Did some research Monday and then met with Jennifer today.
Contribute appears to have no way of allowing you to see the file-and-folder tree, so the only way to address a file included by a php call is to manually enter the url of the included file into the URL box in the Contribute editor.
If the file is a well-formed xhtml structure, though not a full dom, (e.g. an unordered list), then the file will open for reading though what appears may be the xhtml code or may be the default parsing and representation of a list. The file can also be edited, and always is parsed for presentation in the editor (e.g. lists show up as lists and links show up as coloured, underlined text, neither show up in the editor as xhtml code). Changes are saved OK.
Jennifer OK with editing the section nav bar files in each section in this way if necessary. We discussed treating certain elements of page content which are repeated (e.g. department listing) by decided to leave them as duplicate hard-coded instances for the time being.