Reapply "[clang] NFCI: Adopt `SourceManager::getFileEntryRefForID()`"

This reapplies ddbcc10b, except for a tiny part that was reverted separately: 65331da0. That will be reapplied later on, since it turned out to be more involved.

This commit is enabled by 5523fefb and f0f548a6, specifically the part that makes 'clang-tidy/checkers/misc/header-include-cycle.cpp' separator agnostic.