Folder structure before (2 separate repositories):
XXX
|- .git
|- (project files)
YYY
|- .git
This can reduce files to ~15% of their size (2.3M to 345K, in one case) with no obvious degradation of quality.
ghostscript -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH -sOutputFile=output.pdf input.pdf
Other options for PDFSETTINGS: