On/Off switch controlled via IR

Basically the way these circuits work is by relying on the fact that soil conducts electricity, with a resistance of a few hundred kOhm. When it gets wet, the resistance changes allowing the moisture level to be detected by measuring the resistance of the soil.

The measurement is usually achieved using an amplifier circuit which produces a voltage depending on the resistance of the soil. This can be done using an Op-Amp circuit for example, or even just biasing a BJT with the soil probe such as in the example circuit below (Source of image and circuit description here) where S1/S2 are probes in the soil, and the voltage at S1 varies with moisture level.

The LED is almost certainly not in line with the sensor, but is rather turned on or off by the measured voltage. So basically if you want an LED to have the opposite indicator, you would just need a simple inverter circuit driving the second LED.

I'm not that great with Android App development so I'm assuming you can make the headphone jack output a voltage in reference to the "common" ring. This guy got his android to output a waveform that was dependent on the accelerometer device readings.

Most smartphones have TRRS jacks on them, where the breakdown looks like this:

So if you can control the voltage difference between "Left" or "Right" and "Common", then you could exploit that.

Have the voltage difference feed into a transistor, while your external battery drives your LED. This is a much better method because you don't really want your phone to drive your LED, you just want it to say "OK, turn on, now turn off" etc.

^{simulate this circuit – Schematic created using CircuitLab}

So it's just a really simple circuit, where the phone activates/deactivates the transistor. When the voltage of "LEFT or RIGHT" goes HIGH, current will travel from the battery, through the transistor and through the LED. Setting the voltage to ground will stop any current from flowing.