This is a topic in and of itself, but started with Colin's comments on .
I just came across references to the project.
I haven't time to look into it now, but wanted to raise awareness that it exists.Based on their source code, they only support upto the Virtex5 series (last release was mid-2011). They are using the TORC library which is up to date with Zynq support - but not sure that helps any. I haven't seen anyone stating it actually works yet, but a Xilinx guy says on that once you have a partial bitstream, you can load it in the usual way (/dev/xdevcfg).
So we need to establish if this tool works with the Zynq, and if not what is missing - and whether the tool still works in general.
Given the Xilinx version being non-free, this is probably the best hope for partial reconfiguration for the hobbyist.