What I want to do is simply use the eclipse package explorer in hierarchical view but with empty packages being collapsed so I don’t have to open 5+ packages to find the first Java file.
I’m not even sure how I did it in previous versions, but I’ve never had any trouble finding it before, it just seems to be gone now. I have a feeling there was a “flatten hierarchy” tick-box somewhere.
To clarify I get this:
com
example
etc
file1.java
Rather than:
com.example.etc
file1.java
I’m using Eclipse Indigo (v. 3.7.1)

I don’t know what the problem actually was, but I couldn’t get it fixed until I gave up altogether and reinstalled the OS (it was a fresh install anyway), and eclipse. It was completely fine after that. :\