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A search of the Santa Clara County Superior Court's website indicates that in February of this year Kelli McCloughan, Scot McCloughan's wife, filed for divorce for the second time. Kelli originally filed in May of 2009 but the case was dismissed in December. She filed for divorce again in February of this year.
There is nothing as of yet that confirms this to be the reason for the reported "extended leave of absence." However, It would make sense that familial turmoil is the root cause of the problem especially when the issue is described as a "longstanding personal issue."
As information trickles from the 49ers facility, nothing indicates that the fissure between the 49ers and Scot McCloughan has anything to do with job performance. Other news outlets used words and phrases such as "cut ties" and "force out" but this would indicate some kind of power play. At the very least it would indicate that someone at 4949 Centennial was unhappy with McCloughan's performance. The fact that the 49ers have not issued a statement stating a dismissal indicates that this is not a performance related move.
So what happens on draft day? Daniel Jeremiah, a former scout with Baltimore and Cleveland, points out that much of the preparation for the draft is complete by this time of year. The draft board is mostly complete and if there is one part of the organization that has enjoyed continuity, it is the scouting and personnel staff.
The ultimate question is who gains the final personnel say if there is a draft day argument? Supposedly, there was an impassioned argument for Patrick Willis in the draft room that persuaded the team to draft him and not some other player. Who makes the final call when there is a division?
My guess (and it's just a guess)? Mike Singletary.
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So who is left in the personnel department to bear the day-to-day weight? Tom Gamble is the director of pro-personnel and Trent Baalke is the director of player personnel.
Before the 49ers, Baalke worked with the Redskins at a time when Daniel Snyder and Vinny Cerrato made the personnel decisions. Baalke joined the 49ers in 2005 with Mike Nolan and Scot McCloughan. Baalke is responsible for both the college and pro personnel departments so, it would seem, that he is above Tom Gamble on the organizational chart.
It's possible that the 49ers hire an external candidate. But this late in the off-season there aren't many teams willing to let an experienced front-office exec leave. I do not think the 49ers would hire a GM without experience unless it was an internal promotion.
That means that we should see either Baalke or Gamble as the next GM. Whether or not the GM still ranks above the head coach is yet to be seen. I think it would be wise for Jed York to keep the organizational structure if the structure works.