The 'Efficiency' plots are how many optical photons make it to the sensitive volume of the detector (over the gap [air or cookie] and through the SiPM window) vs. length. Each page is a different light guide number, 1-10 for GlueX as normal, and 1-12 for BIC, numbered from smallest to largest.
S12-GlueX is the GlueX light guides with something akin to the 12.7x12.7 mm^2 SiPMs, S13-BIC is the BIC light guides with the 13x13 mm^2 SiPMs. 'QuadrantSource' has optical photons generated only in quadrant 1, and 'Alternate' has some examples of the trapezoidal BIC guides... bt2 has the same base as b5 with the output face altered to be trapezoidal (bottom edge 13 mm, height 13 mm, top edge wider, calculated to whatever it needed to be to make the prism planar), bg2 uses the dimensions of b5 to calculate what the bottom and top base widths would be for GlueX-style guides, with each sector being the same rather than alternating rightside up and upside down.
The 'Extra' plots give more information for each length for the specified light guide/gap/detector combination in the titles. The first page is exit distributions for successful and failed events, the second page has thrown theta, exit theta, exit phi, and exit theta vs. exit phi, the third page has efficiency vs. x, vs. y, vs. theta, and the x-y distribution of detected photons at the face of the sensitive detector volume (useful for looking at light mixing/saturation stuff), and page four has light mixing plots, entrance x vs. exit y etc., repeated for each length, 5 mm through 100 mm. The PDF page titles and plot titles should hopefully have all the information needed to tell what each plot is representing.