I used this command on my mac terminal to only to sync only java files whose size had changed on the remote host:

rsync -rP --size-only --include="/" --include=".java" --exclude="*" /src/dir1/ remote-host:/src/dir1/

However, there were several .git/objects/??/ directories in my source folder but it had no java files in it.

for eg.

ls .git/objects/e3 4704650cf08c9d36c8e6699cf08b6e672e532b <= file but not java

On the remote host it created the exact same .git/objects/e3 folder but completely empty. How do I prevent this?

You can always use --dry-run or -vvv to maybe get a better picture of how your options work.

As I understand rsync and the options as posted.

--include="/" will only include the root directory but not sub-directories regardless of the -r option. Since sub-directories are being created I assume this is a typo?

--include=".java" will only include a file called .java but I assume you actually want --include="*.java"

If you use --include="*/" rsync will include all subdirectories and create them on the destination but since your only including ".java" those directories are empty.

If you use the -m option then empty destination sub-directories will not be created.

Remember that options use a relative path to the source directory.

Thanks -m option worked very well.