Which is the rsync command to “smartly” merge two folders?

I would use:

rsync -abviuzP src/ dest/

• -i turns on the itemized format, which shows more information than the default format
• -b makes rsync backup files that exist in both folders, appending ~ to the old file. You can control this suffix with --suffix .suf
• -u makes rsync transfer skip files which are newer in dest than in src
• -z turns on compression, which is useful when transferring easily-compressible files over slow links
• -P turns on --partial and --progress
• --partial makes rsync keep partially transferred files if the transfer is interrupted
• --progress shows a progress bar for each transfer, useful if you transfer big files