I can build using the Xcode command line tools, is there any way I can actually run the application using them? (E.g. the equivalent to pressing Cmd+R in Xcode)
First decide what device you want to use:
xcrun simctl list
This will give you a list of devices:
-- iOS 9.0 --
iPhone 4s (56632E02-650E-4C24-AAF4-5557FB1B8EB2) (Shutdown)
iPhone 5 (ACD4DB7B-9FC9-49D5-B06B-BA5D5E2F5165) (Shutdown)
iPhone 5s (A8358B76-AD67-4571-9EB7-FFF4D0AC029E) (Shutdown)
iPhone 6 (1D46E980-C127-4814-A1E2-5BE47F6A15ED) (Shutdown)
iPhone 6 Plus (FD9F726E-453A-4A4C-9460-A6C332AB140B) (Shutdown)
Choose the ID (eg. FD9F726E-453A-4A4C-9460-A6C332AB140B) you want (you can create your own device using xcrun simctl create
if you want).
Boot the simulator with that device (replacing YOUR-DEVICE-ID with the ID)
/Applications/Xcode.app/Contents/Developer/Applications/Simulator.app/Contents/MacOS/Simulator -CurrentDeviceUDID <YOUR-DEVICE-ID>
Now you should be able to use simctl to install and launch commands.
xcrun simctl install <YOUR-DEVICE-ID> <PATH-TO-APPLICATION-BUNDLE>
xcrun simctl launch <YOUR-DEVICE-ID> <BUNDLE-ID-OF-APP-BUNDLE>
xcrun simctl help
for more details. Note that booting a device using simctl does not currently (Xcode 7.2) allow you to do anything else with that device such as launch or install applications. You need to launch the device in the simulator to actually do anything interesting. Also, you cannot delete a device that is in use by the simulator, so you will have to quit/kill the simulator before attempting to delete anything.