At each invocation, Sisyphus talks to Portage and asks for information. It is this mechanism that helps Sisyphus know which packages to download during and upgrade for example. Or which packages have been rebuilt and need to be reinstalled (Sisyphus treats rebuilt packages as upgrades and will replace them in place). Or which packages have been configured with a certain USE flag, which packages are masked or keyworded etc. At the very initial step, even before the dependencies are being resolved, a syncronisation of Portage tree and Portage configuration occurs so that Sisyphus has the very latest information.
The problem is that some of that information is then overwritten by Sisyphus, such as the MAKEOPTS variable, which indicates the system how many CPU cores to use when compiling packages, using Sisyphus' "--ebuild" mode. This is a design issue. Sisyphus should never overwrite Portage configuration files, and another mechanism to achieve the same result has to be implemented. Without it, syncronisation failures can occur at any point, leading to potential downgrades and unnecessary package rebuilds.
So, we fixed that design flaw, implementing a new mechanism where overwrites are no longer needed, but now we have a chicken versus the egg problem : the new version of Sisyphus has the new mechanism implemented and works as intended, as long as it is the first package to be updated, but it also syncronises some information before updating itself. So, unfortunately, a manual intervention is required in order to make sure it is the first package to be updated.
sisyphus update
cd /opt/redcore-build
git fetch --unshallow
git fetch --all
git reset --hard 5361e6b8970e53046955ac5071d9122990cf77ec (reject the new mechanism temporary)
emerge -va1 sisyphus sisyphus-qt (this will make sure sisyphus is updated first)
sisyphus branch master (reset the branch configuration and reinstate the new mechanism)
sisyphus upgradeP.S.: This particular system upgrade will take a long time. Since we implemented the new mechanism in Sisyphus, a mass rebuild of all packages have been triggered, in anticipation of the new release, so everything will be replaced. If you're not willing to wait, a new ISO image, containing all the updates, rebuilds and fixes will be released in the next few days, weeks.
P.P.S.: These instructions are only valid for branch master users. Branch next, which is the testing branch already received the new mechanism a while ago.