Unfortunately, it is not possible to turn off URL sanitizing.
If you are willing to ask you users to perform a preparation step when opening your design diagrams, you could try the following approach.
- Add a custom property for nodes (see "Edit" -> "Manage Custom Properties") to your diagram, e.g. MyUrl. Use MyUrl to store your file references - including a variable for user-dependent path prefixes, e.g. file://%ROOT%/my-design-docs/the-other-diagram.graphml
- Create a properties mapper configuration to map MyUrl to the actual URL property using the properties mapper's Regular Expression conversion to replace your variable, e.g.
- Export the properties mapper configuration and distribute it to your users. Have the users import the configuration and adjust the Replacement value for their systems.
- When a user opens the diagram for the first time, have the user run the properties mapper configuration once and save the diagram with the corrected URLs.
Finally, I would like to mention that URLs using the file protocol like file:///home/yguy/Documents/mydiagram.graphml do work. However, if you specify the protocol, you will have to use an absolute path. (There are no relative URLs. If you specify a relative path, yEd will create a corresponding URL internally by adding the relative path to the base URL of the current document.)