COMMUNICATION INTERRUPTED WITH WEB IDE or SERIAL TERMINAL

Looks strange - It looks a lot like you're using some beta version of Chrome? Are you using the Web IDE from the app store?

Looks like you're not initialising the LCD properly on onInit. Try:

var lcd;
var ON=1, OFF=0;
function LCD_bckgnd(status,pin) { digitalWrite(pin,status); }
function onInit() {
   var l=false;
   lcd = require("HD44780").connect(C5,C4,C0,C1,C2,C3); <------ this
   LCD_bckgnd(ON,E7);
   lcd.clear();
  lcd.setCursor(0,0);
   lcd.print(" Board OK …");
   lcd.setCursor(0,1);
  lcd.print("Led1 blinking.");
  setInterval( function() { l=!l; LED1.write(l);},500);
}

onInit();

or you could try executing it all 1 sec after bootup:

var lcd;
var ON=1, OFF=0;
function LCD_bckgnd(status,pin) { digitalWrite(pin,status); }
function onInit() {
 setTimeout(function() {
   var l=false;
   lcd = require("HD44780").connect(C5,C4,C0,C1,C2,C3); <------ this
   LCD_bckgnd(ON,E7);
   lcd.clear();
  lcd.setCursor(0,0);
   lcd.print(" Board OK …");
   lcd.setCursor(0,1);
  lcd.print("Led1 blinking.");
  setInterval( function() { l=!l; LED1.write(l);},500);
 }, 1000);
}

onInit();

The not running when you plug into USB has been covered here so many times I've lost count.

But you've just done WAY too much stuff (custom compile, discovery board, beta chrome, your own SD card connector) for me to have any chance of helping you out properly I'm afraid.