calibre has always allowed people to install anywhere they choose. And yes all three features (desktop icon/start menu folders/adding to path) must be optional, they are optional in the current installer by clicking the advanced button.
Couple more things I thought of:
1) Show the GPL license and have an accept checkbox for it (the license text is in the calibre source tree in txt and rtf formats)
2) Have a minimum amount of clicking Next as I hate that about installers. Ideally it would be like the current installer where you either click install which installs everything with the defaults or previously used settings and an "Advanced" button that allows you to customize the installation path and the other three options.
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