How to find the derivative of the function $f: M_n(\mathbb{R})\to M_n(\mathbb{R}), A\mapsto \sqrt{AA^T},$ where $A^T$ is the transpose of the matrix $A$?
\begin{align} Df_V(A) & = \lim_{h\to 0}\dfrac{f(A+hV)-f(A)}{h}\\ & = \lim_{h\to 0}\dfrac{\sqrt{(A+hV)(A+hV)^T}-\sqrt{AA^T}}{h}\\ & = \lim_{h\to 0} \dfrac{\sqrt{AA^T+hAV^T+hVA^T+h^2VV^T}-\sqrt{AA^T}}{h} \end{align}
Now, what should I do?
Define the matrix $F$ such that $$F = \sqrt{AA^T} \;\implies F^2 = AA^T $$ The vec operation can be used to flatten these matrices into vectors. $$a={\rm vec}(A),\quad f={\rm vec}(F)$$ The requested gradient can be calculated as follows. $$\eqalign{ &F\,F &= AA^T \cr &F\,dF\,(I)+(I)\,dF\,F &= A\,dA^T\,(I)+(I)\,dA\,A^T \cr &(I^T\otimes F+F^T\otimes I)\,{\rm vec}(dF) &= (I^T\otimes A)\,{\rm vec}(dA^T)+(A\otimes I)\,{\rm vec}(dA) \cr &\Big(I\otimes F+F\otimes I\Big)\,df &= \Big((I\otimes A)K+(A\otimes I)\Big)\,da \cr &\frac{\partial f}{\partial a} &= \Big(I\otimes F+F\otimes I\Big)^+ \Big((I\otimes A)K+(A\otimes I)\Big) \cr\cr }$$ where $M^+$ denotes the pseudoinverse of $M$, $I$ is the identity matrix, and $K$ is the commutation matrix associated with the Kronecker product. The solution also takes advantage of the fact that $I$ and $F$ are symmetric.
The true gradient is a fourth-order tensor, while the above result is a flattened version of it. If you want the full tensor result, the components are not too difficult to calculate, since there is a one-to-one mapping between the elements of the tensor and the elements of the flattened matrix.
Upon re-reading the question, it looks like you are interested in the directional derivative, where changes in $A$ are restricted to the matrix direction $V$. $$\eqalign{ v &= {\rm vec}(V) \\ df_v &= \bigg(\frac{\partial f}{\partial a}\bigg)\cdot v \\ }$$ Once again, unflattening this vector into a matrix is just a one-to-one mapping, i.e. $$\eqalign{ F &\in {\mathbb R}^{m\times n} \implies f \in {\mathbb R}^{mn\times 1} \\ F_{ij} &= f_{\alpha} \\ \alpha &= i+(j-1)\,m \\ i &= 1+(\alpha-1)\,{\rm mod}\,m \\ j &= 1+(\alpha-1)\,{\rm div}\,m \\ }$$