I got TinyGPS 12 to work with the maple ide v0.0.12 with some hacking. I had to include stdlib.h in TinyGPS.cpp, and a bit more hacking to get the Examples to compile/run. For static_test I had to add several include's and neuter the PROGMEM stuff. For simple_test I got rid of SoftwareSerial and used Serial1. (I was concerned that the EM-406A GPS ran at 5v, but spec and scope showed TX and pps out were only 2.85v, so any maple pin was good), and changed Serial to SerialUSB. For test_with_gps_device I added stdlib.h string.h and used Serial1 and SerialUSB.
I also tested the GPS pps pulse with attachInterrupt() -- you don't even need TinyGPS to test that. I used the pulse with micros() to test the frequency of the maple, see the gpspps sketch at
https://github.com/manitou48/crystals
gpspps sketch works on Arduino UNO and DUE as well