[Preamble] Check system dependencies in preamble too

Summary:
PrecompiledPreamble hasn't checked if the system dependencies changed
before. This resulted in invalid preamble not being rebuilt if headers
that changed were found in -isystem include paths.

This pattern is sometimes used to avoid showing warnings in third
party code, so we want to correctly handle those cases.

Tested in clangd, see the follow-up patch.

Reviewers: sammccall, ioeric

Reviewed By: sammccall

Subscribers: omtcyfz, cfe-commits

Differential Revision: https://reviews.llvm.org/D48946

llvm-svn: 336528