[clangd] Ignore the static index refs from the dynamic index files.

This patch fixes the following problem:
- open a file with references to the symbol `Foo`
- remove all references to `Foo` (from the dynamic index).
- `MergedIndex::refs()` result will contain positions of removed references (from the static index).

The idea of this patch is to keep a set of files which were used during index build inside the index.
Thus at processing the static index references we can check if the file of processing reference is a part of the dynamic index or not.

Reviewed By: sammccall

Differential Revision: https://reviews.llvm.org/D93393