Assorted cleanups

- fix naming convention for `workingDirectory`
- use type alias for `EvalFiles` everywhere
- move `ponderMode` into `LimitsType`
- move limits parsing into standalone static function

closes https://github.com/official-stockfish/Stockfish/pull/5098

No functional change

src/thread.h

@@ -79,8 +79,7 @@ class ThreadPool {
         }
     }
 
-    void
-    start_thinking(const OptionsMap&, Position&, StateListPtr&, Search::LimitsType, bool = false);
+    void start_thinking(const OptionsMap&, Position&, StateListPtr&, Search::LimitsType);
     void clear();
     void set(Search::SharedState);