[clangd] Explicitly avoid background-indexing the same file twice.

This used to implicitly never happen due to only discovering each CDB
once.

We may want to carefully support reindexing one day, but we need to do
it carefully (tricky tradeoffs) and it would need further support in
background indexer.

Making this explicit here rather than just turning off rebroadcast in
background index for a few reasons:
- allows *new* files in the same CDB to be indexed
- relying on bugs-at-a-distance cancelling each other out is bound to bite us
- gets us closer to actually supporting reindexing, which requires similar tracking

Differential Revision: https://reviews.llvm.org/D94503