回答:
include/exclude
パラメータの順序を変更する必要があります
# rsync -azvr --include lib/project/config.js --exclude config.js . dest
sending incremental file list
./
lib/
lib/project/
lib/project/config.js
代わりに
# rsync -azvr --exclude config.js --include lib/project/config.js . dest
sending incremental file list
./
lib/
lib/project/
sent 73 bytes received 23 bytes 192.00 bytes/sec