Killing kernel from Terminal severely confuses Hydrogen

Description:

Sometimes you run a script that you cannot interrupt. For example a huge NumPy sum that spends most of the time NumPy. Ctrl+C would only work once the sum has returned.

So you go to the terminal, search for the PID of the process and kill it. No problem. But Hydrogen thinks the process is still running and will not accept commands.

Restarting the kernel stops at "Python 3 kernel restarting".

Shutting down the kernel makes the status bar go away, and any following commands will trigger a new kernel to be launched, but the UI does not reflect this.

Sometimes even an Atom restart is needed.

Steps to Reproduce:

1. Do a huge NumPy sum like numpy.sum(numpy.random.rand(2812, 8, 200001), axis=-1)
2. Kill the Python process
3. Try interacting with the Hydrogen UI.

Versions:

$ atom --version
Atom    : 1.24.0
Electron: 1.6.16
Chrome  : 56.0.2924.87
Node    : 7.4.0

$ apm list
...
├── Hydrogen@2.2.2
...

Start by reproducing the issue with a large NumPy sum, then kill the Python process externally and observe Hydrogen's kernel and status-bar state. Done means the UI recognizes the killed kernel, restart and shutdown behave correctly, and later commands launch or use a kernel without requiring an Atom restart.