Right now, a normal (non-HPC) build always sets a single GAP root, pointing to the srcdir. But this way, make bootstrap won't work for out-of-tree builds, because the packages end up in builddir. To solve this, we should set two root directories for out-of-tree builds: First the builddir, then the srcdir.
For HPC-GAP build, that would be three GAP roots: two for the srcdir, and on for the builddir.