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I know very little about visual studio so the answer to this one might be simple; but is it possible to change settings in the project using command line switches to avoid having different project files for minor changes ? As I want to trigger automatic builds changing settings through the ui is not possible.

For example something like /MyOwnSetting="something"

and then have the project file use that.

+1  A: 

There is no command line switch that will modify the project file, If you want to have different setting the way to go is to use configurations.
Each project can have many configurations (Release/Debug for example) and when you compile a project file you can specify which configuration to build.

The last part of you question is a bit unclear.

Shay Erlichmen
I see, I am used to gnu make where it's easy to use commands such as "SETTING=something make" to create a different build based on the specified setting.
Zitrax
A: 

Here are some Visual Studio Command Line Switches (for v2.0 ... see other links on that page for other versions of Visual Studio).

ChrisW