.Words`,
+    :func:`~sage.combinat.words.alphabet.Alphabet`,
+    :class:`~sage.combinat.words.morphism.WordMorphism`,
+    :class:`~sage.combinat.words.paths.WordPaths`.
+
+A list of common words can be accessed through ``words.<tab>`` and are listed in
+the :ref:`words catalog <sage.combinat.words.word_generators>`.
+
+**Internal representation of words:**
+
+- :ref:`sage.combinat.words.word`
+- :ref:`sage.combinat.words.word_char`
+- :ref:`sage.combinat.words.word_datatypes`
+- :ref:`sage.combinat.words.word_infinite_datatypes`
+
+**Options:**
+
+- :ref:`sage.combinat.words.word_options`
+
+See :func:`~sage.combinat.words.word_options.WordOptions`.
+"""
+# install the docstring of this module to the containing package
+from sage.misc.namespace_package import install_doc
+install_doc(__package__, __doc__)
+
 from .alphabet import Alphabet, build_alphabet
 from .morphism import WordMorphism
 from .paths import WordPaths

src/sage/combinat/words/all.py

@@ -23,6 +23,8 @@
 
 from .vector_space_morphism import linear_transformation
 
+from .with_basis.all import *
+
 from sage.misc.lazy_import import lazy_import
 
 lazy_import('sage.modules.filtered_vector_space', 'FilteredVectorSpace')

src/sage/groups/perm_gps/partn_ref/__init__.py renamed to src/sage/groups/perm_gps/partn_ref/all.py

@@ -8,3 +8,6 @@
 
 .. SEEALSO:: The category :class:`ModulesWithBasis`
 """
+# install the docstring of this module to the containing package
+from sage.misc.namespace_package import install_doc
+install_doc(__package__, __doc__)

src/sage/groups/perm_gps/partn_ref2/__init__.py renamed to src/sage/groups/perm_gps/partn_ref2/all.py

@@ -199,6 +199,11 @@ def rebuild(dirname, force=False):
     except OSError:
         if not os.path.isdir(dirname):
             raise
+        # Remove leftover file from before move to namespace packages
+        try:
+            os.remove(os.path.join(dirname, '__init__.py'))
+        except FileNotFoundError:
+            pass
 
     # Although multiple files are generated by this function, since
     # they are all generated at once it suffices to make sure if just
@@ -208,7 +213,7 @@ class NeedToRebuild(Exception):
     try:
         if force:
             raise NeedToRebuild("-> Force rebuilding interpreters")
-        gen_file = os.path.join(dirname, '__init__.py')
+        gen_file = os.path.join(dirname, 'all.py')
         if not os.path.isfile(gen_file):
             raise NeedToRebuild("-> First build of interpreters")
 
@@ -230,5 +235,5 @@ class NeedToRebuild(Exception):
     for interp in _INTERPRETERS:
         build_interp(interp(), dirname)
 
-    with open(os.path.join(dirname, '__init__.py'), 'w') as f:
+    with open(os.path.join(dirname, 'all.py'), 'w') as f:
         f.write("# " + AUTOGEN_WARN)