Gradient & Jacobian
As commented by @whpowell96 :
The more general definition of the gradient is as the transpose of the Jacobian. The Jacobian of the map $(x,y,z)\mapsto (u,v,w)$ is a $3\times 3$ matrix and hence the gradient is the transpose, another $3\times 3$ matrix
Also described here explicitly
$$
{\displaystyle \mathbf {J} ={\begin{bmatrix}{\dfrac {\partial \mathbf {f} }{\partial x_{1}}}&\cdots &{\dfrac {\partial \mathbf {f} }{\partial x_{n}}}\end{bmatrix}}={\begin{bmatrix}\nabla ^{\mathrm {T} }f_{1}\\\vdots \\\nabla ^{\mathrm {T} }f_{m}\end{bmatrix}}={\begin{bmatrix}{\dfrac {\partial f_{1}}{\partial x_{1}}}&\cdots &{\dfrac {\partial f_{1}}{\partial x_{n}}}\\\vdots &\ddots &\vdots \\{\dfrac {\partial f_{m}}{\partial x_{1}}}&\cdots &{\dfrac {\partial f_{m}}{\partial x_{n}}}\end{bmatrix}}}
$$
where $\nabla ^{\mathrm {T} }f_{i}$ is the transpose (row vector) of the gradient of the $i$-th component.
Now I understand both the gradient and Jacobian :)
Understanding the equation
This post helped me make sense of the PDE: https://physics.stackexchange.com/q/101737/115714
Of course, I forgot about this: https://en.wikipedia.org/wiki/Linear_elasticity