Your issue might be different,  depending on what you have installed, but I'll 
write down what solution worked for me(I used socket.io and serialport):
- clean install of Debian 8.3(should be the same for newer dists)
- npm install socket.io
- npm install serialport
- apt-get update
- apt-get dist-upgrade
- cd /var/lib/cloud9 npm update

- create config_custom.sh
- nano /usr/bin/config_custom.sh
#!/bin/bash
config-pin P9.24 uart 
config-pin P9.26 hart

- set execution rights
- chmod u+x /usr/bin/config_custom.sh
- create service 
- nano /lib/systemd/system/config_custom.sh

[Unit]
Description=Config uart1 ex tx pins
After=generic-board-startup.service

[Service]
Type=simple
ExecStart=/usr/bin/config_custom.sh

[Install]
WantedBy=multi-user.target

- enable service
systemctl daemon-reload
systemctl enable config_custom.service

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