»Code Colors«

There were three colors of code: red, green, gold.
Red = "real world", zion, machine city, detached from the Source
Green = matrix, closer to the source
Gold = source

Neo sees the red code outisde of the matrix because, as the oracle says, his power extends beyond the green code of the matrix. It could mean that Zion/Machine City are simulations, matrix within a matrix, whatever. I think it is just there to point out that there is no reality, as Morpheus talks about in M1. I think the computer code is a metaphor for a soul, and where that soul is on its journey to "salvation" or "enlightenment."

The red souls in Zion were anarchic and had rejected the machines all together. THe green souls in the matrix were closer but unaware. The gold souls--Seraph (angel)--were from the Source.

Neo becomes One with the source at the end, exploding in gold light.