The single WAR file approach is the best practice for deploying your projects. 
You can use it to deploy JSP and Freemarker template scripts that reside on the 
file system too. It is the recommended way to deploy a project to a production 
environment. 

http://documentation.magnolia-cms.com/administration/deployment/war-file-with-multiple-configurations.html
http://dev.magnolia-cms.com/~gjoseph/dont-deploy-magnolia-deploy-your-project

However, you can also write Freemarker scripts (.ftl) as "inline templates". In 
this case the scripts are stored in the repository and can be activated using 
the activation mechanism. This may be quicker in development and test 
environments. Create your template script in Templating Kit > Templates in 
AdminCentral and reference it from the page definition. Remember to check the 
Enable Template checkbox in the script editing dialog.

--Antti

-- 
Context is everything: 
http://forum.magnolia-cms.com/forum/thread.html?threadId=488185c5-1ca3-4dbe-a673-f903f3742bf6


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