Hi Henk,

Your good questions stand in their own right so I moved them into a new thread because the thread you used had a clear solution. I will remove the auto generated "off topic" message from the previous thread shortly because this was not off topic.

We are working on some easier solution to this. The native atmel debugger does not understand .ino files so, for now, you have to use "open object file for debugging"

Our next step with this development is to automatically "open the object file for debugging" and to automatically ensure all the source code can be found easily.

You will have seen the atmel studio file mapping window open when you first opened the .elf for debug. It is a strange window because often the source files it is unable to locate are located correctly lower down in the list. In that case you can copy the path and add a \ then atmel should automatically complete the file name for you.

Generally the sources are only in a few places so once you have configured the locations and saved the project you should not need to change it that much in future.

Something else to look at that might help you.... We have only just started to copy the .elf/.hex build files to the /debug /release folders in the last version and have done limited testing. You might find it easier to switch on "tools>options>visual micro>compiler>show build folder". This will give you a link to the real temp build folder where all the .h/cpp files used to actually build the .elf are stored. The .ino will be there as a [sketchname].cpp, in-fact the [sketchname].cpp will be a combination of all .ino files contained in the arduino sketch. 

This build system is how the arduino ide works, we are working on allowing an optional more "native atmel" compile in future versions but there have been so many arduino ide changes recently we have to give them dev priority.

I hope all this helps a bit

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Out of interest. How did you upload the program? Using Visual Micro Atmel programmer?

a. You have to set "debug wire" in the "project properties dialog"?
b. Did you hack the reset pin on your Arduino? 
c. Which board are you using?

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If you have the skill to configure an atmel solution to handle the compile and you are working on just one or two projects then that would be a good solution.

Otherwise you have to use Visual Micro which will give you an automatic Arduino compatible compile (for now).

If you use Visual Micro for the build, you can keep the debug solution open. Atmel will auto detect the changes to the .elf and the mappings dialog is always available by right clicking the debug project in the solution explorer.