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Bug ID https://bugs.eclipse.org/bugs/show_bug.cgi?id=106837 promised something similar as fixed, but it isn't fixed in Eclipse 4.5. The JavaDoc generator remembers settings for the entire Eclipse environment. That is useless and highly annoying when working on multiple projects simultaneously. It should remember its settings per project individually.
The wizard allows you to store all the settings in an Ant script. You can then simply run that Ant script on the next export.
The "save as ant script" feature is neither helpful nor easily discoverable by people new to Eclipse, like myself. If this is the way Eclipse wants developers to use the export feature, saving the settings as an ant script should be the default option, and upon re-export, that same ant script should be loaded automatically. This process should be completely transparent to the developer, rather than forcing them to use (and learn how to use) yet another tool / plug-in / system / whatever. I whole-heartedly disagree with the decision that this bug was marked as "resolved" and "wontfix" due to the arguments presented above.
We can keep it open and see if someone (you?) wants to work on this.