SVN Merge from branch to trunk is not working as expected

In order to do some refactoring I copied the trunk in a new branch. Refactoring included renaming Java Source to src and deleting Web Content folder. But after making desired changes in the branch and executing svn merge from the trunk the refactoring changes were not reflected. Though merging did pull in the code changes from the branch. Am I doing something wrong here?

Trunk structure:

Branch structure:

Merged Trunk structure: (no changes reflected)

Though I was not able to identify the main cause of the problem but my Subversive plug-in was 6 years old and that could be a possible reason. The way I created branch was perfectly correct and to verify that I ended up installing Subclipse plug-in instead and using Team -> Merge everything worked fine!