Site-level preferences are located in TWiki.TWikiPreferences, however this Main.TWikiPreferences prefs topic has override priority and should be used for local customisations. This allows for easier upgrades as you don't need to worry about the shipped preferences clobbering yours. It's easier to keep a handle on if you only copy over the settings you actually change.
Quick edit of existing preferences (edit the topic text to set new preferences)
Site Specific Site-wide Preferences
Skin Settings
Skin overriding the default TWiki templates: (can be overwritten by WebPreferences and user preferences)
Set WEBLISTMAPPING = Main=WikiHelp, KnowledgeBase=Knowledge Base, ResearchSchool=Research School, CMBEducation=CMB Education, CMBEducationIntra=CMB Education Intranet, MedSchool=Study Programme in Medicine, CC1837=Bioinformatics for Cell Biologists, CC2QA006=Advanced Course in Stem Cell Biology and Regenerative Medicine 30hp, CC2188=Developmental Biology for Regenerative Medicine, CC2187=Stem Cell Biology and Bioinformatics Tools, CC2192=Regenerative Medicine of the CNS, CC2189=Correlative Microscopy in Cell Biology, FunktionsSystem=Funktionssystem, BiomedKI=Study Programme in Biomedicine, BiomedKTH=Biomedical Technology at KTH, PostgradCourse=Postgraduate Course Programme, Hippocrates=The Hippocrates Studio, CC2281=Cell Migration and Differentiation - from Development to Disease, CC1837_Y08S=Bioinformatics for Cell Biologists (Spring -08), CC0000=Advanced Course in Stem Cell Biology and Regenerative Medicine 9hp,CC0001=Summer School,CC0002=Differentiation,CC0003=Medical Genetics,FluWeb=Flu Backup Web,CC2339=Academic Careers,CC2192_Y08A=Regenerative Medicine of the CNS (Autumn -08),CC2356=Molecular Localisation in Cells Using Fluorescence Microscopy,CC2271=Yin and Yang of endocytosis,StemCellGame=Stem Cell Game,FunctionalArchitecture=Functional Architecture,CellbiologyGenetics=Cellbiology Genetics,VrgProject=VRG Project,EmergencyMedicine=Emergency Medicine,IndustrySkills=Industry Skills,ConceptsDevelopment=Concepts Development,OphthalmologyStemcells=Ophthalmology Stemcells,Trash.ResearchSchoolCellularReprogramming=Cellular Reprogramming,Foo=Foo Bar, ZebraFish = Zebra Fish, StemcellEngineering = Stemcell Engineering
Final Preferences
FINALPREFERENCES locks site-level preferences that are not allowed to be overridden by WebPreferences or user preferences: