Until now doing a git diff/git status after autogen.sh and before make was showing these files as removed.

Here the rules in the Makefile that generates the files:
baconvideowidget-marshal.h: baconvideowidget-marshal.list
        ( $(GLIB_GENMARSHAL) --prefix=baconvideowidget_marshal $(srcdir)/baconvideowidget-marshal.list --header > baconvideowidget-marshal.h )
baconvideowidget-marshal.c: baconvideowidget-marshal.h
        ( $(GLIB_GENMARSHAL) --prefix=baconvideowidget_marshal $(srcdir)/baconvideowidget-marshal.list --body --header > baconvideowidget-marshal.c )