Project saving and loading is done by two modules, implemented in packages net.sf.mzmine.modules.io.projectsave and net.sf.mzmine.modules.io.projectload.
Project file has a .mzmine extension by default. It is in fact a compressed ZIP archive, which contains several files:
The format of each XML file is intuitive, with tag names defined by the classes RawDataElementName and PeakListElementName in the net.sf.mzmine.modules.io.projectsave package.