Here is a quick dump of what I've done to upgrade my QCubed 1.0 app to 1.1 (as of 07/10/09). I'll try to polish this in the future, but It may be a good reference if you are upgrading:

download the latest version of qcubed 1.1 in a separate dir (I keep my repos under git)

diff -q -r qcubed-1.1/ git/htdocs/ | grep -v '.svn'|grep -i only

move your existing qcodo folder to the qcubed 1.1 style:

mkdir -p assets/_core/php
git mv examples/ assets/_core/php/
git mv includes/data_classes/ includes/model
git mv includes/data_meta_controls/ includes/meta_controls

mkdir includes/configuration/
git mv includes/configuration.inc.php includes/header.inc.php includes/footer.inc.php includes/prepend.inc.php includes/_README.txt includes/_LICENSE.txt includes/configuration/

git mv _devtools/codegen_settings.xml includes/configuration/

git mv includes/qcodo/ includes/qcubed
git mv includes/qcubed/qform includes/qcubed/controls

git mv includes/qcubed/_core/qcodo.inc.php includes/qcubed/_core/qcubed.inc.php
git mv includes/qcubed/_core/qcodo_orm_only.inc.php includes/qcubed/_core/qcubed_orm_only.inc.php

git mv includes/qcubed/_core/codegen/templates/db_orm/class_gen/qcodo_query_classes.tpl includes/qcubed/_core/codegen/templates/db_orm/class_gen/qcubed_query_classes.tpl
git mv includes/qcubed/_core/codegen/templates/db_orm/class_gen/qcodo_query_methods.tpl includes/qcubed/_core/codegen/templates/db_orm/class_gen/qcubed_query_methods.tpl
git mv drafts/dashboard drafts/panels
git mv assets/css/ assets/_core/
git mv assets/images/_core/ assets/_core/images
git mv assets/images/* assets/_core/images/
git mv assets/js/_core/ assets/_core/js
git mv assets/js/_README.txt assets/_core/js/
git mv assets/_core/js/qcodo.js assets/_core/js/qcubed.js
git mv assets/_core/php/examples/qcodo_query assets/_core/php/examples/qcubed_query/
git mv assets/php/* assets/_core/php/
git mv assets/php/friendly_error_page.php assets/php/_README.txt assets/_core/php/

mkdir assets/_core/php/_devtools
git mv  _devtools/codegen.php assets/_core/php/_devtools/codegen.php
mkdir includes/tmp
git mv includes/qcubed/cache/ includes/tmp/

save your current diff:

diff -q -r qcubed-1.1/ git/htdocs/ | grep -v '.svn'|grep -i only > files_diff

commit your changes (to keep separated the renaming from the differences) copy the new files over the old ones

cp -r ../../qcubed-1.1/* .

create wrappers:

echo "<?php require 'configuration/prepend.inc.php'; ?>" > includes/prepend.inc.php
echo "<?php require 'configuration/footer.inc.php'; ?>" > includes/footer.inc.php
echo "<?php require 'configuration/header.inc.php'; ?>" > includes/header.inc.php

add to your configuration.inc.php

// For compatibility with 1.0 generated files
define ('__DATAGEN_META_CONTROLS__',__META_CONTROLS_GEN__);
define ('__DATAGEN_CLASSES__',__MODEL_GEN__);

And the delete files that where present only on 1.0 version (you can find them on the "files_diff" file)