Are you aware of the amazing Java debugger feature of "Drop to Frame"? Combined with "hot-injection" (compile new code, then inject into current debug'd JVM), it is crazy and amazing. (I love C#, but the hot-injection feature is much worse than Java -- more than 50% of the time, C# compiler rejects my hot-injection, but about 80% of the time, JVM accepts my hot-injection.) When working on source code where it is very difficult to acquire data for the algorithm, having the ability to inspect in a debugger, make minor changes the the algorithm, then re-compile, inject new class/method defs, the drop to frame, the re-exec the same code in the same debug session is incredibly powerful.
The plus side of less capable tooling is it tends to limit how complex software can be--the pain is just too noticeable. I haven't liked java in the past because it seems very difficult without the tooling and I never had to do enough java to learn that stuff. Java's tooling does seem quite excellent once it is mastered.
If you are a low level programmer, I understand your sentiment. A piece of advice, when you need to use Java (or other JVM languages), just submit to all the bloat -- use an IDE, like IntelliJ, that needs 4GB+ of RAM. The increase in programmer productivity is a wild ride coming from embedded and kernel programming. (The same can be said for C#.)
What I find is that if my code isn't working, I stop what I'm doing. I look at it. I think really hard, I add some print statements and asserts to verify some assumptions, and I iterate a small handful of times to find my faulty assumption and fix it. Many, many times during the 'think hard' and look at the code part, I can fix the bug without any iterations.
This almost always works if I really understand what I'm doing and I'm being thoughtful.
Sometimes though, I don't know what the hell is going on and I'm in deep waters. In those cases I might use a debugger, but I often feel like I've failed. I almost never use them. When I helped undergrads with debuggers it often felt like their time would be more productively spent reasoning about their code instead of watching it.