I have created a link to folder in unix using ln -s command.. but if I copy the folder structures to windows box the same does not work in windows. is there a way to achieve symbolic/hard links created in one OS works in other also?
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You can't copy them over, but you can create links in Windows. The other operating system probably won't recognize them as links, so if you try to copy you may end up with two of the same folder.
[EDIT on at least some versions of NTFS for Linux, symlinks made under windows are also symlinks under Linux. It works out of the box with Ubuntu Oeneric, which seems to use the FUSE driver]