The auxiliary-field quantum Monte Carlo (AFQMC) method is a general numerical method for correlated many-electron systems, which is being increasingly applied in lattice models, atoms, molecules, and solids. Here, we introduce the theory and algorithm of the method specialized for real materials and present several recent developments. We give a systematic exposition of the key steps of AFQMC, closely tracking the framework of a modern software library we are developing. The building of a Monte Carlo Hamiltonian, projecting to the ground state, sampling two-body operators, phaseless approximation, and measuring ground state properties are discussed in detail. An advanced implementation for multi-determinant trial wave functions is described, which dramatically speeds up the algorithm and reduces the memory cost. We propose a self-consistent constraint for real materials, and discuss two flavors for its realization, either by coupling the AFQMC calculation to an effective independent-electron calculation or via the natural orbitals of the computed one-body density matrix.