This is a really neat concept! The puzzle elements work together quite well, although I'm not sure whether the 15-minute time limit is realistic. I managed to complete it on my third try with one and a half minutes remaining. Reflecting on how I solved the puzzle, I believe there too many things I had to discover and deduce in 15 minutes, but I wouldn't consider this to be too large of a problem, since I can basically just try again, picking up where I left off.
This puzzle was much more involved than I expected it would be, and I really like how well it was put together.
One small nit: One thing that slowed me down was the slower speed at which text is written into a terminal. I wonder if, although the effect is less cool, making it instant would be better for the puzzles. That being said, I had neglected to read the controls until just now, so I didn't realize the terminal was scrollable with page up/down and ended up rerunning commands I didn't need to rerun.
Another small nit: I wish tab completion worked a bit more like Linux, where it completed all the way up until the next character you needed to decide. That would have made reading the logs a bit quicker.