Manipulation of the configuration may cause various problems with eclipse WTP support.
When resolving wtp components:
GRADLE-2496 - forced modules are ignored
2. dependency resolve actions are ignored
3. configuration exclude rules are ignored (https://github.com/gradle/gradle/pull/104)
There may be other problems as well. Basically, in the IDE support we often create configurations on the fly (via detachedConfiguration method) for resolution purposes.However, those transient configurations do not share the configuration settings of the configurations where the dependencies are declared in.