You... study how they evolve, in context. You're going to have to go do real historical research. Read the documentation and source code, absolutely. But also r

You... study how they evolve, in context. You're going to have to go do real historical research. Read the documentation and source code, absolutely. But also read emails, get access to participants' papers, interview participants, study the environment(s) in which the software grew up and spread, study the background contexts (what else was happening in computing at the time: licensing, etc.), and so forth. Do real history, in other words. This is one of the major flaws of research on software history to this day, and it's not like I'm making this up on my own. Real historians who study computer history have commented on this problem. Software history needs to be treated like... history and studied accordingly.