BBEdit 12.6 has been released and this is a very significant update. BBEdit is now a sandboxed application which means there are a number changes to the way permissions are handled.
It is well worth reading the Release Notes which offer a very detailed explanation of the situation.
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.
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.
There are also many additions, changes and fixes.