Extremely slow to package application revision

The code that packages the application revision before uploading and registering to s3 runs really slow when the number of files in the application revision is large. We have one application with small number of files < 500 that runs fast enough, but we have a separate one with well above 5000 and it takes forever. I took a quick look at the code, and it looks like the slowness is because each file is being added to the zip file individually. You can see the area of concern here:

https://github.com/JetBrains/teamcity-aws-codedeploy-plugin/blob/master/aws-codedeploy-agent/src/main/java/jetbrains/buildServer/runner/codedeploy/ApplicationRevision.java#L125

Let me know if you need any more information. I'm going to try to hack my way around it for now, but I'd prefer to use the plugin in the long run.