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When you do a CVS add on a directory, it updates the CVS/Entries file on the filesystem root. This is fine if the directory is at the root level. However, if it's down a level or more, this is wrong. This is happening because the directory CVS is invoked in is the filesystem. CVS needs to be invoked from the directory where the file (or directory) is stored. This is happening in 3.2 Beta RC 2.
Fixed in the main trunk only. The add command now run in the parent directory of the one being added .
Fixed in release32 build #32.
Target milestone -> 3.2
Verified quite easily in development build of NetBeans 3.3 #200106260100 and Forte for Java 3.0 #010625_1.