Is it possible to use build number in Affects Version/s, Fix Version/s?
Is that the right thing to do?
It could be - it depends on your processes and reporting really. The build number of a product can be veryeffectively used to populate the versions list in a project, the only real requirement is that you are working so that projects have a clear 1:1 relationship with products (you can have projects that don't have any product of course)
It probably should be the other way: have custom fields "Reported in build", "Verified in build", where the value stored would be a combination of "Version" and build number. Is that possible?
Could you point me to an example, or suggest how that "a bit of code" should be structured?
Not directly, you'll need a bit of code to populate the options on those fields
Depends on exactly how you want to do it - it's not simple code though. The most simple version would be something that automatically inserts new options into a select-list's list of options (which needs admin rights) and you'll need to decide how and when an insert happens.
Of course, you could just create a new field and add the data manually, but I can't imagine that being sustainable (although it would work while you wrote the code)
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