ARM teensy without arduino

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I am a little confused by the website because as soon as any detail is given it seems to be about simpler teensy boards with an Atmel chip on it. What about the ARM chips ? What sort of support is there if I were to want to program one of the ARM boards not via arduino ? or do I still use arduino but talk normal C to the processor and it's registers ?

At the moment I would start with the arduino but I am wondering what happens when I need specific functionality not available via arduino libraries. This is the same path I took with atmel mega chips where I started with arduino and then moved to directly programming via atmel studio.
 
Mixing and matching the Arduino core code with your own works very well. Teensy is using a standard C / C++ toolchain. The manuals for the different Teensy MCUs are available here.

There are various threads about bare metal (non-Arduino) usage in the forums.

Something to keep in mind is that peripheral compatibility across Kinetis K is extremely good (all the Teensy 3.x are Kinetis K). Many peripherals for Kinetis L (Teensy LC) are a bit different.
 
What sort of support is there if I were to want to program one of the ARM boards not via arduino ?

This depends on what is meant by "support".

If you want technical resources, there are plenty. Teensyduino puts a sample makefile in Arduino's hardware/teensy/avr/cores/teensy3 folder. That's just a starting point. Many other makefiles and other ways exist, which you can find discussed in great detail on this forum. There's a command line loader and lots of other ways to do things, if you're the sort of person who wants to dig into low-level details and really tailor things to your liking. Many, many people have done this and much has been discussed and published.

But if "support" means step-by-step instructions or beginner level guidance, the practical reality is using Arduino. Likewise, if you set up your own build process and run into a possible bug in the Teensy core library code or pretty much any other library, you can expect the first "support" question to be whether the problem happens when you build and run using the Arduino IDE with the latest Teensyduino version installed.
 
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