What happened to the rest of the old mission (e.g. the cemetery, quarters, etc.) and why were they not rebuilt?

Firstly the original quadrangles was never built to last...a temporary outpost until all could be rebuilt in stone which never happened. By mid 1800s the quadrangle and related buildings were in decay and then finally torn down as the city began to be established. The Mexican Gov't sold off the lands associated with the Missions some of which became land grants. For more info see the Mission website: www.sanbuenaventuramission.org

Because