In either case, the Index will be reverted to the HEAD file content.

When unstaging previously staged changes, the staged changes will be moved back to the working tree, if the latter hasn't been modified in the meantime, otherwise the staged changes will be lost. Individual change hunks can be staged and unstaged there. The Changes view of the SmartGit project window can show the changes between the HEAD and the Index, between the HEAD and the working tree, or between the Index and the working tree state of the selected file. If you have staged some file changes and later modified the working tree file again, you can use the Discard command to either revert the working tree file content to the staged changes stored in the Index, or to the file content stored in the repository (HEAD). If you select a file that has Index changes, invoking Commit will give you the option to commit all staged changes.

Explicitly using the Remove command has the same effect, as you may be accustomed to from SVN. If you stage a file that was previously version-controlled, but is now missing in the working tree, it will be marked for removal. The Stage command allows you to save a file's content from your working tree in the Index. With SmartGit, you can make heavy use of the Index, or ignore its presence completely - it's all up to you. The Index is an intermediate cache for preparing a commit.

Smartgit rebase branch on top of master