Ask HN: development collaboration tools & best practices?

INTRO: I'm having difficulty collaborating remotely with a project lead who has little time and specialized knowledge.

BACKGROUND: I am recreating and optimizing a complicated image processing algorithm. The algorithm has been developed within a specialized image processing framework, we are recreating it within OpenGL.

CONSTRAINTS: We are not able to access the original code and framework. We are limited to working with input files generated at various stages in the algorithm, processing these files and compare our output file to that of the output generated by the original framework. MATLAB is relied on heavily. In addition the contact has limited time. Sending zipped folders back and forth for comparison has become quite laborious.

REQUEST: Can anyone share best practices in making the best of this situation? Any suggestions for developing-focused project management and collaboration tools would be extremely helpful.