@User, i guess the SDI and SDO connection between U3 (Flash Memory) and U1 (Caravel) has to be changed . In the schematic both inputs (SI and falsh_io0 ) and outputs ( SO and flash_io1) are connected . Caravel Harness description : pin flash_io0 acting as 

SDI

 (data from flash to CPU) and pin flash_io1 acting as 

SDO

 (data from CPU to flash). Flash datasheet description : SI : Serial Input for single bit data commands or IO0 for Dual or Quad commands. SO : Serial Output for single bit data commands. IO1 for Dual or Quad commands Pls neglect , if its already done .