I've left some of the less important items, like SearchView.cpp "'then' statement is equivalent to the 'else' statement", and RequestBroker::Request::~Request, because I don't feel like spending a few days entirely rewriting those files at the moment (which is what I'd end up doing if I started fixing minor problems and refactoring...)
GameSave::readOPS - not changed. At some point we may have to move to a larger type for element IDs (probably two or four bytes), but PT_NUM isn't likely to be raised to the maximum value of that type immediately, so this check will be needed then. There should be an elements[partsData[i]].Enabled check in there too, but it might be a bit difficult - I'm not sure how to access a Simulation object from GameSave::readOPS...
Notes on changes:
Graphics::textsize, Element_FRZW::Element_FRZW - typos
Button::Draw - the extra case was originally used to invert the icon (draw it in black instead of in white) when the button was clicked. However, the icon colour is now automatically set depending on the background colour. (Note similar conditions "if(Enabled) { if(isButtonDown || (isTogglable && toggle)) " near the start of the function - same logic but in a different place, setting icon colour indirectly).
Simulation::transform_save - unused redundant function, everything uses GameSave::Transform which does much the same thing.
PreviewView::NotifySaveChanged - should be height==YRES/2, it's checking whether the preview image is the correct size, and resizing it if it isn't.
Element_FWRK::update - no idea why that line was there, even though it was my commit that originally added it...
ACEL, changed a range check
DRAY, Fixed repetitive checking
GOLD, less rand()
PLNT, removed range checks, less rand()
PROT, used a switch()
VIBR, less rand()
VINE, less rand(), fixed growing along WOOD
VIRS, less rand()
Fixes http://tpt.io/~1683916 - PLSM was created on top of DMND, which other particles then displaced, leading to lots of stacking and particles escaping through the DMND.
Fix FRZW low temperature transition (accidentally turned into a high temperature transition in b661418d).
FRZZ now melts into FRZW, so that single pixels "form ice that always cools" as in FRZZ description.
ICE update function: was meant to be checking not setting parts[i].ctype. However, turning FRZZ into self-cooling ice seems a logical thing to do, so set ctype of parts[r>>8].ctype, and make all types of ice cause this reaction (not just ICE(FRZW) as was apparently the original intention of the ctype check).