Not the final AWS Elastic Beanstalk deployment for NodeJS. Why not the final? some parts are missing or not tested, like configuration changes. Currently it has been tested for application deployment only.

fix-npm.config

files:
  "/opt/elasticbeanstalk/env.vars":
    mode: "000775"
    owner: root
    group: users
    content: |
      # enable extra logs
      set -xe

      # Defines variables for use by the other scripts below.

      EB_NODE_VERSION=$(/opt/elasticbeanstalk/bin/get-config optionsettings -n aws:elasticbeanstalk:container:nodejs -o NodeVersion)

      # Exported to make sure Node binaries can be found by npm when we run it.
      # And this lets us invoke npm more simply too.
      export PATH=/opt/elasticbeanstalk/node-install/node-v$EB_NODE_VERSION-linux-x64/bin:$PATH

      # For parity with EB https://gist.github.com/wearhere/de51bb799f5099cec0ed28b9d0eb3663#file-ebnode-py-L147
      # and because some npm packages require HOME. This will also get npm to
      # read its configuration from the proper directory.
      export HOME=$(/opt/elasticbeanstalk/bin/get-config container -k app_user_home)

      EB_APP_STAGING_DIR=$(/opt/elasticbeanstalk/bin/get-config container -k app_staging_dir)
      EB_APP_DEPLOY_DIR=$(/opt/elasticbeanstalk/bin/get-config container -k app_deploy_dir)

      # specify architecture
      case $(arch) in
        'i686') export ARCH=x86;;
        'x86_64') export ARCH=x64;;
      esac

      # Export the user's environment variables for use with npm, both because
      # EB does it https://gist.github.com/wearhere/de51bb799f5099cec0ed28b9d0eb3663#file-ebnode-py-L150
      # as well as because we might need NPM_TOKEN.
      #
      # I wish this was a heredoc but I can't get the syntax right in YAML,
      # EB gives an error "warning: here-document delimited by end-of-file (wanted `EOS`)"
      /opt/elasticbeanstalk/bin/get-config --output YAML environment|perl -ne "/^\w/ or next; s/: /=/; print qq|\$_|" > /var/tmp/envvars
      source /var/tmp/envvars

  "/opt/elasticbeanstalk/hooks/appdeploy/pre/40install_node.sh":
    mode: "000755"
    owner: root
    group: users
    content: |
      #!/usr/bin/env bash

      /opt/elasticbeanstalk/containerfiles/ebnode.py --action node-install

      . /opt/elasticbeanstalk/env.vars

      #make sure node binaries can be found globally
      ln -sf /opt/elasticbeanstalk/node-install/node-v$EB_NODE_VERSION-linux-$ARCH/bin/node /usr/bin/node
      ln -sf /opt/elasticbeanstalk/node-install/node-v$EB_NODE_VERSION-linux-$ARCH/bin/npm /usr/bin/npm
      ln -sf /opt/elasticbeanstalk/node-install/node-v$EB_NODE_VERSION-linux-$ARCH/bin/node-gyp /usr/bin/node-gyp

      echo "checking npm..."
      if [ ! -f "/opt/elasticbeanstalk/node-install/npm_updated" ]; then
      cd /opt/elasticbeanstalk/node-install/node-v$EB_NODE_VERSION-linux-$ARCH/bin/ && /opt/elasticbeanstalk/node-install/node-v$EB_NODE_VERSION-linux-$ARCH/bin/npm update npm -g
      touch /opt/elasticbeanstalk/node-install/npm_updated
      echo "YAY! Updated global NPM version to `npm -v`"
      else
        echo "Skipping NPM -g version update. already installed"
      fi

  "/opt/elasticbeanstalk/hooks/appdeploy/pre/50npm.sh":
    mode: "000755"
    owner: root
    group: users
    content: |
      #!/usr/bin/env bash
      #
      # Only install modules, don't rebuild like Elastic Beanstalk does by default:
      # https://gist.github.com/wearhere/de51bb799f5099cec0ed28b9d0eb3663.
      # New modules will be built when they are installed, and cached modules don't
      # need to be rebuilt. When the Node version changes, the configdeploy script
      # will rebuild.
      #
      # Note that this *overwrites* Elastic Beanstalk's default 50npm.sh script.

      . /opt/elasticbeanstalk/env.vars

      cd $EB_APP_STAGING_DIR

      sudo -u ec2-user -H npm install --production
      if [ -d /tmp/.npm ]; then
        chown -R nodejs:nodejs /tmp/.npm
      fi

  "/opt/elasticbeanstalk/hooks/appdeploy/pre/55npm_cleanup.sh":
    mode: "000755"
    owner: root
    group: users
    content: |
      #!/usr/bin/env bash
      #
      # Remove all npm tmp files leftover by npm shrinkwrap flow.
      # https://github.com/npm/npm/issues/6855

      rm -rf /tmp/npm-*

  "/opt/elasticbeanstalk/hooks/configdeploy/pre/50npm.sh":
    mode: "000755"
    owner: root
    group: users
    content: |
      #!/usr/bin/env bash
      #
      # Only rebuild modules, don't install like Elastic Beanstalk tries to do
      # by default: https://gist.github.com/wearhere/de51bb799f5099cec0ed28b9d0eb3663.
      # package.json isn't changing on a config deploy, and all the existing
      # modules should be cached.
      #
      # Note that this *overwrites* Elastic Beanstalk's default 50npm.sh script.
      # But their default script actually doesn't work at all, since the app
      # staging dir, where they try to run `npm install`, doesn't exist during
      # config deploys, so ebnode.py just aborts:
      # https://gist.github.com/wearhere/de51bb799f5099cec0ed28b9d0eb3663#file-ebnode-py-L140

      . /opt/elasticbeanstalk/env.vars

      cd $EB_APP_DEPLOY_DIR

      sudo -u nodejs -H npm rebuild --production
      if [ -d /tmp/.npm ]; then
        chown -R nodejs:nodejs /tmp/.npm
      fi