The problem is that the FitCanvasToDrawing verb doesn't 'dirty' the document, so the Save verb doesn't save the changes. You can see this by running:
inkscape --verb=FitCanvasToDrawing tree.svg, then choosing File->Save and then File->Save As... and saving a second copy. Only the second copy is saved with the cropping. I'm not sure if this is a general problem with verbs, or specific to FitCanvasToDrawing. If the former, I'll open a separate bug.
OK, I get it! Although this actually exposes another bug. The following doesn't work:
cp tree.svg tree_copy.svg; FitCanvasToDraw ing --verb=FileSave --verb=FileClose tree_copy.svg ;
inkscape --verb=
inkscape -A tree_crop.pdf tree_copy.svg
The problem is that the FitCanvasToDrawing verb doesn't 'dirty' the document, so the Save verb doesn't save the changes. You can see this by running:
inkscape --verb= FitCanvasToDraw ing tree.svg, then choosing File->Save and then File->Save As... and saving a second copy. Only the second copy is saved with the cropping. I'm not sure if this is a general problem with verbs, or specific to FitCanvasToDrawing. If the former, I'll open a separate bug.