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PuTTY stores its configuration and host keys in the registry under HKEY_CURRENT_USER, because we think that by and large that is the best single location for the job. However, not everybody agrees, and often for good reason. People carrying PuTTY around on a USB key tend to want to store their configuration in a disk file on the same device, so they can take absolutely everything with them from place to place. (See the docs for a current hack to do this, which assumes you have write access to your registry.) Sysadmins could very well want to store system-wide configuration in HKEY_ALL_USERS or HKEY_LOCAL_MACHINE.
The major difficulty with this work is one of design: if there are contradictory things stored in several of these locations, which one should take priority? It seems fairly obvious that HKEY_CURRENT_USER or a disk file represent the choices of an individual user, and therefore they should override HKEY_ALL_USERS or HKEY_LOCAL_MACHINE which merely set defaults over a large number of users. But which of CURRENT_USER and a disk file takes priority? Which of ALL_USERS and LOCAL_MACHINE? You can make a case for either one either way.
After some consideration, I think that probably the simplest thing would be for each config location (CURRENT_USER, ALL_USERS, LOCAL_MACHINE and disk files) to contain a single "Priority" field - so that a sysadmin could arrange for either of ALL and LOCAL to have higher priority than the other, depending on local needs. PuTTY should scan all config locations and use the priority order it finds. Priorities should be unbounded, so that the local user can always ensure they have a setup which supersedes the systemwide one.
Another question is how to tell PuTTY about a disk file. Specifying it on the command line is one obvious way, but not a particularly convenient one to set up. Alternatively it could be stored in the Registry somewhere - but where? Within one of these interchangeable config locations (in which case, what happens if a disk file specifies another disk file? Should that be allowed?), or in one single place?
Should PuTTY look for a disk file in the directory it was run from, and if found, use that in the first instance? (Supports convenient `run from a pen-drive' operation.)
Finally, although the above design makes it obvious how PuTTY should read its configuration, how should it write it? When the user wants to save a config change, where should it be saved to?
Some people have got fed up waiting for us to sort the design issues out, and made forks of PuTTY which store settings in files; some of these can be found on our Links page.