A while back, I stumbled upon a version of PuTTY that used file configurations instead of registry configurations (http://jakub.kotrla.net/putty/). I've been using this configuration for a while for local use, but now that I'm getting on the road, I'm loading up my flash drive with Portable Apps, including PuTTY Portable. I've noticed that Putty Portable uses registry keys to store info, and I was wondering if it was possible to store it in separate files for ease of editing, and to reduce fragmentation and corruption.
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Search for puttytray on this site, or the putty portable apps page.
You can run portable putty (to load reg settings), then run puttytray AT THE SAME TIME. Then you can load settings in puttytray, select "settings from file" and save them there. When all are copied over, exit puttytray, exit putty, then change the portableapps config files to point to puttytray.