Uggh. Please let me explain a few things.
I only use windows and Visual Studio. I have no knowledge of Linux.
I did not know you are using Atmel Studio, most users are using Visual Studio
I provide a free plugin and free forum for Atmel Studio and Visual Studio for people who use Arduino. My software replicates the Arduino build process 100%. The process is designed by Arduino and makes it very simple for people to build their sketches and upload without need for any complexity.
I have clearly described to you how to build windows programs, not Linux programs. The simple fact is that you say you use windows but you have no experience of how to build a windows program.
The pre and post build feature of the Arduino system is again designed by Arduino. Visual Micro is advertised as being 100% arduino compatible to build Arduino programs.
The pre and post build events are new and only in the beta because Arduino also have only just designed and released the feature.
So to recap.
You have jumped in making a seriously strange number of assumptions. Not read anything about what Arduino is. Not followed a simple set of instructions which other people happily work with. Consumed free support time, not read posts properly or answer my questions.
I am sorry you have not achieved what you wanted to achieve but I really have invested time in trying to help you and you really have made many wrong assumptions. I've put a great deal of effort into the software and this forum and fortunately people who really want to use their Arduino's get satisfaction from the software and support.
In this case I feel like you are shooting the messenger. All I have done is educated you and explained how you can make arduino work on windows. I am not Arduino, they are a hardware company that make a lot of money from selling hardware and I am not Atmel, they are the company who asked me to make Visual Micro work in Atmel Studio for free and also a company that makes a lot of money from selling hardware.
So what exactly are you saying to me about Linux? (I suggested writing your command.exe in Visual Studio which is the Microsoft dev environment and suggested build a windows console app or windows form app etc)
Arduino is excellent for most exactly because you don't have to mess with any build events. Doesn't sound like the tool for you at all.
edit: Maybe you thought you needed to use command line but you don't that is simply an option for advanced users.. Please don't shoot the messenger that has tried to help you. ps:
I just reread your message. Maybe you are confused about how to build arduino programs. You just pick your board from the tool bar and click debug>start with or without debugging.
http://www.visualmicro.com/page/User-Guide.aspx?doc=index I think this is just a whole bunch of confusion from reading the beta release notes. Please see the compile and upload docs they are designed for students