DotNetNuke has long supported building modules as separate projects in Visual Studio.  With the release of Visual Studio 2005, Microsoft added a new compilation mode for web projects called Web Site Projects.  This required module developers to figure out how to work in the new paradigm since our previous module development methodologies would no longer work.  Anyone who was around for that transition knows how painful it was to relearn how to create modules.  The old methods no longer worked and the WSP model did not provide many of the same benefits as the compilation model in VS 2003.  Microsoft listened to the complaints of the DotNetNuke community and many other web developers who still wanted the old compilation model.  Their solution: Web Application Projects (WAP). 

WAP brought back the more traditional development style that DNN developers were used to.  Unfortunately there were some new kinks as well.  I have long advocated keeping my module projects separate from the DotNetNuke installation.  I create and destroy DNN installs quite a bit and don’t want to inadvertently delete some of my code during my frequent site purges.  Keeping my modules in a separate project directory allows me to delete websites without harming my modules.