The C refers to the program being written in the C programming language as opposed to Fortran in which TranSIESTA was written. This code had been completely reengineered and further developed into the commercial products marketed by the company today.
This passage highlights a shift from Fortran to C programming for the development of TranSIESTA. The original Fortran version was replaced with a reengineered C-based program that is now commercially available.