Meld is a visual diff and merge tool. It integrates with most version control systems. The diff viewer lets you edit files in place (diffs update dynamically), and a middle column shows detailed changes and allows merges. The margins show location of changes for easy browsing, and it also features a tabbed interface that allows you to open many diffs at once.
CVS, GIT, and Mercurial as well as other well-known version control systems cannot version directories. In other words, you cannot add empty directories. A "workaround" for this issue is to use placeholder files that are placed into empty directories. These placeholder files can then be committed into the repository and will make sure that, upon checkout, the directory tree is entirely reconstructed. The problem with using placeholder files is that you need to create them, and need to delete them if they are not necessary anymore (because sub-directories or real files were added). With big source trees, managing these placeholder files can be cumbersome and error prone. MarkEmptyDirs can manage the creation/deletion of such placeholder files automatically. It creates placeholder files in all empty "leaf" directories. If later on new files or directories are put into such directories, the placeholder files are not necessary anymore, and are removed automatically.