I heard the intention was that sometimes it's against the public good to prosecute some people even though they have comitted crimes. Good examples of it being used as intended was pardoning the perpetrators of the whiskey rebellion, the confederate army, vietnam draft dodgers and more controversially, Nixon. I guess it's also intended in cases where obvious miscarriages of justice have been committed. It made sense in 1785 or whenever but along with lots of the rest of the constitution it's long obsolete and has been twisted, stretched and mangled into a hideous caricature of itself over the centuries.