AppendApplicationVersion.cs

using System.Web.Optimization;
using LOR.PDCA.Web.Infrastructure;

namespace Foo.Bar.Baz
{
    public class AppendApplicationVersion : IBundleTransform
    {
        private readonly IAppSettings _appSettings;

        public AppendApplicationVersion(IAppSettings appSettings)
        {
            _appSettings = appSettings;
        }

        public void Process(BundleContext context, BundleResponse response)
        {
            foreach (var file in response.Files)
            {
                file.IncludedVirtualPath = string.Concat(file.IncludedVirtualPath, "?vbuster=", _appSettings.ApplicationVersion);
            }
        }
    }
}

AppendFileHash.cs

using System.IO;
using System.Security.Cryptography;
using System.Web;
using System.Web.Hosting;
using System.Web.Optimization;

namespace Foo.Bar.Baz
{
    public class AppendFileHash : IBundleTransform
    {
        public void Process(BundleContext context, BundleResponse response)
        {
            foreach (var file in response.Files)
            {
                using (var fs = File.OpenRead(HostingEnvironment.MapPath(file.IncludedVirtualPath)))
                {
                    var hash = new SHA256Managed().ComputeHash(fs);
                    var version = HttpServerUtility.UrlTokenEncode(hash);
                    file.IncludedVirtualPath = string.Concat(file.IncludedVirtualPath, "?hbuster=", version);
                }
            }
        }
    }
}

Debugging.cs

using System.Diagnostics;

namespace Foo.Bar.Baz
{
    // See: http://stackoverflow.com/questions/2104099/c-sharp-if-then-directives-for-debug-vs-release/15288676#15288676.
    public interface IDebugging
    {
        bool RunningInDebugMode();
        bool RunningInReleaseMode();
    }

    public class Debugging : IDebugging
    {
        private bool _debugging;

        public bool RunningInDebugMode()
        {
            // #if DEBUG
            // return true;
            // #else
            // return false;
            // #endif
            AreWeInDebugMode();
            return _debugging;
        }

        public bool RunningInReleaseMode()
        {
            AreWeInDebugMode();
            return !_debugging;
        }

        [Conditional("DEBUG")]
        private void AreWeInDebugMode()
        {
            _debugging = true;
        }
    }
}

gistfile1.cs

var js = new ScriptBundle("~/bundles/js").Include("~/Scripts/foo.js", "~/Scripts/bar.js");

// Set EnableOptimizations to false for debugging. For more information visit http://go.microsoft.com/fwlink/?LinkId=301862.
var debugging = new Debugging();
BundleTable.EnableOptimizations = debugging.RunningInReleaseMode();

// An "append file hash" bundle transform that adds the cache breaker in debug mode...
var appendFileHash = new AppendFileHash();

// Only append the file hash if in debug mode (as release mode has a built in version buster).
if (debugging.RunningInDebugMode())
{
    bundle.Transforms.Add(appendFileHash);   
}

bundles.Add(bundle);