Well, you may be able to use a more sophisticated file transfer programme for uploading the modified code, e.g. rsync. Or you might find an Eclipse synchronise plugin that does the job. Or you might want to think about using CVS to administer your site http://docs.moodle.org/en/CVS_for_Administrators.
You might also try posting this question in a more appropriate forum, go get more experienced answers.
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