Move Inkscape::IO::fixupHrefs to Inkscape::XML::rebase_hrefs in new file xml/rebase-hrefs.*.  Give it the old and new base directory, so that it can change hrefs without relying on sodipodi:absref.
Also create a new function sp_repr_save_rebased_file that changes all xlink:href attributes as it writes them, so that we don't need to modify the owning document.  (Especially useful for "Save a copy" or exporting.)
extension/system.cpp: (Inkscape::Extension::save): Don't call sp_document_set_uri even temporarily other than at the same time as calling rebase_hrefs.  (Otherwise, existing relative hrefs will point nowhere.)
When exporting plain SVG, change the relative hrefs according to the destination filename.

(bzr r7643)