The EDH Rules committee has officially changed the way tucking works with Commanders.  

 
As of today, if your commander would go into the library or your hand, you may choose to put it into the command zone. It’s as simple as that. Just like with the graveyard, if you want it to go into the library/hand, you’re more than welcome to let it. Note that this is a replacement effect, but it can apply multiple times to the same event.

 

According to the Rules Committee, there were are four major points in how they arrived at this decision:

 

  •  We want to engender as positive an experience as we can for players. Nothing runs the feel-bads worse than having your commander unavailable to you for the whole game.
  • The presence of tuck encourages players to play more tutors so that in case their commander gets sent to the library, they can get it back—exactly the opposite of what we want (namely, discouraging the over-representation of tutors).
  • While we are keenly aware that tuck is a great weapon against problematic commanders, the tools to do so are available only in blue and white, potentially forcing players into feeling like they need to play those colors in order to survive. We prefer as diverse a field as possible.
  • It clears up some corner case rules awkwardness, mostly dealing with knowing the commander’s locationin the library (since highly unlikely to actually end up there).

 

They have also ruled on Manifested commanders:

 

When FRF came out, manifest led us to talking about what it meant to be a commander—which is what got us talking about tuck in the first place. After a long discussion, we decided the best course regarding commander-ness was no change. Your commander is always your commander regardless of where it is or its status. That means enough hits from a face-down commander can kill you. 

Source:  http://mtgcommander.net/Forum/viewtopic.php?f=1&t=17560