Switch File functions, classes, and types to ValueStores (#3316)

Building on #3313, start using ValueStore on File. Functions and classes
are straightforward. Types here I present as a borderline case where
maybe we want a more bespoke API, but maybe this is okay? Most other
things probably need a slightly different API, which although I might do
that for a consistent interface, felt more out-of-scope for this change.

toolchain/check/handle_call_expression.cpp

@@ -29,7 +29,7 @@ auto HandleCallExpression(Context& context, Parse::Node parse_node) -> bool {
   }
 
   auto function_id = function_name->function_id;
-  const auto& callable = context.semantics_ir().GetFunction(function_id);
+  const auto& callable = context.semantics_ir().functions().Get(function_id);
 
   // For functions with an implicit return type, the return type is the empty
   // tuple type.