[clangd] auto-index stores symbols per-file instead of per-TU.

Summary:
This allows us to deduplicate header symbols across TUs. File digests
are collects when collecting symbols/refs. And the index store deduplicates
file symbols based on the file digest.

Reviewers: sammccall, hokein

Reviewed By: sammccall

Subscribers: ilya-biryukov, MaskRay, jkorous, arphaman, kadircet, cfe-commits

Differential Revision: https://reviews.llvm.org/D53433

llvm-svn: 346221