[clangd] Perform system include extraction inside CommandMangler

It needs to run after edits from config files are applied to
the compile command (because the config file may specify the
compiler), and before resolveDriver() runs at the end of
CommandMangler.

As part of this change, QueryDriverDatabase is renamed to
SystemIncludeExtractor and is no longer a GlobalCompilationDatabase.

Fixes https://github.com/clangd/clangd/issues/1089
Fixes https://github.com/clangd/clangd/issues/1173
Fixes https://github.com/clangd/clangd/issues/1263

Differential Revision: https://reviews.llvm.org/D133757