Sorry if this is the wrong forum.

So, in order to make the sketches as small and fast as possible, I'm trying to take off the training wheels and program the Arduino (a Sparkfun Pro Micro, 32u4, very similar to the Leonardo) in AVR C. (preferably using Atmel Studio, but whatever), but, at the same time, rely on Visual Micro to do the uploading (reset the Arduino (leonardo-style, at 1200 baud, upload the sketch, etc). Also (if it is needed) I'd like to also have no problems with the bootloader (when uploading without Visual Micro / Arduino IDE, i.e. straight through avrdude something happens to the bootloader and, as a result, the board does no longer have a COM port. When I upload a sketch as I should, that problem is fixed. It might be a quirk with the pro micro.) 

The problem is that Visual Micro includes the arduino headers, links the core, and as a result an empty sketch takes up to 15% of the program space.

So, how can I get rid of the arduino headers, the arduino core, etc and keep just what I need and include manually, while letting Visual Micro do the uploading? As a bonus, I'd like to have the extension .c or .cpp, an not .ino (code completion doesn't work on .ino files, for some reason).

What I've tried:
-make a new (copy) board with the core set to something else (i picked avr, might do nothing). I get some linking error about 'undefined reference to main' in the arduino files.
-remove include statements from the "[project].vsarduino.h". Overwritten by Visual Micro.

Any ideas?

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I -can- already program the Pro Micro by running the avrdude command while the Pro Micro is in bootloader mode (for 8 seconds). That mode can be 'called' with the 1200 baud port open/close and with a double-tap on reset. (more info here: https://dlnmh9ip6v2uc.cloudfront.net/datasheets/Dev/Arduino/Boards/32U4Note.pdf). So, basically, I can flash with avrdude while the board is in the bootloader mode. The thing is, visual micro does that MUCH, MUCH better (not overriding the bootloader, opening/closing the port at 1200 baud, letting me pick the port much easily)

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(as far as I know, this is the same with the Leonardo, to which the Pro Micro is very much alike) There are two ports, one for the normal usage and one for the bootloader. The 1200 baud connection is opened on the normal port, the board resets and the program is uploaded on the bootloader port. Again, this works flawlessly with Visual Micro/Arduino IDE. When my port is gone, I manually reset the board (double-tap on the reset button) and I upload a blank sketch with the arduino IDE or Visual Micro. This fixes everything.

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(I might not understand correctly what you mean) I am already 'set' on port manipulation, I can pull the init() function from the source code, the delay() function (or write my own). I can #define HIGH, LOW, INPUT, whatever. I don't really need access to the main() function, but it would be a bonus. I asked this question because I've seen just how configurable Visual Micro is and I've wondered if there is a way to use a trick (either with a custom board or with something else) to keep the uploading functionality, but not to be forced to use the arduino headers and core (just plain AVR C), because this kind of bloats the code. Basically to use an empty core.

Thanks for the extension, it's very useful even if I can't find a solution to this.

ps: idea

Copy the arduino ide, set the location against the Teensy option in Visual Micro then hack the arduino.h to do whatever you need, hack the boards.txt and remove entries you don't want.

Teensy is the same as arduino 1.0.x

Visual Micro plus allows you to create new Ide entries such as My Arduino C Ide but using the built-in Teensy option works the same

The only reason for using Teensy or ano Ide option in Visual Micro is to preserve your normal arduino ide for reference purposes.

I made it! Well, sort of. I followed the Teensy route and I created my own core. The thing is that I had to include almost 60% of the core to get it working (including USB functionality).

About the programmer... yeah, probably not going to happen very soon. But who knows, I guess I'll see.

Thank you very much for the assistance.

A couple more things.
1) Is it possible to change the extension from .ino to .c/.cpp? There are some extensions (Resharper on Visual Studio and the whole code completion on Atmel Studio) that don't work on unknown extensions.
2) What optimization does Visual Micro tell the compiler to do? If I want to, can I change them? (basically I'd like "optimize for size")

Awesome! Can't wait! Good luck