meta: Clean up various class-native* RDEPENDS overrides

meta: Clean up various class-native* RDEPENDS overrides

With PACKAGES functioning more correctly for native recipes combined
with classextend improvements over the years, there are various overrides
of RDEPENDS which look unecessary now, clean them up.

There some some minor changes in dependencies, specifically:

"python3-numpy-native.do_populate_sysroot" -> "python3-native.do_populate_sysroot"
"python3-mako-native.do_populate_sysroot" -> "python3-native.do_populate_sysroot"
"itstool-native.do_populate_sysroot" -> "libxml2-native.do_populate_sysroot"

however there are already:

XXX-native.do_prepare_recipe_ssysroot -> YYY-native.do_populate_sysroot

mappings from DEPENDS so this is effectively a null op.

Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>