Xdebug is a necessary plugin for development. Just make sure you don't use it in production.
I recommend subversion database and develop from there. When you're ready to test, you can then checkout to your dev server to test it. You can update the production server the same way. You can setup a script that you can run with one command or maybe a editor plugin whenever you want to update either the dev or production server.
Of course, this is getting all complex, but if you're familiar with linux, it should be pretty straight forward. To get rid of all the busywork, just install ubuntu and then virtualmin. From virtualmin, you can create svn databases, virtualhosts, cron jobs and anything else you want with a few clicks.
For something simple, setup subversion and a test server on your local machine.
For something a little more complex, but very handy, setup redmine. You can check out redmine here: http://darkbit.devstorm.co.uk/redmine