The following code will create an external coverage store in GeoServer also publishing the layer

// layer encoder
final GSLayerEncoder layerEnc = new GSLayerEncoder();
String style=getDefaultStyle();
if (style==null || style.isEmpty())
 style="raster";
layerEnc.setDefaultStyle(style);

// coverage encoder
final GSImageMosaicEncoder coverageEnc=new GSImageMosaicEncoder();
coverageEnc.setName(mosaicDescriptor.getCoverageStoreId());
coverageEnc.setTitle(mosaicDescriptor.getCoverageStoreId());
if (config.getCrs()!=null){
 coverageEnc.setSRS(config.getCrs());
}
coverageEnc.setMaxAllowedTiles(Integer.MAX_VALUE);

// ... many other options are supported

// create a new ImageMosaic layer...
final boolean published = gsPublisher.publishExternalMosaic(workspace, storeName, baseDir, coverageEnc, layerEnc);

// check the results
if (!published) {
 final String msg="Error creating the new store: " + layerName;
 Exception ex = new Exception(this.getClass(), msg);
}