protobuf.js version: 6.0.0

When decoding messages with empty arrays or initializing a blank message with new(), all arrays are non extensible and inherited from the builder prototype.
It makes sense to freeze those array on the prototype, but when using new() or decode() we should have a working object, not frozen.

Can't we have usable objects without duplicating with Builder.from(message.toJSON()) and setting util.toJSONOptions.defaults to true?

Basically this shouldn't throw any error:

var message = new TestMessage({testList: []})
var buffer = TestMessage.encode(message).finish()
var decoded = TestMessage.decode(buffer)

// decoded.testList is undefined so it falls back to TestMessage.prototype.testList which is frozen       
decoded.testList.push('test str')

Replace {testList: []} with {testList: ['something']} and everything works back again.

I made a small repro repo to demonstrate what's going on.
Just run make and it should install everything and launch mocha. The first three tests should pass, the last two should fail.