I work daily with HTML templates and CGI, and founded that...
- If you keep the template in a separated file, you can drop the template into a browser and look how it looks like.
- If you keep the template in a separated file, you can edit it with an WYSIWYG editor.
- In a CGI enviroment, avoiding to open an extra file will bring a very small performance gain, and very very small if the extra file is already in the OS file cache.
Normally, there are some more expensive tasks: forking the process, loading modules, connecting to DB (if any), parsing template, doing some real process...
If you are worried about CGI performance, I would suggest to take a look at SpeedyCGI: mod_perl comparable performance (slower, obvious) under CGI.
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