Same sentiment here. Basically, the options are as follows:
1) no attempt at separation - the perl script contains both code and html
2) some attempt at separation - part of the logic is moved to the template
3) strict separation - no html in code
(3) gives you clean and highly maintainable code but is hard to achieve in some cases. I've been through (1) and the result is ugly and difficult-to-maintain code (which has lots of html in it). (2) seems like a neat solution :)
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