CLE fails to load Android apps if classes referenced in the manifest are not part of the classes.dex

Hi team.

I'm trying to load an Android app in angr and it gave me the following error message:
(CLE & angr version: 9.2.18. Most recent on Pip)
```
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File ~/[FOOBAR]/angr_solver.py:59
57 logging.getLogger("angr.factory").setLevel("DEBUG")
58 logging.getLogger("angr.manager").setLevel("DEBUG")
---> 59 main()

File ~/[FOOBAR]/angr_solver.py:44, in main()
41 print(f"Using Sample:\t\t{sample_path}")
42 print(f"Using Entrypoint:\t{entry_point}")
---> 44 project = angr.Project(sample_path, main_opts=loading_opts, auto_load_libs=True)
46 # project.hook(SootMethodDescriptor(class_name="java.lang.String", name="valueOf", params=('int',)).address(), Dummy_String_valueOf())
48 entry = project.factory.entry_state()

File ~/.local/lib/python3.10/site-packages/angr/project.py:138, in Project.__init__(self, thing, default_analysis_mode, ignore_functions, use_sim_procedures, exclude_sim_procedures_func, exclude_sim_procedures_list, arch, simos, engine, load_options, translation_cache, support_selfmodifying_code, store_function, load_function, analyses_preset, concrete_target, eager_ifunc_resolution, **kwargs)
136 l.info("Loading binary %s", thing)
137 self.filename = str(thing)
--> 138 self.loader = cle.Loader(self.filename, concrete_target=concrete_target, **load_options)
140 # Step 2: determine its CPU architecture, ideally falling back to CLE's guess
141 if isinstance(arch, str):

File ~/.local/lib/python3.10/site-packages/cle/loader.py:133, in Loader.__init__(self, main_binary, auto_load_libs, concrete_target, force_load_libs, skip_libs, main_opts, lib_opts, ld_path, use_system_libs, ignore_import_version_numbers, case_insensitive, rebase_granularity, except_missing_libs, aslr, perform_relocations, load_debug_info, page_size, preload_libs, arch)
131 self._main_opts.update({'arch': arch})
132 self.preload_libs = []
--> 133 self.initial_load_objects = self._internal_load(main_binary, *preload_libs, *force_load_libs, preloading=(main_binary, *preload_libs))
135 # cache
136 self._last_object = None

File ~/.local/lib/python3.10/site-packages/cle/loader.py:689, in Loader._internal_load(self, preloading, *args)
687 l.info("Skipping load request %s - already loaded", main_spec)
688 continue
--> 689 obj = self._load_object_isolated(main_spec)
690 objects.append(obj)
691 objects.extend(obj.child_objects)

File ~/.local/lib/python3.10/site-packages/cle/loader.py:871, in Loader._load_object_isolated(self, spec)
868 # STEP 4: LOAD!
869 l.debug("... loading with %s", backend_cls)
--> 871 result = backend_cls(binary, binary_stream, is_main_bin=self.main_object is None, loader=self, **options)
872 result.close()
873 return result

File ~/.local/lib/python3.10/site-packages/cle/backends/java/apk.py:96, in Apk.__init__(self, apk_path, binary_stream, entry_point, entry_point_params, android_sdk, supported_jni_archs, jni_libs, jni_libs_ld_path, **options)
94 self.components = {'activity': [], 'service': [], 'receiver': [], 'provider': []}
95 self.callbacks = {'activity': [], 'service': [], 'receiver': [], 'provider': []}
---> 96 self._set_lifecycle(apk_parser)
97 else:
98 self.components = None

File ~/.local/lib/python3.10/site-packages/cle/backends/java/apk.py:116, in Apk._set_lifecycle(self, apk_parser)
114 for key, getter in component_getter.items():
115 class_names = getter()
--> 116 self.components[key], self.callbacks[key] = self._extract_lifecycle(class_names, key)

File ~/.local/lib/python3.10/site-packages/cle/backends/java/apk.py:133, in Apk._extract_lifecycle(self, cls_name, component_kind)
130 callbacks = []
132 for cls in cls_name:
--> 133 components.append(self.classes[cls])
134 callbacks.extend(self.get_callbacks(cls, callback[component_kind]))
136 return components, callbacks

KeyError: 'com.foo.bar.SomeActivity'
```

I also think I know where the issue comes from: The class `com.foo.bar.SomeActivity` is referenced in the APKs Manifest and therefore returned by `pyaxmlparser` on https://github.com/angr/cle/blob/e2776162d623441f9d1e3070bb344cb148b0e32b/cle/backends/java/apk.py#L109, but is not part of the apps `classes.dex` and therefore not found in the list of classes at https://github.com/angr/cle/blob/e2776162d623441f9d1e3070bb344cb148b0e32b/cle/backends/java/apk.py#L133.

The missing class is part of a second stage payload that gets decrypted at runtime. Since the app runs fine on devices and emulators the Dalvik Vm seems to be able to support this, meaning it's not a malformed apk. I'm happy to assist in debugging/testing fixes but am unable to share the apk. I'm also happy to write a PR, but want to get an opinion on how this should be fixed first.