Honestly, you just listed some of the best reasons to use Java.
Other languages are less dependent on a heavy IDE; I can write Python or even Scala in vim (+ repl in another tab) reasonably comfortably, and while vim has its warts it's a lot less fragile than eclipse.
Spring is IMO not worth the complexity compared to explicitly constructing things, but if you really want to do that there are ways to do it in Scala (e.g. just using implicits, reader monad) that don't require annotations or XML and don't have anything like the number of quirks (e.g. autoproxying, about 10 magic lifecycle methods, configuration-dependent behaviour on duplicate beans) that Spring does.
Likewise Hibernate is nice but it has some irritating misbehaviour (e.g. passing empty lists can cause it to make SQL syntax errors) that isn't present in ActiveRecord or even modern JVM alternatives.
I didn't expect my comment to be so negative when I started writing it, but as I started to try and explain the basics I realized how many arbitrary workarounds a very basic Java app needs. A lot of this is 10 years of accumulated cruft rather than fundamental problems, but at the sharp end new users still have to deal with it.
Install eclipse. Get a non-JavaEE version - probably "eclipse for java developers". It's flaky software and you will have to babysit it sometimes, but it's still the best choice.
Use maven, then you don't need a sysadmin to maintain your libraries. You just add libraries as dependencies (you can even use a search wizard in Eclipse) and it Just Works. Start by using the new maven project wizard; I would skip archetype selection entirely, but if you want to use a particular framework you can choose one of those and get a "hello world".
Add libraries one at a time. If you're writing a web application I love Wicket which is literally the best-designed library ever. Aside from that you're facing things that, like eclipse, are a bit clunky; sooner or later you will have to learn Spring and Hibernate. Everyone loves to hate them and with good reason, but people will expect you to know them, and they do have good parts.
Try to do as much as possible in pure java. Use embedded jetty and write a normal application rather than messing with war packaging. Use annotation-based Spring configuration rather than XML, and the same for Hibernate.
The whole ecosystem is old and crufty. You will have to get used to random crappy workarounds for all sorts of problems, and you will probably have to cargo-cult some things to get stuff working. This is unfortunate, but I guess it's the price of stability. There are good sides to the ecosystem too. Sorry to be such a downer.