Set permissions for executables in modules dir, also update new commons-io to fatjar.
Set permissions for executables in modules dir, also update new commons-io to fatjar.

chipster/chipster,chipster/chipster,chipster/chipster,chipster/chipster,chipster/chipster,chipster/chipster,chipster/chipster,chipster/chipster,chipster/chipster,chipster/chipster