One idea is common on many well-organized servers. Graphics are kept together in one directory. This might be pictures of Aunt Jane, or it could be small images that are used to decorate your web pages. Other files that users may wish to download are kept together, possibly in a directory named download, such that when the site is cleaned out, these additional files aren't cleaned out too!

Reflecting this, it may be good housekeeping to organise such files on your disk in a similar manner, collecting these oddments as they are added, all ready to be uploaded to the same place on the server.

This means finding a home for each Website that you maintain, within that organising content in an organized manner (for xml files, html files generated from the xml files and 'other' material). As an example I will use three types of 'other' material.

A suitable layout for a Website called drinks might be:

/websites
  /drinks
  layout.xml
  build.xml
    /xml
     ... xml files
    /html
      /download
      /graphics
      index.html
      ..... html files

This means that all the files needed on the server may be found in the html directory! In this example, in directory /websites/drinks/html. The other directories contain the other types of files. They are segregated simply to keep different types of files together for ease of management. /downloads for word files, PDF files, spreadsheets, photographs, technical files etc. Whatever non-html files you create yourself or have legitimate access to and use for, on your Website.

The /graphics directory is there to keep the small images used for site navigation in some Websites. Docbook provides a whole directory full. It would be nice to be able to upload a new set, perhaps when Docbook is updated!

A final point for the perfectionist. One thing that Website doesn't do is remind you when you delete an xml file, that it has within it, a link to abc.doc, a Word file in the download directory! If you need reminding (quite reasonable if you uploaded the Word file and wrote the xml file two years ago?), then perhaps it is worthwhile keeping a simple file which relates to the files in the download directory, and the xml files which make some reference to them? Something as simple as

If this file is somehow associated with the Website (perhaps within the /websites/drinks directory, then you have a means of checking the files on the Website and the files in the download directory. Of course this only works if you keep the file up to date!

A simple case of you get out what you put in