I've just committed basic support for configurable keymaps. You'll probably need to do a fresh ./configure to get share/keys -- and a 'make install' to install share/keys/default.xml and get your keyboard shortcuts back!

share/keys/default.xml contains the default key configuration for Inkscape; until I document the format further, you can use it for reference when developing your own keymaps. The key names in it are GDK keysym names.

share/keys/default.xml gets loaded first, followed by ~/.inkscape/keys/default.xml if it exists. At present, a user keymap is overlaid on the system keymap rather than clearing it completely.

-mental