Hard links are not like symbolic links, they are not merely pointers to other files, but alternative names for the same file. The name of every file is a hard link, the first so to speak. You can add additional names which really are the file, they are not just pointers. For the technically minded, they are not separate inodes, they are additional directory references to the same inode. When you perform a copy operation on multiple files, cfengine attempts to preserve hard links but this is a difficult task.
Because a hard link just looks like an ordinary file (it cannot be distingiushed from the original, the way a symbolic link can) there is a danger that any copy operation will copy two hard links to the same file as two separate copies of the same file. The difference is that changes a hard-linked file propagate to the links, whereas two copies of a file are completely independent thereafter. In order to faithfully reproduce all hardlinks to all files, cfengine needs to examine every file on the same filesystem and check whether they have the same inode-number. This would be an enourmous overhead, so it is not done. Instead what happens is that cfengine keeps track of only the files which it is asked to examine, for each atomic copy-command, and makes a note of any repeated inodes within this restricted set. It does not try to go off, wandering around file systems looking to other files which might be hardlinks.
To summarize, cfengine preserves hardlinks during copying, only within the scope of the present search. No backups are made of hard links, only of the first link or name of the file is backed up. This is a necessary precaution to avoid dangling references in the inode table. As a general rule, hard links are to be avoided because they are difficult to keep track of.
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