[Serialization] Place command line defines in the correct file

Fix several problems related to serialization causing command line
defines to be reported as being built-in defines:
 * When serializing the <built-in> and <command line> files don't
   convert them into absolute paths.
 * When deserializing SM_SLOC_BUFFER_ENTRY we need to call
   setHasLineDirectives in the same way as we do for
   SM_SLOC_FILE_ENTRY.
 * When created suggested predefines based on the current command line
   options we need to add line markers in the same way that
   InitializePreprocessor does.
 * Adjust a place in clangd where it was implicitly relying on command
   line defines being treated as builtin.

Differential Revision: https://reviews.llvm.org/D144651