Add extended similarity comparison functionality

[drroe]

Adds two new commands, crdtransform and extendedcomp.

crdtransform is for manipulating trajectories in various ways.

[help crdtransform]
        <input crd set> [name <output crd set>]
        { rmsrefine [mask <mask>] [mass] [rmstol <tolerance>] |
          normcoords |
          trim [metric <metric>] [{ntrimmed <#>|cutoff <val>}]
               [criterion {comp|medoid}]]
        }
  <metric> = msd bub fai gle ja jt rt rr sm ss1 ss2
  Transform a trajectory in one of several ways:
  - rmsrefine  : Do an iterative RMS refinement of all frames.
  - normcoords : Normalize coordinates between 0.0 and 1.0.
  - trim       : Remove trajectory frames using extended similarity metrics.

The iterative refinement procedure is similar to that found in J. Chem. Theory Comput. 2022, 18, 3218−3230.

extendedcomp is for calculating extended similarity comparison values (see J. Comp.-Aid. Mol. Design, 2022, 36, 157-173). Based on work done by @ramirandaq and @lexin-chen.

 [help extendedcomp]
        <input crd set> [name <output data set>]
        [metric <metric>] [out <file>]
  <metric> = msd bub fai gle ja jt rt rr sm ss1 ss2
  Calculate extended comparison similarity values for each trajectory frame.

Adds a test and updates manual.