If you used this client before 0.2.0, you have a different directory structure than the current one. If you want to upgrade, but keep all your data, here's a migration guide.
# Start in ./data
cd data
# Move your account key to new location:
mkdir accounts
mv account/key.pem accounts/acme-v01.api.letsencrypt.org.directory.pem
# or accounts/acme-staging.api.letsencrypt.org.directory.pem if it's a staging key
# account should now be empty or contain just a config.json, you can delete the folder then
rm -rf account
# Migrate certificates to new location:
cd certs
mkdir acme-v01.api.letsencrypt.org.directory
# Move all your certificate directories
# Repeat for all directories!
mv example.com acme-v01.api.letsencrypt.org.directory
# or acme-staging.api.letsencrypt.org.directory
# Delete all config.json files which may exist
find -name "config.json" | xargs rm
# Update to current version
# Alternatively have a look at the new installation instructions and use the Phar
git checkout master && git pull
# Check out latest release
git checkout $(git describe --tags `git rev-list --tags --max-count=1`)
# Update dependencies
composer update --no-dev
# Reconfigure your webserver to use the new paths
# and check (and fix) your automation commands.