Take care of user-supplied function by checking whether mode_compute is numeric

Fixes #508
Add options for providing the variances, an identity matrix , and user specified matrices as proposal densities

Deals with #507 and #112
Includes a unit test
Merge remote-tracking branch 'jpfeifer/mode_compute'
Ref. manual: fix reference
Finish implementation of mcmc_jumping_covariance option

Closes #112, #514
Merge remote-tracking branch 'github/master'