[clangd] Adjust compile commands to be applicable for tooling

Summary:
As can be seen in https://github.com/llvm-mirror/clang/blob/master/lib/Tooling/Tooling.cpp#L385
clang tool invocations adjust commands normally like this. In clangd we have
different code paths for invoking a frontend action(preamble builds, ast builds,
background index, clangd-indexer) they all work on the same GlobalCompilationDatabase
abstraction, but later on are subject to different modifications.

This patch makes sure all of the clangd actions make use of the same compile
commands before invocation.

Enables background-index to work on chromium codebase(since they had dependency
file output in their compile commands).

Reviewers: gribozavr, hokein

Subscribers: ilya-biryukov, ioeric, MaskRay, jkorous, arphaman, jdoerfert, cfe-commits

Tags: #clang

Differential Revision: https://reviews.llvm.org/D59086

llvm-svn: 355669