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That's a bad thing that you can't quickly change your implementation: this means, that your code is not flexible.
"Out of boundary" is too trivial error, try finding it yourself. Just remember, that...

Your generationNextCalc method. Try to trace the life of a cell (from the beginning of the method) throughout the loops. Then reason, what changed on your field.
Also, your cells have only 2 states....

The very same NullPointerException, I guess, with the very same array. Java's multidimensional array is just an array of references to other arrays. So, if one dimension is initialized, that does not...

I see the calculations. I mean, what is created after this operation? What object? What it consists of?

Can you explain in details what happened when you wrote Cell[][] cells = new Cell[lnr.getLineNumber()+2][]; - in your opinion?