I just posted this in response to a question elsewhere about Pablo Sandoval's salary. This is a new provision in this CBA, regarding the competitive balance tax. From XXIII.C.2.f:

(f) Outright Assignment to a Minor League club
Any Uniform Player’s Contract that is assigned outright to a Minor League club during the term of this Agreement shall be included in the Club’s Actual Club Payroll. Any Uniform Player’s Contract that was assigned outright to a Minor League club prior to the effective date of this Agreement shall be excluded from Actual Club Payroll; provided, however, that if any Uniform Player’s Contract that was assigned outright to a Minor League club prior to this Agreement is subsequently selected to a Club’s 40-man roster, the entire remaining Salary under that Uniform Player’s Contract shall be included in Actual Club Payroll, even if the Player is thereafter assigned outright to a Minor League club.

This closes the loophole that allowed teams not to count (for the purposes of the tax) salary for players removed from the 40-man roster. Prior loopholed players are grandfathered, which means Boston still doesn't count Allen Craig and Rusney Castillo toward the tax. But Sandoval will count, even if he's eventually outrighted to the minors by SF.