Move files from `Overlap/Analysis` to Overlap

There were only three files in `Overlap/Analysis`.

Overlap/Analysis/plot_traj.py → Overlap/plot_traj.py

@@ -94,7 +94,7 @@ if __name__ == "__main__":
     import argparse
     import sys
     from os import path
-    sys.path.append(path.join(sys.path[0], "../../Common"))
+    sys.path.append(path.join(sys.path[0], "../Common"))
     import util_eddies
     import time