Eigen fix 3007

Fix a logical error in EigenKernel. It will show when we have eigen=false EigenKernels on an EigenSystem, which will set 'eigenvalue' parameter.

Sebastian had an input which shows 'consistency_tolerance = 1e-12' is too tight. This is probably caused by machine round-off error, so we make it to 1e-10.

Others are just output improvements. Turned off any output through moose output system when solving, so on and so forth.