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However, I dont know if it is better to create separate repositories for each project or to create a single repository and just make folders within it.
It's an organizational question up to you. When I used Subversion, I would group tightly coupled projects together. By that I mean those in charge of working one project are definitely going to want access to the development source of the other. For example, if my code used zlib, this would be an example of
not having such coupling. I just want the library. I don't care about the actual repository. On the other hand, a repository where I had two projects, one for a library, and one for the GUI, made sense. If you're trying to extract some kind of rule on grouping projects, you shouldn't. Heck, for configuration purposes, you might as well dump all projects into one single repository. If it becomes unmanageable later on, just split up the projects.
The wildcard is Fisheye. I haven't used it, and I don't know what the configuration quirks are. From briefly looking at their online documentation, it looks like Fisheye has approached the issue (
the relevant document page on repository layout)) in a rather sane and intuitive manner. So it looks like Fisheye won't interfere in your choices. One repository, multiple repositories: all up to you.