I am not a developer on this project, but thought this could be helpful to people here.
Analysis/fix tool for extension and customization conflicts resulting from the Magento SUPEE-6788 patch.
All results are output to screen and to var/log/fixSUPEE6788.log.
We recommend patching your site in two phases: First, apply the SUPEE-6788 patch and immediately run this script with the fixWhitelists flag to fix any functionality broken by the whitelist changes. (Verify that all entries added should in fact be there.) Then, run this script with analyze and/or fix to correct controller conflicts. Verify all is well, then disable the admin controller compatibility mode.
After patching, scan with MageReport.com to confirm your site is up to date.
Nice. We used this on several and it was very handy.
Unfortunately, there are some problems with this one.
One of them is that it requires shell access while some hostings still don't provide that.
Another problem is that on multiple environments this is not handy anymore.
To make everyone's lives easier we created an extension for this - http://supee6788.magebit.com
It adds all blocks to whitelist. Once it has ran once it disables itself so the security is still as it should be.
Another great feature here is that you can set whitelist till date. For example, you have a site under development on multiple environments. Install this extension and set the date to golive date. After the golive date it will not whitelist automatically anymore. You can also use this to scan all blocks used in code to see/add/remove blocks manually via admin panel.
NOTE: This extension will be publicly available at 5PM (GMT+2), Oct 30 as we need to make sure all is ruuning great on different stores etc. If you need it faster - contact us and we can send you the beta version.