$$
\newcommand{\uex}{{u_{\small\mbox{e}}}}
\newcommand{\half}{\frac{1}{2}}
\newcommand{\tp}{\thinspace .}
\newcommand{\Oof}[1]{\mathcal{O}(#1)}
\newcommand{\x}{\boldsymbol{x}}
\newcommand{\dfc}{\alpha} % diffusion coefficient
\newcommand{\Ix}{\mathcal{I}_x}
\newcommand{\Iy}{\mathcal{I}_y}
\newcommand{\If}{\mathcal{I}_s} % for FEM
\newcommand{\Ifd}{{I_d}} % for FEM
\newcommand{\basphi}{\varphi}
\newcommand{\baspsi}{\psi}
\newcommand{\refphi}{\tilde\basphi}
\newcommand{\xno}[1]{x_{#1}}
\newcommand{\dX}{\, \mathrm{d}X}
\newcommand{\dx}{\, \mathrm{d}x}
\newcommand{\ds}{\, \mathrm{d}s}
$$
The equation for the Neumann boundary condition
\( i=0 \): insert
$$
u_{-1} = u_1 -\frac{2\Delta x}{\dfc(u_0)}
$$
in \( A_{0,0} \). The expression for \( A_{i,i+1} \)
applies for \( i=0 \), and \( A_{i,i-1} \) for \( i=0 \) does not enter the system.