Ok, so this is how I develop custom magnl module, I don't know another 
(simpler) way:

1) get magnolia sources from SVN (you can find tags with all versions <= 4.5.2) 
or GIT (version 4.5.2+)
SVN: 
[url]http://svn.magnolia-cms.com/svn/community/magnolia/tags/magnolia-4.5.2[/url]
GIT: look here [url]http://git.magnolia-cms.com/gitweb/[/url]
2) in those sources you'll find an artifact "magnolia-empty-webapp"; this is an 
empty web application which you can start from your favorite ide or just deploy 
it under your favorite servlet container (tomcat or jetty will do the work)
3) duplicate this project, add your custom module as dependency (just like you 
add it to any other webapp)
3.1) you can add more standard/custom modules to it
4) start this webapp in debug mode from your IDE or inside a servlet container 
having remote debug enabled
5) enjoy debugging

-- 
Context is everything: 
http://forum.magnolia-cms.com/forum/thread.html?threadId=41ff8790-9429-4ab7-a768-bd47c3d90f13


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