They have also made a change where packages not offered in their official repository will no longer appear in Package Manager as an installed package.
In the release notes the pfSense team has said:
The upgrade process will automatically remove pfSense-pkg-* packages installed from alternate repositories. After the upgrade completes, the user can reinstall these packages. Packages from alternate repositories will not appear in the Installed Packages list in the GUI, and must be entirely managed in the command line.
As a result, our team has changed the name of our package to dnsthingy from pfSense-pkg-dnsthingy. Our automatic upgrade will convert installations to the new package name and has verified that DNSthingy does continue to operate in the pfSense 2.4.4 snapshots from our alternate repository when managed from the command line.
How to Remove DNSthingy from pfSense
Under Diagnostics / Command Prompt run the following command:
pkg remove -y dnsthingy