I tried this on on one of my testinstallations after upgrade failed and it worked.
But only follow this if you have the tar.gz installation.
First I renamed my magento2 directory to magento2-bad.
mv magento2 magento2-bad
made a new directory for magento2.
mkdir magento2
uploaded Magento-CE-2.0.1-2016-01-20-02-11-21.tar.gz to my new directory, entered the directory and extracted the files.
cd magento2
tar -zxf Magento-CE-2.0.1-2016-01-20-02-11-21.tar.gz
then i copied configuration and media files from the old bad installation.
cp ../magento2-bad/app/etc/config.php app/etc/config.php
cp ../magento2-bad/app/etc/env.php app/etc/env.php
cp ../magento2-bad/.htaccess .htaccess
cp -rf ../magento2-bad/pub/media/* pub/media
then i copied my custom modules (in the tar.gz version i had to create the code directory first).
mkdir app/code
and then copy my modules
cp -rf ../magento2-old/app/code/* app/code
I didnt have any theme in this installation but i suppose that it's possible to just copy them as well.
Ex:
cp from magento2-bad/app/design/frontend/<Vendor>/* to app/design/frontend/<Vendor>
Then i set the file owner and right and ran upgrade.
sudo chown -R [fileuser]:apache .
sudo chmod -R 770 .
sudo find . -type f -exec chmod 660 {} \;
./bin/magento setup:upgrade
And now it seem to work ok.
I do have more installations to upgrade so i'm waiting to see what happening from the magento team