Our folder structure for glslify + ThreeJS.
src/
shaders/
glsl-voronoi/ (depends on glsl-random on npm)
glsl-displace/ (depends on glsl-voronoi)
glsl-src-over/
glsl-blend-overlay/
glsl-blend-screen/
fancy.js
fancy.frag
pass.vert
main.js
Each of the glsl-*
folders is a "shader cunk" or util. At the end of the project, they will be stable enough to split into npm modules so they can be required and depended on in future projects (like glsl-random and glsl-lut).