On a recent project I have been working on in C#/ASP.NET I have some fairly complicated JavaScript files and some nifty Style Sheets. As these script resources grow in size it
The MSBuildCommunityTasks Project has a few MSBuild tasks that may do what you are looking for including Merge and JSCompress.
You could add these into your MSBuild project in the AfterBuild target to allow the project to perform this action every time the project is built and nothing would ever be out of sync. Your web application could then reference the compacted version for run but the developers would edit the full versions.
Nothing else would be needed on the server except the MSBuild community tasks assembly. You can put this assembly in your own source tree and reference from there and your CI build should get that assembly and everything it needs when it builds.