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Any Apps you have installed with ports, can be updated using the ports system. Appliactions you download from PC-BSD's website and install, will have to be re-downloaded and installed, or you can just install the next release... Since he seems to be releasing about once a month, thats about as fequent of an update I can take!
It can be very boring to update every application and I guess that libraries are statically linked just like I guess it happens on MacOS X.
IMHO system libraries are part of the operating system, application specific libraries *may* be included in a self-contained environment for the app itself.
With dpkg is possible to create a kind of package - a task, so you can create a task named xyz, the user install xyz and apt downloads and installs the whole dependencies chain, so the user experience is just the same as download a .pbi that installs a self-contained app.