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How do I efficiently manage the updating of the source code and patching of a website in a live environment?

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You can use any of Versioning tools like SVN or Git Hub which basically manage your source code as well as maintain complete change logs / history.
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Experience Trainer for C, C++, .Net, Java, Python, Php, Networking

Changing Source code Will not affect much except a small down time. You just need to ensure that there are no operations being done on file-system or database.
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