Expand use of CheckIRId stores (#5820)

This is trying to make it clearer when vectors are being indexed with
`CheckIRId`.

The only one that I still kind of want to change is the
`SmallVector<std::unique_ptr<CompilationUnit>>`, but because it's a
`unique_ptr` that's a little more complex. I may not bother.

Note, some of the changes around nuanced `SmallVector` interactions were
based on trying to copy the way `SmallVector` itself takes arguments,
like with range passing.

toolchain/language_server/context.cpp

@@ -166,13 +166,14 @@ auto Context::File::SetText(Context& context, std::optional<int64_t> version,
   // TODO: Include the prelude.
   Check::CheckParseTreesOptions check_options;
   check_options.vlog_stream = context.vlog_stream();
+  auto getters =
+      Parse::GetTreeAndSubtreesStore::MakeWithExplicitSize(1, getter);
 
   auto clang_invocation =
       BuildClangInvocation(consumer, fs, {context.installation().clang_path()});
 
-  Check::CheckParseTrees(units,
-                         llvm::ArrayRef<Parse::GetTreeAndSubtreesFn>(getter),
-                         fs, check_options, std::move(clang_invocation));
+  Check::CheckParseTrees(units, getters, fs, check_options,
+                         std::move(clang_invocation));
 
   // Note we need to publish diagnostics even when empty.
   // TODO: Consider caching previously published diagnostics and only publishing