SOLR-4475: Fix various places that still assume File based paths even when not using a file based DirectoryFactory.
SOLR-4551: CachingDirectoryFactory needs to create CacheEntry's with the fullpath not path.

git-svn-id: https://svn.apache.org/repos/asf/lucene/dev/branches/branch_4x@1454915 13f79535-47bb-0310-9956-ffa450edef68