Well, looks like noone tried that before :-)
It should work if you put "pages/home.rst" in index.rst and "generalnotes.rst" in home.rst
However, that will *NOT* work because when it builds home.rst it will not find generalnotes.rst
A quick and dirty solution is to create a symlink to pages/generalnotes.rst outside pages.
A more complicated solution is to not have things that at the same time are pages and get included in pages.
For example:
index.rst includes pages/home.inc and pages/generalnotes.inc
home.rst includes pages/generalnotes.inc
generalnotes.rst includes pages/generalnotes.inc