First ensure that the web.home property in build.xml points to the www folder in your Map Server web tier deployment. If it doesn't, edit and save the file. Then run the command:
ant deploy
This will combine and compress the files to the build folder and then deploy them to the web tier. Yet another option is:
ant deploymin
This deploys only the combined/compressed files. This supports a fully-functioning deployment, but does not allow for debugging of the individual files, so it's useful once your application is complete.
ant clean
can be run to clean up the build folder.
ant deployandcleanup
will deploy compressed and individual files to the web tier and clean up the build folder in one step. This is very useful when developing and debugging the application, since it precludes the possibility of making edits to a file in the build folder instead of the main folder by accident. This is also the default build target, so if you run 'ant' with no parameters, this will be the effect.