CAPSL is a Common Authentication Protocol Specification Language intended to support analysis of cryptographic protocols using formal methods. CAPSL is adapted for use by various protocol analysis tools using an intermediate language, CIL. This report includes a CAPSL tutorial, the syntax of CAPSL and CIL, and the abstract rewriting model underlying CIL. Algorithms are given for translating CAPSL to CIL and for CIL rule optimization. Methods are given for integration of CAPSL and CIL with analysis tools, specifically PVS, Maude, and Athena, and for protocol analysis using PVS and Maude.