I originally added the CellArray class to consolidate those methods into one place and make it so that operations involving multiple cells would be performed on the object itself. I didn't like having new CellArray([]) in so many places even at the time, though basically went for it just because the alternatives also had disadvantages.

Generally I've have tried to avoid adding methods to prototypes because of the side effects e.g. when going for (let i in o) for arrays:

let o = [];
Array.prototype.foo = function() {}
for (let k in o) {console.log(k);} // -> outputs `foo`

will output foo as one of the keys. Although I don't do it myself I've sometimes seen other people's code use [] instead of {} to define an associative object e.g. let o = []; o.property = 'value';.

I'm wondering whether it might be an idea to move those methods into a utility object e.g. cellArrayFns or cellArrayOps to avoid these kinds of bugs at the same time as removing the need for the CellArray class, as think they could be quite tricky bugs to track down.

Yeah, I agree it's an anti-pattern. I thought about hiding the methods with defineProperty(), but apparently it doesn't work with multiple argument setter functions.
If this were a brand new project, I'd probably go for a new data structure something like 'CellCollection' without extending Array. After all, inheritance can't be free from potential method shadowing.

As @mcyph mentioned, I think moving the methods to utility functions is a better idea. These methods are not used that frequently, so migration wouldn't be too overwhelming.

Hi guys, I am also ok to move the methods to utility functions.

I've created a file named cellArrayUtils.ts inside util directory and transferred all the CellArray related functions.
Also updated the examples as well, but let me know if something doesn't work.