Fix startup when data_manager_config_file config option is set to…

… an empty value

by not resolving it to the `path_resolves_to` directory in such a case.

planemo (which we use in the converters tests) set this option to an
empty value when not testing data managers:

https://github.com/galaxyproject/planemo/blob/master/planemo/galaxy/config.py#L452

Resulting in this traceback:

```
Traceback (most recent call last):
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 68, in app_pair
    app = galaxy.app.UniverseApplication(global_conf=global_conf, is_webapp=True, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/app.py", line 777, in __init__
    self.data_managers = self._register_singleton(DataManagers)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/di.py", line 27, in _register_singleton
    instance = self[dep_type]
               ~~~~^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 381, in __getitem__
    return self.resolve(dep)
           ^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 265, in resolve
    return self._reflection_build_with_err_handling(dep_type, suppress_error)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 392, in _reflection_build_with_err_handling
    return self._reflection_build(dep_type)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 408, in _reflection_build
    return dep_type(**sub_deps)  # type: ignore
           ^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/tools/data_manager/manager.py", line 44, in __init__
    self.load_from_xml(filename)
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/tools/data_manager/manager.py", line 58, in load_from_xml
    tree = util.parse_xml(xml_filename)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/util/__init__.py", line 360, in parse_xml
    with source.open("rb") as f:
         ^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IsADirectoryError: [Errno 21] Is a directory: '/tmp/tmps2qq5htq'
```

Why this has become a problem
-----------------------------

Before commit 3282aa3 `util.parse_xml()`
would raise a `XMLSyntaxError` exception if passed a directory, but
now it raises `IsADirectoryError`, which is a subclass of `OSError` with
errno 21.
As a consequence when `load_from_xml()` in lib/galaxy/tools/data_manager/manager.py
calls `util.parse_xml()` passing a directory, the resulting exception
is now re-raised in the `except OSError as e:` branch instead of
just being logged, which is good since this is a misconfiguration.

N.B.: This will also need to be fixed in Planemo by not setting the
`data_manager_config_file` option when not needed.

lib/galaxy/config/__init__.py

@@ -301,7 +301,7 @@ def is_set(self, key):
         # To check only schema options, change the line below to `if property not in self._raw_config:`
         if key not in self._raw_config:
             log.warning(f"Configuration option does not exist: '{key}'")
-        return key in self._kwargs
+        return key in self._kwargs and self._kwargs[key]
 
     def resolve_path(self, path):
         """Resolve a path relative to Galaxy's root."""
@@ -511,10 +511,10 @@ def resolve(key):
             if not parent:  # base case: nothing else needs resolving
                 return path
             parent_path = resolve(parent)  # recursively resolve parent path
-            if path is not None:
+            if path:
                 path = os.path.join(parent_path, path)  # resolve path
             else:
-                path = parent_path  # or use parent path
+                log.warning("Trying to resolve path for the '%s' option but it's empty/None", key)
 
             setattr(self, key, path)  # update property
             _cache[key] = path  # cache it!