\begin{align}I =\displaystyle\int_0^{\pi / 4} x\ln\left(\tan x\right)\left(1-\frac{1}{\cos^2 x}\right)\,dx\end{align}
Perform the change of variable $y=\tan x$,
\begin{align}I&=\int_0^1 \arctan x\ln x \left(\frac{1}{1+x^2}-1\right)\,dx\\
&=-\int_0^1 \frac{x^2\arctan x\ln x}{1+x^2}\,dx\\
&=\Big[\left(\arctan x-x\right)\arctan x\ln x\Big]_0^1+\int_0^1 \left(x-\arctan x\right)\left(\frac{\ln x}{1+x^2}+\frac{\arctan x}{x}\right)\,dx\\
&=\int_0^1 \frac{x\ln x}{1+x^2}\,dx+\int_0^1 \arctan x\,dx-\int_0^1 \frac{\arctan x\ln x}{1+x^2}\,dx-\int_0^1 \frac{\arctan^2 x}{x}\,dx\\
&=\left[x\arctan x-\frac{1}{2}\ln(1+x^2)\right]_0^1+\frac{1}{4}\int_0^1\frac{2x\ln(x^2)}{1+x^2}\,dx-\int_0^1 \frac{\arctan x\ln x}{1+x^2}\,dx-\\
&\Big[\ln x\arctan^2 x\Big]_0^1+2\int_0^1 \frac{\arctan x\ln x}{1+x^2}\,dx\\
&=\frac{\pi}{4}-\frac{1}{2}\ln 2+\frac{1}{4}\times -\frac{\pi^2}{12}+\int_0^1 \frac{\arctan x\ln x}{1+x^2}\,dx\\
\end{align}
And from,
Compute this following integral without Fourier series : $\int_0^{\pi/4}x\ln(\tan x)dx$
One knows that,
\begin{align}\int_0^1 \frac{\arctan x\ln x}{1+x^2}\,dx=\frac7{16}\zeta(3)-\frac{1}{4}\pi\text{G}\end{align}
Therefore,
\begin{align}\boxed{I=\frac{\pi}{4}-\frac{1}{2}\ln 2-\frac{1}{48}\pi^2-\frac{1}{4}\pi\text{G}+\frac7{16}\zeta(3)}\end{align}