[clangd] [Modules] Use ASTReader directly in IsModuleFileUpToDate (#113879)

@kadircet mentioned in
https://github.com/llvm/llvm-project/commit/448d8fa880be5cae0f63c3b248f07f647013a5a4#diff-fb3ba8a781117ff04736f951a274812cb7ad1678f9d71d4d91870b711ab45da0L285
that:

> this is definitely a functional change, clangd is used in environments
that solely relies on VFS, and doesn't depend on ASTUnit at all.

> right now this is both introducing a dependency on ASTUnit, and making
all the logical IO physical instead. can you instead use the regular
compiler utilities in clangd, and get the astreader from
CompilerInstance directly, which is VFS-aware, and doesn't depend on
ASTUnit ?

This tries to resolve the problem by creating ASTReader directly and use
VFS to create the FileManager.