[clangd] Use URIs instead of paths in the index file list

Without this patch the file list of the preamble index contains URIs, but other indexes file lists contain file paths.
This makes `indexedFiles()` always returns `IndexContents::None` for the preamble index, because current implementation expects file paths inside the file list of the index.

This patch fixes this problem and also helps to avoid a lot of URI to path conversions during indexes merge.

Reviewed By: kadircet

Differential Revision: https://reviews.llvm.org/D97535