The Java Language Specification says:
An object is a class instance or an array.
And it also says:
arrays [...] may be assigned to variables of type Object
But the part that confuses me is:
The class Object is a superclass of all other classes
If arrays may be assigned to variables of type Object, then it must mean that arrays can be Objects (not only behave as, but to be instead). Then it means that an array is a class instance, which does not seem to be consistent with the first quote (if it were, then why would it be listed as a different thing?).
How can all this fit together?
Yes... and no. It is true, indeed, that new Object[100] instanceof Object → true, but this is missing the true nature of arrays in Java. Arrays are objects (lowercase), but not Objects (capitalized). Being objects, for example, you have to use the new operator to allocate space for them.
However, the Java Language Specification is right to say that "An object is a class instance or an array", because arrays are fundamentally different from a regular Object. They are inherited from languages such as C++, that were much more deeply rooted in the low-level architecture of computers.
"arrays [...] may be assigned to variables of type Object" only because Java provides an interface for us, programmers, to refer to arrays as Objects. In fact, the JLS says:
All methods of class Object may be invoked on an array
Which of course is true, but it does not logically imply they are Objects. Arrays are not true Objects; therefore, they are not true class instances, and therefore the sentence "The class Object is a superclass of all other classes" doesn't apply here.
All in all, Java is not a pure Object-Oriented programming language (primitives are not objects, for example, but they are nonetheless present in Java). And arrays are a language feature that Java includes that behave as if they were class instances of the Object class, but are not actually class instances of it.
[This is my attempt at summarising the main points made here. Thanks a lot to all of you for your ideas, and feel free to add more!]