diff --git a/src/sage/ext/__init__.py b/src/sage/ext/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/graphs/__init__.py b/src/sage/graphs/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/graphs/graph_decompositions/__init__.py b/src/sage/graphs/graph_decompositions/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/arith/__init__.py b/src/sage/graphs/graph_decompositions/all.py
similarity index 100%
rename from src/sage/arith/__init__.py
rename to src/sage/graphs/graph_decompositions/all.py
diff --git a/src/sage/interfaces/__init__.py b/src/sage/interfaces/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/libs/__init__.py b/src/sage/libs/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/matrix/__init__.py b/src/sage/matrix/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/misc/__init__.py b/src/sage/misc/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/numerical/__init__.py b/src/sage/numerical/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/numerical/backends/__init__.py b/src/sage/numerical/backends/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/categories/__init__.py b/src/sage/numerical/backends/all.py
similarity index 100%
rename from src/sage/categories/__init__.py
rename to src/sage/numerical/backends/all.py
diff --git a/src/sage/rings/__init__.py b/src/sage/rings/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage/sets/__init__.py b/src/sage/sets/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/src/sage_docbuild/builders.py b/src/sage_docbuild/builders.py
index b6b723976cd..9cc99254e64 100644
--- a/src/sage_docbuild/builders.py
+++ b/src/sage_docbuild/builders.py
@@ -1011,6 +1011,10 @@ def get_new_and_updated_modules(self):
                 raise
 
             module_filename = sys.modules[module_name].__file__
+            if module_filename is None:
+                # Namespace package
+                old_modules.append(module_name)
+                continue
             if (module_filename.endswith('.pyc') or module_filename.endswith('.pyo')):
                 source_filename = module_filename[:-1]
                 if (os.path.exists(source_filename)):
diff --git a/src/sage_setup/command/sage_install.py b/src/sage_setup/command/sage_install.py
index 8571b4e9813..abfc142eec4 100644
--- a/src/sage_setup/command/sage_install.py
+++ b/src/sage_setup/command/sage_install.py
@@ -71,9 +71,12 @@ def clean_stale_files(self):
 
         # Determine all Python modules inside all packages
         py_modules = []
+        ordinary_packages = []
         for package in dist.packages:
             package_dir = cmd_build_py.get_package_dir(package)
-            py_modules += cmd_build_py.find_package_modules(package, package_dir)
+            if os.path.exists(os.path.join(package_dir, '__init__.py')):
+                ordinary_packages.append(package)
+            py_modules.extend(cmd_build_py.find_package_modules(package, package_dir))
         # modules is a list of triples (package, module, module_file).
         # Construct the complete module name from this.
         py_modules = ["{0}.{1}".format(*m) for m in py_modules]
@@ -97,7 +100,7 @@ def clean_stale_files(self):
         for output_dir in set(output_dirs):
             log.info('- cleaning {0}'.format(output_dir))
             clean_install_dir(output_dir,
-                    dist.packages,
+                    ordinary_packages,
                     py_modules,
                     dist.ext_modules,
                     data_files,
diff --git a/src/sage_setup/find.py b/src/sage_setup/find.py
index 71fddc3e4ef..28467135c12 100644
--- a/src/sage_setup/find.py
+++ b/src/sage_setup/find.py
@@ -404,7 +404,7 @@ def installed_files_by_module(site_packages, modules=('sage',)):
     Namespace packages::
 
         sage: files_by_module['sage.graphs.graph_decompositions']
-        {...'sage/graphs/graph_decompositions/__init__.py'...}
+        set()
 
     This takes about 30ms with warm cache::