[clangd] Improve clangd-indexer performance

This is a try to improve clangd-indexer tool performance:
- avoid processing already processed files.
- use different mutexes for different entities (e.g. do not block insertion of references while symbols are inserted)

Results for LLVM project indexing:
- before: ~30 minutes
- after: ~10 minutes

Reviewed By: kadircet

Differential Revision: https://reviews.llvm.org/D91051