Is there any way to make subclipse checkout a repository into a non-root folder of a project. In particular, I want to checkout into folder src/wavedev rather than just to the project root.
Not sure if this is a solution to your situation, but you could use SVN:Externals
The SVN:Externals property lets you checkout an external repository within your current repository. Changing code in this external repository will update in your current project and changing code in your current project from the external repository will commit to that repository.
To set the external property in subclipse:
right-click your root foolder
select team > set property
From the property dropdown select "svn:externals"
set the value to:
src/wavedev http://svn.yourrepository/wavedev
As far as I know subclipse uses the same .svn folders as the svn commandline tool or for instance tortoisesvn. So if you can't get it to work with subclipse you could try this workaround
If your top level project isn't under version control, then you probably can't do the svn:externals trick.
However, you could work your way around it:
Check out the code you want into a new project (let's call this Project B).
In the project your working in (let's call it Project A), create a new folder (src/wavedev), but in the New Folder Dialogue, use the Advanced button to link it to an external folder in the filesystem. You can point it to the location of Project B.
It might make more sense, though, to add Project B to the build path of Project A...?