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Run configurations are used to run a project. This will compile the necessary classes, link them together, load the resulting binary to a target and run it.
All the run configurations of all projects in a workspace can be edited with Properties - > Run/Debug Settings.
With Run/Debug setting you can choose which run configuration of the chosen board you want to run. All the available run configuration (must be defined in the board description file) are listed. One of them can be chosen.
Within a run configuration you can also specify where your program will be written to. This can be RAM or flash memory (see Flashing your Program).