Your path of least resistance is to use Maven (as opposed to Gradle or Ant/Ivy). If you’re working in Java, you definitely want an IDE - Eclipse and IntelliJ both have their following. I think most people will be happier with IntelliJ but you have to pay for it.
There are two viable maven plugins right now:
com.google.appengine:appengine-maven-plugin is the older and more mature plugin
com.google.cloud.tools:appengine-maven-plugin is the newer and not yet perfect plugin
I would say we are on the cusp of the newer plugin being ready for default use. It currently has trouble deploying the queue/cron configs, but it looks like it’s getting fixed fast. I actually have both enabled in my project right now.
You also have the choice of “older vs newer” plugin for Eclipse/IntelliJ. I would go with the newer one.
Someone else will have to give you endpoints advice.
Jeff