Assorted typing cleanups

[mwichmann]

Fix various niggly typing and checker complaints.

Environment.py:

• To avoid modifying a dict-like thing while iterating over it, we did .copy(), making an awkward chained construct that checkers don't like. Simpler (and the more common idiom) is to make a list from the keys view, that way you're iterating over that new list and not the dict (and save creating a dict copy).
• Another use of copy() was in detecting a CPPDEFINES deque, where we want to keep a copy of it and not modify the original - use the deque constructor for this instead of calling copy() method.
• A few complaints about calling subst with a bad type were due to us defeating type narrowing - checkers don't know that is_String evaluating true means the object is a string type. Added casts for certain instances of this.
• Align the names of vars in overridden dunder methods in BuilderDict with parent UserDict for more consistency (one of ours used the same name as a different arg in the parent). Similar for the JSONEncoder default method.
• arg2nodes node_factory argument could be passed a None, indicate that in the signature.
• Multiple uses of CacheDir (it was both an import from CacheDir for type checking, and the name of a function in Environment.py). This was confusing to at least one type checker, so just use the qualified name.
• The environment Base class _update and _update_onlynew methods were annotated to take an EnvironmentBase argument, but in fact they're designed to update the internal dict from a passed dict. Adjusted the annotation.
• Used the global Environment hook directly by name rather than fully qualified, as SCons.Environment doesn't have an import of itself. That's namespace niggling, because it worked as written.
• The Repository method (public API level) was written to take kwargs and pass those on to the FS layer's Repository - which doesn't take kwargs. Repository() was never documented as accepting any keyword arguments (and no tests ever poked at that usage), so just removed to align the two.
• In VariantDir, make a small readability change and also avoid reassigning the function parameters: the index-zero access occurs on the call to self.fs.VariantDir, not on the end of the call to arg2nodes.

Node/FS.py: Glob and glob annotation adjusted to show the exclude argument could also be a single string, as that could be passed down from the public API level, as documented: "The optional exclude argument may be set to a pattern or a list of patterns describing files or directories to filter out of the match list."

Tool/FortranCommon.py: fix an error where returns were annotated Tuple, which is not imported; changed to tuple.

Util/__init__.py: use a typevar for semi_deepcopy, which is a dispatch function, type checkers don't seem to read through to the return types of the various copy functions it calls.

No test changes - for the small code changes, we want to show behavior didn't change.

Contributor Checklist:

• I have created a new test or updated the unit tests to cover the new/changed functionality.
• I have updated CHANGES.txt and RELEASE.txt (and read the README.rst).
• I have updated the appropriate documentation

[Repiteo]

Everything seems to check out!

Will need RELEASE.txt updated, though

[mwichmann]

Everything seems to check out!

Will need RELEASE.txt updated, though

I dodged it as there are already three entries there that collectively say Environment was tweaked for typing and docstrings. I figure it's covered... will wait to hear.