Let's talk about Windows first:
First if it's not a CGI, but a command line utility it is necessary to give those files an extension. The only other solution would be to force the users to use a Unix shell. That's be even harder on most of them.
Second ... the fact that you do not have to enter the .exe should lead to a question "Is it possible to set the system so that you do not have to type .pl?" And of course it is. You just have to add that extension to the list in PATHEXT system variable. Easy to do in a network login script or something, isn't it?
So then the script files do end with .pl, but everybody may call them without.
Then CGIs under Windows:
if you use Apache you do not need the extensions, if you use IIS you do. In either case it's not such a big problem to make a redirect there somewhere so that both addresses work.
For Unix:
yeah you are right that there the extensions are not needed. I find that way of handling files a bit crazy, but that's another point.
Jenda
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