Starting with today's update, BBEdit is a sandboxed app, which is a change that Bare Bones Software needed to make because it plans to bring BBEdit to the Mac App Store in the future.
Sandboxing on macOS limits apps to their intended use and is a protection implemented to prevent malicious software from working. BBEdit will require explicit permission to access files and folders on the Mac.
To work properly, though, BBEdit often requires advanced access to file and folder contents, a problem Bare Bones Software is solving with a prompt to enable Sandbox Access. This setting, says Bare Bones Software, will allow for the full functionality of BBEdit without compromising security.
Without unrestricted access to your files and folders, many of BBEdit's most useful features, from the basic to the most powerful, won't work at all; or they may misbehave in unexpected ways. At the very least, this hinders your ability to work done.Due to the changes, BBEdit is no longer able to access support folder items in iCloud Drive, so those previously using iCloud Drive/Application Support/BBEdit will need to make some manual changes as outlined in the update's release notes.
In order to resolve this fundamental conflict between security and usability, we have devised a solution in which BBEdit requests that you permit it the same sort of access to your files and folders that would be available to a non-sandboxed version.
For this reason, the first time you start BBEdit, it will prompt you to allow this access. The prompt will not be repeated; so if you decline to allow this access and later reconsider, go to the Application preferences, and click on the "Allow" button in the "Sandbox Access" section.
The new version of BBEdit also includes a number of tweaks to the app and a whole slew of bug fixes, all of which are also listed in the release notes.