How does Superposition principle follow from Maxwell's equation's linearity? It is said that whole of electromagnetism can be completely described by the Maxwell's equations. 
The thing that intrigues me is that how does superposition principle follow?
First, I take an example, where $2$ charges $q_i$ are placed at a distance $d_i$ from a point, $i=1,2$. Now to calculate the field at that at point, we simply add the electric field due to individual charges at that point if the other charge was not there (Field calculated using Gauss' law). But how do we know that now, after the charges are placed together, the electric field due to both of them there is unaffected and also, that it adds up?
Edit: For all those who are saying that since Gauss' Law is a linear equation, that is why the SP follows. Please read the question again. I am asking the reasoning behind it, why SP follows from linearity (Or how). 
It would be appreciated if someone explains it in the simple example I chose above. (2 point charges)
 A: To put it simply superposition does NOT follow from Maxwell's equations.  It is a mathematical principle and it holds for any linear equation or system of equations.  Maxwell's equations are just one of many that fall into this category.  The general form is:
D(Field) = Source
where D() is some abstract differential linear operator.  Linearity means that if F1 is a solution for S1, and F2 is a solution for S2 then F1 + F2 is a solution for S1 + S2.  The proof can be found in most math texts on ordinary or partial differential equations, also linear algebra or operator theory.  Once you "prove" that a set of equations is in fact linear you can immediately apply this result.
You state using Gauss' law to calculate the field.  The more fundamental equation is Coulomb's law, which was discovered as an empirical law, along with its linearity, by experiments conducted by Coulomb.  This is how we know that the field behaved linearly.  When we learn all this physics today we sometime forget the history, how our knowledge is connected to history, and what comes first (i.e. what piece of knowledge is fundamental rather than derived).   
A: Superposition principle (SP) holds for every physical phenomenon which may be modeled by linear equations. 
A frequently neglected consequence is that, in the case of macroscopic electromagnetic fields, SP is not unconditionally true, even if Maxwell's equations are linear, due to the completely general (non-linear) relation between the fields $\mathbf{E}$, $\mathbf{D}$, $\mathbf{B}$, $\mathbf{H}$. It is only in the cases of vacuum and linear materials that the full set of Maxwell's equations and constitutive equations is globally linear and SP holds.
A: Maxwell's equations did not answer all electromagnetic theory. Actually Maxwell equation + Lorenz gauge + superposition principle together solve the current electromagnetic problems. Hence superposition principle is an independent principle. It is not included in Maxwell's theory.
Lorenz gauge is very important. Lorenz gauge is a correct gauge. Maxwell uses the Coulomb gauge. That is a wrong gauge. Hence in order to solve the electromagnetic problem, Lorenz gauge is required. Lorenz gauge should be as 5th Maxwell equations. (Here is Lorenz not Lorentz). Lorenz introduced Lorenz gauge in 1867. Only a few years later than Maxwell's theory. He also introduced retarded potential in the same paper. The concept of retarded potential is equivalent to the displacement current of Maxwell. Lorenz introduce the retarded potential is base on his study in optic and elastic wave. Hence Lorenz should get the respect similar to Maxwell.
As I know the suppositions of the static field electric field and static electric magnetic field is self-explained. However it is difficult to prove the radiation field can be superposed.
For radiation fields, there are two kind of fields retarded potential and advanced potential. They are the solutions of Maxwell equations. As I know the transmitting antenna sent retarded wave. The receiving antenna sends the advanced wave. Most scientists do not accept the advanced wave because of the causality problem. However the absorber theory of Wheeler and Feynman, Transactional interpretation of John Cramer supports the advanced wave. The mutual energy flow theorem also supports the advanced wave. We know there is current in the receiving antenna when it receives wireless waves. This current should produce some wave, if this wave is retarded wave, the receiving antenna actually is a transmitting antenna but not a receiving antenna. Hence the advanced wave should exist. Can the retarded wave and advanced wave be supposed? This is not clear.
Radiation is a very complicated phenomena, our today's theory still does not answer the problem of wave-particle duality problem. Wave can be supposed, but it is clear that the particle cannot be supposed.
Feynman and his doctor father Wheeler tell us if the space is empty, the sun cannot shine. In order to let the sun shine there needs the absorbers. Our current electromagnetic field theory (Maxwell theory) did not reflect this point of view. This means something is wrong in classical electromagnetic field theory. If something is wrong we first need to test whether or not the superposition principle is correct. There are some publications that tell us the supposition principle is correct at 15%, (I forget the cite place). Anyway superposition principle is not tested like Coulomb's law.
There is the concept of wave collapse. The wave collapse process if it exists should be some kind of waves. As I know the wave collapse is related to the concept of time-reversal waves.  Can this kind wave be supposed? It is not clear.
Summary: Maxwell theory is not a complete theory (Otherwise do not need QET), superposition principle should be an independent principle to Maxwell equations. It needs to be tested again and again in case there is some new theory developed in electromagnetic field theory or quantum mechanics.
A: First, superposition principle and linearity is the same thing, exactly how @Cuspy Code wrote in a comment above.
The answer to why you could add electric fields in the first place, or more precisely, what causes the equations of motion to become linear (instead of something else random), comes from symmetry. Interactions in a theory are mediated by gauge fields. In quantum electrodynamics(QED), there is one gauge field called the photon and is denoted by $A_\mu$. The key point is that the local symmetry group in QED, which is U(1), is Abelian. You can change the order of 2 successive gauge transformations without changing anything. The resulting equations of motion are linear in $A_\mu$: there are no self-interaction terms. If the local symmetry was non-Abelian, you would get self-interactions between the gauge fields, as happens for gluons that describe the strong nuclear force in quantum chromodynamics. In general relativity (GR) too, there are graviton self-interactions. So although for many purposes you can add Newtonian potentials, we really should be taking the non-linearities into account. The non-linear structure of GR explains Mercury's perihelion precession, for instance; see my answer here.
But in all this analysis, it must be noted that we considered an idealized situation where the sources are fixed. In reality, everything is affected by everything else and all backreaction effects (which cause non-linearity) must be taken into account in order to be as precise as possible.
A: After a few comments and the last edit of the original question, I think that the original question has been better focused and it is more a question about how to prove SP for linear electrodynamics (Maxwell's equations plus linear constitutive equations) using Gauss' law in the integral form.
Answer to this question is that it cannot be done at the same level of simplicity one is able to derive Coulomb's low from Gauss' law. Indeed, in the case of Coulomb's law, one exploits heavily  the symmetry of the field due to a point-like charge. The symmetry allows to obtain from a unique number (the flux through the surface of a sphere with the charge at the centre) the value of the electric field at all the points on the spherical surface.
Missing the simplification offered by symmetry, Gauss' law is not able to provide directly the electric field at one point. It can be done indirectly by using  the integral form to derive the differential form and the differential form of Gauss'law plus the condition on the curl of $\mathbf{E}$ and the boundary conditions allow to get the value of electric field everywhere.
As far as the derivation of SP from Maxwell's equations in differential form, it is basically contained in the first comment by Cuspy Code.
