Remove annoying messages

No more "Function has been initialized!"
Clean up
Fix a change directory bug
Add restart mechanism for some solvers.

Restart mechanism is applied to CMA-ES, JADE, and YaDE.
Let error smaller than 1e-8 take zero
Disable restart mechanism in yade

Restart mechanism is implemented and tested in yadev6
Fix restart mechanism in cmaesshellv4
Update comparison results