Stopping an Android app from console

Edit: Long after I wrote this post and it was accepted as the answer, the am force-stop command was implemented by the Android team, as mentioned in this answer.

Alternatively: Rather than just stopping the app, since you mention wanting a "clean slate" for each test run, you can use adb shell pm clear com.my.app.package, which will stop the app process and clear out all the stored data for that app.

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If you're on Linux:
adb shell ps | grep com.myapp | awk '{print $2}' | xargs adb shell kill

That will only work for devices/emulators where you have root immediately upon running a shell. That can probably be refined slightly to call su beforehand.

Otherwise, you can do (manually, or I suppose scripted):
pc $ adb -d shell
android $ su
android # ps
android # kill <process id from ps output>

The clean way of stopping the app is:

adb shell am force-stop com.my.app.id

This way you don't have to figure out the process ID.