I think that's not really what's being asked for here. Julia looks in JULIA_PKGDIR, which defaults to ~/.julia, but it also looks in the paths in the LOAD_PATH global variable, which on my system defaults to this:
2-element Array{Union(UTF8String,ASCIIString),1}:
"/Users/stefan/projects/julia/usr/local/share/julia/site/v0.3"
"/Users/stefan/projects/julia/usr/share/julia/site/v0.3"
If you have a system-installed julia, it should have system directories in LOAD_PATH by default. Thus, you can clone package repos there and they will be found when loading packages. However, the package manager will not do this for you – unless you set JULIA_PKGDIR to one of those directories. So you may want to run julia as root and temporarily set the JULIA_PKGDIR environment variable to one of the default LOAD_PATH entries to use Pkg to install system-wide packages. After that, those packages will be visible but the package manager will consider them to be pre-installed.