The information about the thumbnail management use by freedesktop.org window managers is at http://jens.triq.net/thumbnail-spec/introduction.html.
You have it, the hash is normally generated by referencing the file path and modification time, but other apps may make thumbnails in which the hash includes additional information like the camera model, resolution, etc...
The .directory file is used to store the view properties for the directory that contains the file. That file is used to store the following for each directory:
[ul][li]view mode[/li][li]if previews are enabled[/li][li]when the view mode was last modified[/li][li]if hidden files should be shown[/li][li]if it is set to display the contents sorted[/li][li]sort order[/li][li]If the files will be grouped[/li][li]the icon associated with the directory[/li][/ul]
Other options may also be stored in the file, but I have not yet identified them.
Shown below is the contents of a .directory file with grouping, sorted entries, previews, to show hidden files and icon view enabled.
After looking all of this up I am impressed with the work of the freedesktop.org community, this is a good method that is built for efficiency and accuracy, but it is still prone to duplication of thumbnails if the same file is present in multiple directories, which is probably why it is just a proposed standard at this time.