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We present a comprehensive analysis of the deuteron charge and quadrupole form factors based on the latest two-nucleon potentials and charge density operators derived in chiral effective field theory. The single- and two-nucleon contributions to the charge density are expressed in terms of the proton and neutron form factors, for which the most up-to-date empirical parametrizations are employed. By adjusting the fifth-order short-range terms in the two-nucleon charge density operator to reproduce the world data on the momentum-transfer dependence of the deuteron charge and quadrupole form factors, we predict the values of the structure radius and the quadrupole moment of the deuteron: $r_{\rm str}=1.9729\substack{+0.0015\\ -0.0012}\ \text{fm},\ Q_d=0.2854\substack{+0.0038\\ -0.0017}\ \text{fm}^2. $ A comprehensive and systematic analysis of various sources of uncertainty in our predictions is performed. Following the strategy advocated in our recent publication Phys. Rev. Lett. 124, 082501 (2020), we employ the extracted structure radius together with the accurate atomic data for the deuteron-proton mean-square charge radii difference to update the determination of the neutron charge radius, for which we find: $r_n^2=-0.105\substack{+0.005\\ -0.006} \, \text{fm}^2$. Given the observed rapid convergence of the deuteron form factors in the momentum-transfer range of $Q \simeq 1-2.5$ fm$^{-1}$, we argue that this intermediate-energy domain is particularly sensitive to the details of the nucleon form factors and can be used to test different parametrizations.