Create directory "classes" with exploded module m
modules/m/module-info.class
modules/m/p/D.class

invoke fm.setLocationFromPaths(StandardLocation.SYSTEM_MODULES,classes);

Exception will be thrown
java.lang.IllegalArgumentException: path too long for directory
at com.sun.tools.javac.file.Locations$SystemModulesLocationHandler.setPaths(jdk.compiler@9-internal/Locations.java:1377)
at com.sun.tools.javac.file.Locations.setLocation(jdk.compiler@9-internal/Locations.java:1548)
at com.sun.tools.javac.file.JavacFileManager.setLocationFromPaths(jdk.compiler@9-internal/JavacFileManager.java:807)

JavaCompiler compiler = ToolProvider.getSystemJavaCompiler();
        StandardJavaFileManager fm = compiler.getStandardFileManager(null, null, null);
        Path modules = base.resolve("modules");
        Path classes = Files.createDirectories(base.resolve("classes"));
        tb.writeJavaFiles(modules.resolve("m"), "module m { }", "package p; public class D { }");
            tb.new JavacTask()
                    .options("-modulesourcepath",modules.toString())
                    .outdir(classes)
                    .files(modules.resolve("m/p/D.java"))
                    .run();
            fm.setLocationFromPaths(StandardLocation.SYSTEM_MODULES,classes);