* Flag was being ignored, now added and passed in to tracking function
* Added a pre-filter output of tracking result if debug is set
* Added in a proper trajectory length filtering function;
  original function was too simple and relied on forward-tracking

* Removed unneeded vecs list

* removed some commented out plotting

* Also added well stack saving for debug

Merge from forgotten pull :/

* Tested various potential fixes, only
  one that seems to work is simply switching to using a
  different automatic threshold selection algorithm
* Also added in debug plotting used during diagnosis
* Currently still contains stubs of other attempts such as the
  modified canny code
TODO:
  * Remove these stubs and any commented out plotting sections