The full moduli space M of a class of N=1 supersymmetric gauge theories is studied. For gauge theories living on a stack of D3-branes at Calabi-Yau singularities X, M is a combination of the mesonic and baryonic branches, the former being the symmetr
ic product of X. In consonance with the mathematical literature, the single brane moduli space is called the master space F. Illustrating with a host of explicit examples, we exhibit many algebro-geometric properties of the master space such as when F is toric Calabi-Yau, behaviour of its Hilbert series, its irreducible components and its symmetries. In conjunction with the plethystic programme, we investigate the counting of BPS gauge invariants, baryonic and mesonic, using the geometry of F and show how its refined Hilbert series not only engenders the generating functions for the counting but also beautifully encode ``hidden global symmetries of the gauge theory which manifest themselves as symmetries of the complete moduli space M for arbitrary number of branes.
We discuss in detail the problem of counting BPS gauge invariant operators in the chiral ring of quiver gauge theories living on D-branes probing generic toric CY singularities. The computation of generating functions that include counting of baryoni
c operators is based on a relation between the baryonic charges in field theory and the Kaehler moduli of the CY singularities. A study of the interplay between gauge theory and geometry shows that given geometrical sectors appear more than once in the field theory, leading to a notion of multiplicities. We explain in detail how to decompose the generating function for one D-brane into different sectors and how to compute their relevant multiplicities by introducing geometric and anomalous baryonic charges. The Plethystic Exponential remains a major tool for passing from one D-brane to arbitrary number of D-branes. Explicit formulae are given for few examples, including C^3/Z_3, F_0, and dP_1.
