In SVN 1420992, SolrCore#getIndexDir() changed it's implementation from a version that would reflect the value of the index property in index.properties to one that does not.
In 3.6, SolrCore#getIndexDir() was:
In 3.6, SolrIndexSearcher would be passed the value of SolrCore#getNewIndexDir() – which reads index.properties – in its constructor and return it when SolrIndexSearcher#getIndexDir() was called.
In 4.1, SolrCore#getIndexDir() is:
Clients of SolrCore#getIndexDir() that were expecting the previous behavior are likely to have issues. E.g.:
--In CoreAdminHandler#handleUnloadAction(SolrQueryRequest, SolrQueryResponse) if the deleteIndex flag is set to true, it calls core.getDirectoryFactory().remove(core.getIndexDir()). If a value other than index/ is set in index.properties, the wrong directory will be deleted.
--In CoreAdminHandler#getIndexSize(SolrCore), the existence of SolrCore#getIndexDir() is checked before SolrCore#getNewIndexDir(). If a value other than index/ is set in index.properties, this will return the size of the wrong directory.