There might be some ideas in these threads:
- Memorizing Network Diagrams
- Method of loci for graph/hierarchical information
- "Six Degrees" memory feat - memory method?
- How to memorize flow charts and graphs for economics
Just brainstorming here:
Without knowing the details, one idea is to start by drawing the graph on paper and then figuring out how much information there is and how you want to recall it. (What questions will you ask to recall the information?)
I don’t know what the program looks like, but if you draw it first, it might give hints on whether the information should be grouped by package or by functionality. The more of it that you can offload into natural memory, the fewer memory palace locations you’ll need.