Linux: Force different set of directory/file permissions

I would use rsync as it means that if it is interrupted for any reason, then you can restart it easily with very little cost. And being rsync, it can even restart part way through a large file. As others mention, it can exclude files easily. The simplest way to preserve most things is to use the -a flag – ‘archive.’ So:

rsync -a source dest

Although UID/GID and symlinks are preserved by -a (see -lpgo), your question implies you might want a full copy of the filesystem information; and -a doesn't include hard-links, extended attributes, or ACLs (on Linux) or the above nor resource forks (on OS X.) Thus, for a robust copy of a filesystem, you'll need to include those flags:

rsync -aHAX source dest # Linux
rsync -aHE source dest  # OS X

The default cp will start again, though the -u flag will "copy only when the SOURCE file is newer than the destination file or when the destination file is missing". And the -a (archive) flag will be recursive, not recopy files if you have to restart and preserve permissions. So:

cp -au source dest

In order to have all files under a given directory inherit group rights, you need to use the setgid bit on your directory. See this link.

 $ mkdir test
 $ sudo chown raphink.staff test
 $ ls -lhd test
     drwxr-xr-x 2 raphink staff 4.0K 2009-12-21 16:19 test
 $ sudo chmod g+s test # Set the setgid bit
 $ ls -lhd test
     drwxr-sr-x 2 raphink staff 4.0K 2009-12-21 16:21 test
 $ touch test/foo
 $ ls -lh test
     total 0
     -rw-r--r-- 1 raphink staff 0 2009-12-21 16:23 foo