Harvest's JP location was costing them an arm and a leg in maintenance and repair due to the building (an old mansion) being in very poor shape, and then Whole Foods bought up a property from a local ethnic 'super' market whose owners were done being in the grocery business.
Harvest built out a very fancy new store very close to a major subway/bus terminus that was gorgeous but everyone went to the Whole Foods which was closer to the higher population-dense areas. Location, location, location - but also WF was very stiff competition.
I never saw rotten produce. I have no idea what the other commenter is on about. Organic, locally-sourced, heirloom produce often isn't as pretty as the stuff genetically modified or bred to survive being shipped halfway around the world and stored in a warehouse for 6 months.