Currently, the Repository module is a .net 1.1 module. While the module can be installed using the 'Install' package on both DotNetNuke 3.X and 4.X, the source code can ONLY be modified/rebuilt using .net 1.1 (Visual Studio 2003)
So, if you are running DotNetNuke 3.X / Visual Studio 2003, the process is straightforward
If you are running DotNetNuke 4.X / Visual Studio 2005, then it's not. You need to setup a .net 1.1 development environment, install the corresponding DNN version ( for example if you're running DNN 4.3.5, then you should install DNN 3.3.5 ).
Once you have a working DotNetNuke 3.X installation. Install the latest Repository 'Source' package (3.01.13). Using Visual Studio 2003, open the DotNetNuke.Repository.sln solution file. Check the references to make sure they are pointing to the correct folders ( the assumption is that your DotNetNuke web site is located in c:\inetpub\wwwroot\dotnetnuke, if different you'll need to modify the project references). You should then be able to build the solution and debug/modify the source.
Once you're all done, rebuild the entire solution in 'Release' mode. Exit Visual Studio. In the /DesktopModules/Repository folder you'll see a batch file named 'build'bat'. Make sure you have Nant installed ( if not, search the internet, download and install it ). Just run the batch file. It will rebuild and create a new install and source package. The packages will be located in the /DesktopModules/Repository/package folder. You can then install your new 'Install' package on either a DotNetNuke 3.X OR 4.X web site using the Host->Module Definitions screen.