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How can I best compare two profiles?

So, I've been tweaking a special-purpose profile, and now I'm trying to recreate it from scratch (to make sure that I understand and can explain the effect of each configuration step)...I've checked critical points in the GUI (e.g. disabled/enabled protocols, per-protocol configurations, etc.), and two seem to "match" visually, but I'm getting different responses between the two when using the same display filters against the same capture file.

What's the best way to do a detailed comparison of two profiles? Run diff against the various files in the two profile directories?