It helps to use the same file name on both ends...
# The directory containing the source code. Relative to $(srcdir)
DOC_SOURCE_DIR=$(top_srcdir)/gio
-HFILE_GLOB=$(addprefix $(top_srcdir)/gio/,$(shell cat $(top_srcdir)/gio/gio-public-header-files.txt))
+HFILE_GLOB=$(addprefix $(top_srcdir)/gio/,$(shell cat $(top_srcdir)/gio/gio-public-headers.txt))
CFILE_GLOB=$(top_srcdir)/gio/*.c
# Headers to ignore
MKDB_OPTIONS=--sgml-mode --output-format=xml --name-space=g
# Used for dependencies
-HFILE_GLOB=$(addprefix $(top_srcdir)/glib/,$(shell cat $(top_srcdir)/glib/glib-public-header-files.txt)) $(top_srcdir)/gmodule/*.h
+HFILE_GLOB=$(addprefix $(top_srcdir)/glib/,$(shell cat $(top_srcdir)/glib/glib-public-headers.txt)) $(top_srcdir)/gmodule/*.h
CFILE_GLOB=$(top_srcdir)/glib/*.c $(top_srcdir)/gmodule/*.c
# Images to copy into HTML directory