The current master (3cf28720fc18a042e911b038bc1c5db271383275) don't send the classpath file. So eclipse don't show them correct and mark the files with errors.
On the filesystem, everything seems to be transmitted correctly.
The Files must be in a package (src/foo/bar.java)
The error don't exist in the current release
This was a change by request. We had several concerns about the classpath file. Endusers simply did not used partial sharing because the classpath file was always overwritten which result in broken projects on the receiver side. It is up to the enduser to decide whether to include the meta information file or not.
http://saros-build.imp.fu-berlin.de/gerrit/1289