Here I go again with the William Westwater quote. I copy and paste this so many times I'm afraid someone's going to write it on my tombstone. 
"As we saw in the movies, operators in the hovercraft can download programs directly into the Matrix. After the Smith incident (in The Matrix Revolutions), Zion developed more direct transmitters that allow operatives to access the hovercraft remotely. This led to experiments in more directed attacks on the simulation itself--viruses that target the stability and coherence of the Residual Self-Image (RSI), the manifestation of self and other within the system.
In other words, hackers do have the ability to attack their opponents at a distance by targeting them with a virus."
Here's the article where this is mentioned.
http://www.gamespot.com/news/2004/08/20/news_6105301.html
There were a few other pre-release articles that described what the Hacker/Coder abilities (again, why do people single out Hacker abilities? Nobody formed simulacra within the Matrix, and Static Barrage has more "lightning bolts" that any Hacker ability ) are and how they work. Unfortunately I can't find those articles (if anyone can find them I'd appreciate it).
But what they basically said was that the characters access programs on their hovercrafts and direct them towards other characters. It's based off two concepts we saw in the trilogy: the ability to transmit in and out of the Matrix, and the virtual controls seen in the Zion Control construct towards the beginning of Reloaded.
Though you don't have to accept this if you don't want to.
"Archival Science in a Post-War Simulation".
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"Logging Tips for New People and Veterans Alike".
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"Submit Your Logs".