For a long time I have struggled to make sense of "input-output theory." And unfortunately, I still cannot make any intuitive sense out of it. The key equation (found in this famous resource) is this boundary condition
$$ \alpha_\text{out}(t) = \alpha_\text{in}(t) - \sqrt{\kappa}\alpha(t) \, , $$
but immediately, this is already unclear. If for example I have a one-sided cavity that sends light into a cavity, then this suggests that what I get is a linear combination of the light that has originally entered, and destructive interference of the light in the mode of the cavity.
What this actually physically represents is not clear to me. What I would expect would be linear interference of light that was rejected from the cavity, interfering with the light that is leaking from the cavity.
$$a_{out} = R(a_{in}) a_{in}(t) + \sqrt{\kappa} a_{cavity}(t).$$
Something like this would be more sensible. $R(a_{in})$ is the reflection coefficienct of transmission function of the cavity, which is dependent on the input frequency of the light. And this interferes with some leackage light, which has some amplitude and phase.
So how exactly do I make physical sense of this weird form for the boundary condition. It has been for a long time really unclear to me what this actually represents.