At present, references to pages in the proofs file sometimes are a few pages off. This can most likely be fixed by making it run XeTeX one more time - which is unfortunately rather CPU-intensive.
On a related note, the makefile should delete auxilliary/output files to reduce the likelihood that the XeTeX runs will fail in the common case where the previous attempt failed ungracefully. These two issues will probably be fixed by the same change.
mskala 
Tsukurimashou Font Family and IDSgrep
At present, references to pages in the proofs file sometimes are a few pages off. This can most likely be fixed by making it run XeTeX one more time - which is unfortunately rather CPU-intensive.
On a related note, the makefile should delete auxilliary/output files to reduce the likelihood that the XeTeX runs will fail in the common case where the previous attempt failed ungracefully. These two issues will probably be fixed by the same change.