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We're occasionally asked for a means of generating keys non-interactively with the Windows version of PuTTYgen; for instance, command-line arguments to specify the key type and so on.
There are a few wrinkles to this:
For generating keys, interaction would still be required; there isn't a source of sufficiently good randomness on Windows, so for key generation we make the user generate some by waving the mouse around.
It would be possible to pare the interaction down to the bare minimum (mouse-waving and perhaps passphrase entry); this might make PuTTYgen suitable for use in an installation procedure, which specifies the parameters and does something with the resulting keypair.
The randomness issue can be ignored for some operations, such as automated format conversions. However, Windows PuTTYgen is currently a GUI application, which makes using it from a batch file slightly tricky. Normally, it will not block the batch file, but this can be dealt with with START /WAIT; but it's still not clear how such a setup might e.g. indicate errors (given that it probably won't be able to interact with the console).
Since we already have a command-line PuTTYgen (for Unix), it might be better to just port that to Windows as a console application, disabling key generation on the way. (The Unix version can and does run in a batch mode, as we use /dev/random there, which is assumed to be a sufficiently good source of randomness and doesn't require us to interact with the user.)