DesignTools.copyImplementation() not reproducing SitePinInst objects on copied nets correctly

[clavin-xlnx]

It has been found that DesignTools.copyImplementation() is not generating SitePinInst objects on the nets it copies correctly. These missing pins can lead to issues, especially when the route uses dual-output pins and a separate route tree is created as certain route flags need to be set accordingly on the output node of these trees. Logic based on SitePinInst objects is used as input to determine these flags and, if they are missing, have a bad flag causing Vivado to crash or unroute the net.

[eddieh-xlnx]

Not sure if this is helpful, but could it be because https://github.com/Xilinx/RapidWright/blob/5aaa678493e56f069ca8e5d58a10b95196d4ef64/src/com/xilinx/rapidwright/design/DesignTools.java#L1835 is doing a "raw" setting of the cell type, without updating the port refs inside the EDIFCellInst's portInsts?

I was in this general area while working on #346.