Java: Some CodeQL classes don't extend `Top`

**Description of the issue**
The [documentation](https://codeql.github.com/codeql-standard-libraries/java/semmle/code/Location.qll/type.Location$Top.html) for `Top` says:
> Top is the root of the QL type hierarchy; it defines some default methods for obtaining locations and a standard `toString()` method.

However, some CodeQL classes don't extend it.
Affected (list might be incomplete):
- `SuppressionScope` (internal, so might not matter)
- `TypeBound`
- `Module`
- `Directive`
- `XMLParent`