How to copy file preserving directory path in Linux?

The switch you need is --parents, e.g.:

jim@prometheus:~$ cp --parents test/1/.moo test2/
jim@prometheus:~$ ls -la test2/
total 42
drwxr-xr-x   3 jim jim    72 2010-09-14 09:32 .
drwxr-xr-x 356 jim jim 43136 2010-09-14 09:32 ..
drwxr-xr-x   3 jim jim    72 2010-09-14 09:32 test
jim@prometheus:~$ ls -la test2/test/1/.moo
-rw-r--r-- 1 jim jim 0 2010-09-14 09:32 test2/test/1/.moo

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