Many of the web site configuration details for Sitefinity 3.x were stored in the web.config file. Web.config is the main settings and configuration file for an ASP.NET web site. This file is an XML document that defines configuration information for the web application.
However, because this file is used for ASP.NET configuration (in addition to Sitefinity configuration), the web.config file became a place where Sitefinity configuration, Sitefinity customizations and ASP.NET configurations collided. This overlap could then become an issue during Sitefinity upgrades.

I am now blogging primarily on the official Sitefinity Blogs. This full blog post can be seen there.