Options for 'bare-metal' development

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It's still alive. I was interruped for 9 months due to an unforseen extra project.
But I will resume the development in march 2018..
Current status is :
* hardware (PCB) has been tested and is 100% functional.
* sw : GCODE interpreter has been tested about 80%
* use of SD card has been added : gCode can be saved onto SD card and then executed from there
* host-communication flow control has been tested

I understand you'd like things to move faster, but this is my hobby and sometimes my daytime job consumes all my time.
 
However, as for the title of this post, I am still struggling with a number of TeensyDuino things

1. I can't easily hook a more suitable driver for Hardware Serial 1, because the interrupt handlers are already defined in the TeensyDuino boot code..
* I can either use Serial as it is and wrap my driver around it, but it's not beautiful and not efficient..
* If I outcomment parts of the TeensyDuino code, it is possible to have my own Serial handler, but in this case the code no longer compiles on a vanilla TeensyDuino installation..

2. Same problem for PIT0. I need this timer to drive the outputs to the stepper drivers. Paul has provided an IntervalTimer library, but in my project, I need to reload the timer with a different value every time..
I had this working before (doing a direct configuration of the K64/K66 peripherals registers), but it's no longer working in the latest TeensyDuino
 
However, as for the title of this post, I am still struggling with a number of TeensyDuino things
...
2. Same problem for PIT0. I need this timer to drive the outputs to the stepper drivers. Paul has provided an IntervalTimer library, but in my project, I need to reload the timer with a different value every time..
I had this working before (doing a direct configuration of the K64/K66 peripherals registers), but it's no longer working in the latest TeensyDuino

Does this TD change give you what is needed?

This is the full list of changes, from 1.40 to 1.41:

Add IntervalTimer update()
 
I understand that this is a side project. I am what you would call a rookie with all the code and jargon that is being used but I get the jist of it for the most part. I was wondering if this would still work with the gshield that the Arduino uses ? assuming the pin map is correct.
 
All the source can be found here, and of course there's a copy installed within Arduino, in hardware/teensy/avr/cores/teensy3/.

If any part of this interferes (which seems quite unlikely), of course you can edit the code any way you like.

So if I wanted to create a new USB Type as explained there I would need to clone that repository and copy it in \Arduino\hardware\teensy\avr.
It looks like boards.txt and platform.txt are missing. Are they generated somehow?
 
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