Option 1: go back in time and read this: http://lincolnloop.com/blog/2012/jan/6/detecting-file-moves-renames-rsync/
This uses a trick with hardlinks to optimise the operation (note carefully the omission of trailing "/" in the example though, that might be different to what you are used to). If you have a local backup copy prior to the reorg, you can perhaps restore and use that (the complication is being able to create the hardlink copy as required).
Option 2: if you have no spaces/quotes in your file or directory names, and do not intend keeping any duplicates, you can create a quick and dirty copy/rename script like this.
On source:
cd /wherever
find . -type f | xargs sha1sum | sort > /tmp/src.out
On destination
cd /wherever
find . -type f | xargs sha1sum | sort > /tmp/dst.out
Copy the dst.out file over to source, and then on source do:
join -j 1 /tmp/src.out /tmp/dst.out | while read sum src dst; do
if [ "$src" != "$dst" ]; then
echo mkdir -p $(dirname "$src")
echo cp -ipl "$dst" "$src"
fi
done > fixup.sh
This will output a set of mkdir/cp commands that you can run (fixup.sh) in the top directory of your copy on the destination. Make sure that the script output will do what you require it to do. cp -ipl will not overwrite without prompting, and will copy by hard-linking. A subsequent rsync --delete ... will delete the old files, assuming that want an identical copy. Use rsync --dry-run ... afterwards to confirm the extent of any remaining differences.
(It is possible to use "mv -i" instead of the non-destructive "cp -ipl", saving the duplication and cleanup.)
If you have problematic file/directory names, you'll need to do some intermediate processing of filenames, or try one of the solutions here: https://unix.stackexchange.com/questions/6411/any-way-to-sync-directory-structure-when-the-files-are-already-on-both-sides
Update:
If you can tolerate the explosion-in-a-punctuation-factory that passes for a sed command line:
find . -type f -print0 | xargs -0 sha1sum |
sed -re $'s/(^[0-9a-z]*) /\\1__/;
s/ /\\\\x20/g; s/\'/\\\\\'/g;
s/(^[0-9a-z]*)__/\\1 /;
s/ (.*)$/ $\'\\1\'/g;'
This will handle spaces and single/double quotes (though we're approaching perl territory for proper heavy lifting). It uses the bash $'' construction for quoting troublesome strings.
