Due: issues about Wire plus SPI, DueTimer + Scheduler + pwm + PID_v1

_From @shiftleftplusone on December 14, 2015 9:25_

is it possible that there are still unresolved issues about the DUE using Wire plus SPI, DueTimer + Scheduler +pwm + PID_v1 ?
I'm always runing into issues for SD init (either if SD.h or SdFat) when running those different other libs additionally, simultaneously - when outcommenting SD init, everything runs fine though.

see, e.g.
http://forum.arduino.cc/index.php?topic=365405.msg2520360#msg2520360

_Copied from original issue: arduino/Arduino#4301_

Start by reproducing SD initialization on an Arduino Due with Wire, SPI, DueTimer, Scheduler, pwm, PID_v1, and either SD.h or SdFat enabled together. Compare the failing setup with the configuration where SD initialization is commented out, and use the linked forum thread for context; done means identifying and documenting the interaction or a reproducible fix.

Written by the indexing model from the issue text.