"at the end of the operation" - this sounds weird to say. Also, notes about it should be added to the single methods as well.

Maybe something like this, added to the doc of every method that does recalculation?
```java
/**
 * Sets a permission to the given value by its fully qualified name.
 * <p>
 * This method will recalculate the permissions on the attached {@link Permissible}. If it is
 * desired to set multiple permissions at once,
 * {@link #setPermissions(blah blah blah blah blah blah)} is preferred, as the recalculation is
 * only done once.
 * 
 * @param name Name of the permission
 * @param value New value of the permission
 * @see setPermissions(Map<String, Boolean> permissions)
 */
public void setPermission(String name, boolean value) {
```
Hmm.. still don't like the language. I'll be thinking.