Removed convertIndex function, as there's a pyQCD_utils function for this.
Added a function to set individual links
Added function to convert list to Eigen matrix
Modified getLinkP function to accept a list rather than a series of coordinates
Added function to accept a list and set the corresponding link to this list.
Brought pyQCD pickling and wrappers inline with new getLinkP function
Exposed set_links function in pyQCD, added interface and updated readme.
Removed epsilon member variable as it's unnecessary.
Removed item from todo list.
Merge from master