the installer of NSIS should remember the settings previously specified. such as "uninstall before installation" (because i always use the other option) and also for the components page. previously disabled sections should be deselected by default when upgrading.
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It's funny that you suggest this right now. I've been working on such a solution yesterday, called Memento.
http://stashbox.org/14314/Memento.zip
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First version that remembers only sections is in CVS.
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I do not want the desktop icon, this setting should be remembered, too. I install updates /S (silent) so the previous settings (no desktop icon) should be used for this (silent) update install, too.