Currently, the context menu actions provided by the File System Browser are all performed on the file/directory that is selected in the file list pane, even if invoked from the directory tree pane. So, for example, if I right-click some directory along the path in the tree pane (e.g. the root directory), and select "Search in directory...", the Search dialog that opens specifies the path to the selected item in the file list pane rather than the directory that was right-clicked in the tree pane (and the selected item in the tree pane is changed to the leaf item). This is not a standard behavior.
"Search in directory..." is only an example. I think the tree pane should have a different context menu than the file list pane, since all actions actually work on the selected item in the file list pane.