Build the entire project (not just the scratch/ or web/) via ./gradlew build.
Copy the web/build/libs/web-1.0.0-SNAPSHOT-all.jar into your spongepowered.org Minecraft, typically the mods/ directory of a Vanilla server.
Start a web server for the ScratchX extension:
cd scratch
npm start
Make sure you CLOSE the page that just opened on http://localhost:3000, because its only used for testing, but the Vert.X EventBus client on it will interfere with the one in the ScratchX page.
Start the Minecraft server, and pass the URL where the ScratchX extension is available now:
java -Dstoreys_jsURL=http://localhost:3000/minecraft.scratchx.js -jar spongevanilla-*.jar
Connect to your Minecraft server with the Minecraft client GUI, and use the console command as documented here.
To develop new extensions to our Vert.x-based Minecraft remote API, we often first (before doing above) start the main() method of the SeleniumTest, which starts the TestMinecraft implementation, use npm start as above to run the client, and then open http://localhost:3000/?eventBusURL=http://localhost:6060/eventbus, and try out things in the Browser's Console.
To only just test Scratch (v2) integration issues in dev, you can also npm start and then open
http://scratchx.org/?url=http%3A%2F%2Flocalhost%3A3000%2Fminecraft.scratchx.js (the EventBus won't work, but you can debug problems with blocks).
You can also hack away at the Minecraft plugin server side with Java code hot reloading using https://github.com/vorburger/ch.vorburger.minecraft.osgi. This will reload the plugin when you re-build it. You can use ./gradlew build --continuous to have it rebuilt automatically on each change you make. In this mode, you don't use the web-*-all.jar, but you /osgi:install file:/... for the two smaller web/build/libs/web-1.0.0-SNAPSHOT.jar and the storeys/build/libs/storeys-1.0.0-SNAPSHOT.jar, and put all dependencies into the server's osgi/boot directory:
1_org.apache.felix.log-1.0.1.jar
2_org.everit.osgi.loglistener.slf4j-1.0.0.jar
3_guava-18.0.jar
3_guava-19.0.jar
3_guava-20.0.jar
3_guava-22.0.jar
4_ch.vorburger.osgi.gradle-1.0.0-SNAPSHOT.jar
4_org.gradle.tooling.osgi-3.3.jar
5_ch.vorburger.minecraft.osgi.dev-1.0.0-SNAPSHOT.jar
6_jackson-annotations-2.9.0.jar
6_jackson-core-2.9.0.jar
6_jackson-databind-2.9.0.jar
6_netty-buffer-4.1.16.Final.jar
6_netty-codec-4.1.16.Final.jar
6_netty-codec-dns-4.1.15.Final.jar
6_netty-codec-http2-4.1.16.Final.jar
6_netty-codec-http-4.1.16.Final.jar
6_netty-codec-socks-4.1.16.Final.jar
6_netty-common-4.1.16.Final.jar
6_netty-handler-4.1.16.Final.jar
6_netty-handler-proxy-4.1.16.Final.jar
6_netty-resolver-4.1.16.Final.jar
6_netty-resolver-dns-4.1.15.Final.jar
6_netty-transport-4.1.16.Final.jar
6_vertx-auth-common-3.5.0.jar
6_vertx-bridge-common-3.5.0.jar
6_vertx-core-3.5.0.jar
6_vertx-web-3.5.0.jar