The first snapshot ignores the loaded fileformat and the save-action write always an extended fileformat. This one dont work with the , because it uses unsupported tags to store additional information.
People, who run in this trouble should load the saved file and choose the the "Cocoon CLI xconf fileformat" from the "Save as" dialog. This will generate a correct cli.xconf file. The "broken-links" and the "uri-list"-tags are unfortunately lost, you have to add this by hand, if there was one of them before.
Sorry
The current snapshot handles more carefully filesaving. Have a look at the User guide, it is now updated and explain, how paths are handled.
First, this software is not stable and has bugs.
Use the sourceforge-page to report bugs or send an email to me.
If possible attach the stackstrace (Windows user take simple the "jre.log" from the dist-folder), but have a look for private data and remove this before sending (for example: if the publishing throws exception there will be the uri with password and username in the error-message).