It's not clear to me what the exact question within the code is. Java is pass-by-value, but arrays are pass-by-reference as they pass no object but only pointers! Arrays consist of pointers, not real objects. This makes them very fast, but also makes them dangerous to handle. To solve this, you need to clone them to get a copy, and even then it will only clone the first dimension of the array.
For more details see my answer here: In Java, what is a shallow copy? (also see my other answers)
By the way, there are some advantages as arrays are only pointers: you can (ab)use them as synchronized objects!
