I'm planning to use OpenCart to build a web site. According to the licence (GPLv3) it's necessary to provide the source code of any modifications made. Is it acceptable to provide this on request or should it be linked to from every page on the shop?
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You only need to provide source if you distribute the software, not when you use it.
I don't think there is anythin legally wrong with providing the source on a per-request basis, but this is generally frowned upon for two reasons. 1) it requires action on your part to respond to each and every request, and 2) a simple download link is scalable and instant.
Note that you are only required to provide the modifications if you are redistributing the program, as explained in the other answer.