Is it now possible to change the method of congruence analysis?
I wonder why do you believe that someone plans to implement a further method for deformation analysis in JAG3D.
I would like to use the Pezer method rather than this implemented in JAG3D which is like Karlsruhe.
It is up to you to implement the methods you prefer.
"Pursuant to the results obtained by [Sušić et al. (2015)], the conclusion can be drawn that modified Karlsruhe Method and method implemented in the JAG3D Open-Source Software provide satisfying results regarding the discovery of unstable points, against the most commonly applied Deformation Analysis Methods–by Pelzer and Karlsruhe."
From this point of view, there is no reason to simply implement the same thing the other way around.
applied-geodesy.org - OpenSource Least-Squares Adjustment Software for Geodetic Sciences