It appears James Macdonald isn't really back in the Astros system. Recently, it was posted here (thanks to Baseball America) that the Astros 2009 draft pick had been reinstated from the restricted list. Macdonald had retired prior to the 2010 season to pursue a career in journalism. Word from the Astros media office today is that Macdonald has been released. I think that a player has to be reinstated before he can be officially released, so it sounds like the reinstatement was just a formality.
NOTE: Thanks to Appy Astros for clarifying via Twitter that a player like Macdonald is placed on the restricted list, even though he is retired, to retain his rights in case he changes his mind. If I remember correctly, Chris Sampson was "retired" for several seasons before he came back to the Astros system. I assume he was on the restricted list during that time.