atom: force a fresh instance instead of using portage's intern cache

portage.dep.Atom.__new__ now interns instances in a module-level cache
keyed only by the atom string and parse flags, not by the constructor's
class. Constructing gentoolkit.atom.Atom with a string already interned
elsewhere as a plain portage.dep.Atom silently returns that cached
instance instead of one of our subclass, so methods we override (like
intersects()) resolve to portage's implementation instead of ours.

Reproduced with portage d52efac67: gentoolkit.atom.Atom() returned a
plain portage.dep.Atom whenever the same atom string had already been
interned by portage itself, which happens constantly in normal use. This
also explains why equery d was under-reporting some reverse
dependencies: portage.dep.Atom.intersects() and our own implementation
don't always agree.

Bug: https://bugs.gentoo.org/981521
Signed-off-by: Matt Turner <mattst88@gentoo.org>

Author: mattst88

pym/gentoolkit/atom.py

@@ -45,6 +45,14 @@ class Atom(portage.dep.Atom, CPV):
     # Necessary for Portage versions < 2.1.7
     _atoms = weakref.WeakValueDictionary()
 
+    def __new__(cls, *args, **kwargs):
+        # portage.dep.Atom.__new__ interns instances in a module-level
+        # cache keyed only by the atom string (not by cls), so calling
+        # this subclass's constructor with an already-interned string can
+        # silently hand back a plain portage.dep.Atom instead of one of
+        # ours. Always build a fresh instance so we stay this subclass.
+        return object.__new__(cls)
+
     @property
     def operator(self):
         # Old portage stored operator as a plain instance attribute in