A South Korean programmer is suspected of stealing (for a foreign customer) government software, stuff that he worked on from 2005-10. The suspect, who is still being investigated, was arrested in 2002 for posting pro-North Korean data on web sites. Thus the investigation is seeking to discover if the classified software went to North Korea.
This could be a serious intelligence breach. That's because, for the last decade, South Korea has been planning to take over command of all military forces in South Korea. That would include American troops, and those of any other nation that came to help repel a North Korean invasion. As part of that switch, South Korea had to acquire additional communications capabilities, software and trained officers (both staff and command) that enable them to run the entire operation.
To that end, the U.S. and South Korea ran a series of wargames, where the South Koreans could practice being in charge. Everything went better than expected, but many problems were encountered. These included South Korean information systems, including databases that did not work well with their American counterparts. In addition to the wargames, there are also political games. Procedures are being worked out to coordinate how the two nations will handle the escalation that would lead to a war. Even if the North Koreans execute the dreaded surprise attack, the two nations have to be on the same page when it comes to mobilizing and moving additional military and diplomatic resources towards the war effort. The South Koreans have to have an idea of what additional forces the U.S. could, or would, provide, and when. The U.S. has to be kept informed of South Korean strategy, because what the South Korean generals do is a matter of life or death for the American forces involved.
The United States has long practiced operating as part of a NATO force in Europe, including having American units subordinate to foreign commanders. During the Cold War, the NATO alliance involved armed forces from over a dozen nations operating together. To make that happen with a minimum of confusion and errors, all NATO members spent decades establishing standards for command, communications, logistics and diplomacy. In South Korea, while there has long been a similar standardization with the U.S., the former subordinates are finding that even more standardization and synchronization is required if South Korea is to switch roles and be in charge. It's not a simple or quick process.
Being in possession of an early version of this new command and control software, including the overall design documents, could be a big help to North Korea, especially if they were planning more military action against South Korea.