Currently I do all updates manually, meaning when I make changes to the code I manually ftp the files that were changed to the server. Obviously Im playing with fire, so want to start using a more structured process of releasing updates for my php projects. Im using Windows 7 with Eclipse as my IDE. I have a linux dev box, what version control program would you recommend that I can interact with Eclipse to check out a copy from my dev box? Make changes and commit those changes back to dev, test the code and be able to commit the changes to a production box? (Im assuming that is the correct process?)
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Subversion or Git are good choices. They both have plugins that integrate into eclipse and will do what you need.
They do use somewhat different paradigms so choose the one that you are most comfortable with.