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The PuTTY .exe uninstaller has a /silent switch (and some others such as /verysilent); however, none of these actually allows a silent uninstall, as the user is always prompted to decide whether they want to remove all traces of PuTTY use (saved sessions and random seed file) from the machine:
PuTTY Uninstallation Remove saved sessions and random seed file? If you hit Yes, ALL Registry entries associated with PuTTY will be removed, as well as the random seed file. THIS PROCESS WILL DESTROY YOUR SAVED SESSIONS. (This only affects the currently logged-in user.) If you hit No, uninstallation will proceed, but saved sessions etc will be left on the machine.
Last time we looked, this was unavoidable with the Inno Setup installer engine we were using (the "skipifsilent" flag was not supported in the [UninstallRun] section), as long as we wanted to offer this choice to users uninstalling interactively.
This is fixed in 0.67 by the provision of a MSI installer (which doesn't offer the option of clearing out old settings at all). The Inno Setup (.exe) installer still has this problem in 0.67.
For existing installations of the Inno Setup installer where you want to silently migrate to the MSI installer (which requires uninstalling the Inno Setup one first) or just uninstall, there are a couple of options:
(A suspected problem with the above migration is that if a program such as Pageant is running at the time you run the Inno Setup uninstaller, the machine can end up with no Pageant; we think the Inno Setup uninstaller leaves a note to remove the currently-in-use pageant.exe on next reboot, which the MSI installer is unaware of, so the MSI's pageant.exe gets removed. Or something like that.)
(The git commit id listed in Fixed-in is actually after 0.67, even though 0.67 has an MSI installer. That's not an error; I prepared the 0.67 MSI ad-hoc, after 0.67 itself was released.)