Can a commander be tucked into a library and what happens if it is?

As of the 2015 Commander rules update, whenever a commander would be put into a library (or hand) from anywhere, its owner may choose to put it into the command zone instead. This is a replacement effect defined by the Commander format's additional rules, not the Comprehensive Rules themselves, but it is universally recognized in official Commander play.

Before this rule change, 'tucking' — burying a commander into the middle of a library with cards like Hinder or Condemn — was a permanent solution that prevented the commander from being recast. That is no longer the case. The owner always has the choice to redirect it to the command zone.

Critically, this is a choice, not mandatory. If for some reason a player wants their commander in their library (perhaps to tutor it later), they may decline to use the replacement effect and let it go to the library normally. However, doing so means it is no longer tracked as a commander for zone-tracking purposes while it sits there.

Concrete example: Your opponent casts Hinder targeting your commander spell on the stack, which would put it third from the top of your library. You may choose to send it to the command zone instead, where you can recast it by paying its mana cost plus any applicable commander tax.

Relevant rules: CR 903.9 governs the command zone replacement effect for commanders going to graveyards or exile, and the official Commander rules (maintained by the Rules Committee) extend this to libraries and hands as well.