I’ve already filed issue #2924, but I’m posting here in case someone else runs into the same problem:
My code that had worked with previous versions of the Arduino IDE suddenly failed to work with 1.6.3 (didn’t adequately test with 1.6.2). The SD card on an Arduino Ethernet was no longer readable. The SD card itself tested OK, but testing with the SD example sketch “listfiles” produced the same failure.
Adding the line
digitalWrite(10, HIGH); after
pinMode(10, OUTPUT); to the “listfiles” sketch caused it to function normally. No other changes were made to the sketch.
Commit 0e898d5 modified how SPI influences the state of the SS pin. I believe that a corresponding change needs to be made in the SD library in order for everything to work properly.