If you used VS2010 for Sharepoint development you most probably encountered with the famous problem: when you add a new element (e.g. new module) to the project created using Sharepoint project template, VS implicitly adds this element to the randomly selected feature. Waldek Mastykarz even created extension for VS, which prevents this behavior: Mavention Cancel Adding SharePoint Project Items. Surprisingly this bug (can’t call it feature) is still in VS2012 in Sharepoint 2013 project templates. Don’t know why MS still didn’t address it.
On this week I had a meeting with Microsoft guys from Redmond from product group which develop Sharepoint office dev tools. Although meeting was about another subject, in the end I asked them to fix this problem. Hope it will be fixed sometime, and I hope that my request will help to make it a little bit quicker :).