building: collect built-in extensions into lib-dynload sub-directory

On macOS and linux, some of the python's built-ins have extension
modules that originally reside in python3.X/lib-dynload directory.
This directory is in sys.path, therefore the collected extensions
have no parent directory and end up directly in the _MEIPASS.

This commit explicitly diverts such extensions into lib-dynload
sub-directory in the _MEIPASS.

In addition to decluttering the _MEIPASS on linux and macOS, this
also prevents ctypes.CDLL() from picking up the extensions'
shared libraries and causing inconsistent behavior between
frozen and unfrozen application, which in some corner cases
leads to issues with shadowing, such as in pyinstaller#5583.

PyInstaller/building/api.py

@@ -42,6 +42,16 @@
     from PyInstaller.utils.win32 import winmanifest, icon, versioninfo, winresource
 
 
+def _is_libdynload_extension(typ, dst, src):
+    """
+    Determines if the given TOC entry is an EXTENSION coming from
+    python's lib-dynload directory.
+    """
+    return typ == 'EXTENSION' \
+           and not os.path.dirname(os.path.normpath(dst)) \
+           and os.path.basename(os.path.dirname(src)) == 'lib-dynload'
+
+
 class PYZ(Target):
     """
     Creates a ZlibArchive that contains all pure Python modules.
@@ -233,6 +243,11 @@ def assemble(self):
                 # file is contained within python egg, it is added with the egg
                 continue
             if typ in ('BINARY', 'EXTENSION', 'DEPENDENCY'):
+                if _is_libdynload_extension(typ, inm, fnm):
+                    # Place extensions that originate from python's
+                    # lib-dynload directory into _MEIPASS/lib-dynload
+                    # instead of directly into _MEIPASS
+                    inm = os.path.join('lib-dynload', inm)
                 if self.exclude_binaries and typ == 'EXTENSION':
                     self.dependencies.append((inm, fnm, typ))
                 elif not self.exclude_binaries or typ == 'DEPENDENCY':
@@ -734,7 +749,13 @@ def assemble(self):
                or os.path.isabs(inm):
                 raise SystemExit('Security-Alert: try to store file outside '
                                  'of dist-directory. Aborting. %r' % inm)
-            tofnm = os.path.join(self.name, inm)
+            if _is_libdynload_extension(typ, inm, fnm):
+                # Place extensions that originate from python's
+                # lib-dynload directory into _MEIPASS/lib-dynload
+                # instead of directly into _MEIPASS
+                tofnm = os.path.join(self.name, 'lib-dynload', inm)
+            else:
+                tofnm = os.path.join(self.name, inm)
             todir = os.path.dirname(tofnm)
             if not os.path.exists(todir):
                 os.makedirs(todir)