Customize material in ThreeJS - three.js

Question

I would like to customize the shaders of a material in ThreeJS, the MeshStandardMaterial, by making it work as a ShaderMaterial. Here is the material code :
const material = new THREE.ShaderMaterial({
uniforms: THREE.UniformsUtils.merge([
{
color: { value: new THREE.Color( 0xeeeeee ) },
opacity: { value: 1.0 },
map: { value: null },
offsetRepeat: { value: new THREE.Vector4( 0, 0, 1, 1 ) },
specularMap: { value: null },
alphaMap: { value: null },
envMap: { value: null },
flipEnvMap: { value: - 1 },
reflectivity: { value: 1.0 },
refractionRatio: { value: 0.98 }
},
THREE.UniformsLib.aomap,
THREE.UniformsLib.lightmap,
THREE.UniformsLib.emissivemap,
THREE.UniformsLib.bumpmap,
THREE.UniformsLib.normalmap,
THREE.UniformsLib.displacementmap,
THREE.UniformsLib.roughnessmap,
THREE.UniformsLib.metalnessmap,
THREE.UniformsLib.fog,
THREE.UniformsLib.lights,
{
emissive: { value: new THREE.Color( 0x000000 ) },
roughness: { value: 0.5 },
metalness: { value: 0 },
envMapIntensity: { value: 1 } // temporary
}
] ),
vertexShader: `
#define PHYSICAL
varying vec3 vViewPosition;
#ifndef FLAT_SHADED
varying vec3 vNormal;
#endif
#include <common>
#include <uv_pars_vertex>
#include <uv2_pars_vertex>
#include <displacementmap_pars_vertex>
#include <color_pars_vertex>
#include <fog_pars_vertex>
#include <morphtarget_pars_vertex>
#include <skinning_pars_vertex>
#include <shadowmap_pars_vertex>
#include <specularmap_pars_fragment>
#include <logdepthbuf_pars_vertex>
#include <clipping_planes_pars_vertex>
void main() {
#include <uv_vertex>
#include <uv2_vertex>
#include <color_vertex>
#include <beginnormal_vertex>
#include <morphnormal_vertex>
#include <skinbase_vertex>
#include <skinnormal_vertex>
#include <defaultnormal_vertex>
#ifndef FLAT_SHADED
vNormal = normalize( transformedNormal );
#endif
#include <begin_vertex>
#include <displacementmap_vertex>
#include <morphtarget_vertex>
#include <skinning_vertex>
#include <project_vertex>
#include <logdepthbuf_vertex>
#include <clipping_planes_vertex>
vViewPosition = - mvPosition.xyz;
#include <worldpos_vertex>
#include <shadowmap_vertex>
#include <fog_vertex>
}`,
fragmentShader: `
#define PHYSICAL
uniform vec3 diffuse;
uniform vec3 emissive;
uniform float roughness;
uniform float metalness;
uniform float opacity;
#ifndef STANDARD
uniform float clearCoat;
uniform float clearCoatRoughness;
#endif
varying vec3 vViewPosition;
#ifndef FLAT_SHADED
varying vec3 vNormal;
#endif
#include <common>
#include <packing>
#include <color_pars_fragment>
#include <uv_pars_fragment>
#include <uv2_pars_fragment>
#include <map_pars_fragment>
#include <alphamap_pars_fragment>
#include <aomap_pars_fragment>
#include <lightmap_pars_fragment>
#include <emissivemap_pars_fragment>
#include <envmap_pars_fragment>
#include <fog_pars_fragment>
#include <bsdfs>
#include <cube_uv_reflection_fragment>
#include <lights_pars>
#include <lights_physical_pars_fragment>
#include <shadowmap_pars_fragment>
#include <bumpmap_pars_fragment>
#include <normalmap_pars_fragment>
#include <roughnessmap_pars_fragment>
#include <metalnessmap_pars_fragment>
#include <logdepthbuf_pars_fragment>
#include <clipping_planes_pars_fragment>
void main() {
#include <clipping_planes_fragment>
vec4 diffuseColor = vec4( diffuse, opacity );
ReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );
vec3 totalEmissiveRadiance = emissive;
#include <logdepthbuf_fragment>
#include <map_fragment>
#include <color_fragment>
#include <alphamap_fragment>
#include <alphatest_fragment>
#include <specularmap_fragment>
#include <roughnessmap_fragment>
#include <metalnessmap_fragment>
#include <normal_flip>
#include <normal_fragment>
#include <emissivemap_fragment>
#include <lights_physical_fragment>
#include <lights_template>
#include <aomap_fragment>
vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveRadiance;
gl_FragColor = vec4( outgoingLight, diffuseColor.a );
#include <premultiplied_alpha_fragment>
#include <tonemapping_fragment>
#include <encodings_fragment>
#include <fog_fragment>
}`
});

Answer 1

As of r88 the THREE.Water code implements an example of using a ShaderMaterial along with some internals code chunks from ThreeJS internals.
The onBeforeCompile material method introduced in r86 provides an easy and short way to apply changes to built-in materials.