Removed some redundant logic from DependencyGraphBuilder.

No tests have barfed after this change. Either this logic is redundant or we're missing coverage. I came across this while working on the component replacement. @Adam, it would be good if you reviewed this and let me know what coverage we're missing or bless this removal.
Added some corner cases to the component replacement feature planned test cases.
Added a story related to replacing a module with a set of modules (or vice versa) into the conflict-resolution spec.
Added more context to the javadoc generation exception.
Added more trace so that debugging javadoc generation issues is easier for us and for end users.