linked folders are evil ,)
Report the issues with details on how the layout are (project example) in jira and we will see if we can acoomodate for it.
Unfortunately we might not be able to fix all linked folder issues since "j2ee module dependencies" is part of WTP not just jboss tools ,(
p.s. having a policy of not having eclipse or any other IDE related files where it makes sense (next to the source) is a policy that will give more troubles than it is worth IMO.
I didn't make this policy, but IMO a powerful IDE like Eclipse should be able to handle linked folders ;)
The consequence is that the plugins should be able too.
OK, I'll open an issue.
note: just because the IDE supports linked folders does not mean all plugins automatically will support - not all areas of wtp supports linked folders.
Anyhow - open an issue with the details and we will look at it.