Если вы можете использовать Python, это очень просто:
import yaml
# read your first file
with open("basefile.yaml", 'r') as f:
conf = yaml.load(f)
# read your second file
with open("devfile.yaml", 'r') as f:
devconf = yaml.load(f)
# update the first dictionnary with the values of the second
conf.update(devconf)
# write it in a new file
with open("result.yaml", 'w+') as f:
yaml.dump(conf, f)