Do I have to unlock the espionage 3 (or Espionage 2) )folders when I do a clean upgrade from Lion to Mountain Lion or can I leave them locked? Do I follow the same procedure if I am going to clone the data hard drive Espionage is on to a larger hard drive?
Just leave everything locked.
And if possible try not to change your home folder path. The hard drive size does not matter.
All should continue to work after upgrade.
Let me know if it doesn't
Rgds
Zsolt