read.js

function isChatMessage(message) {
    if (message.__x_isSentByMe) {
        return false;
    }
    if (message.__x_isNotification) {
        return false;
    }
    if (!message.__x_isUserCreatedType) {
        return false;
    }
        return true;
}
function getUnreadChats() {
    var Chats = Store.Chat.models;
    var Output = [];

    for (chat in Chats) {
        if (isNaN(chat)) {
            continue;
        };
        var temp = {};
        temp.contact = Chats[chat].__x_formattedTitle;
        temp.id = Chats[chat].__x_id;
        temp.messages = [];
        var messages = Chats[chat].msgs.models;
        for (var i = messages.length - 1; i >= 0; i--) {
            if (!messages[i].__x_isNewMsg) {
                break;
            } else {
                if (!isChatMessage(messages[i])) {
                    continue
                }
                messages[i].__x_isNewMsg = false;
                temp.messages.push({
                    message: messages[i].__x_body,
                    timestamp: messages[i].__x_t,
                    type : messages[i].__x_type,
                    e : messages[i]
                });
            }
        }
        if(temp.messages.length > 0) {
            Output.push(temp);
        }
    }
    console.log("Unread messages: ", Output);
    return Output;
}

send.js

function sendMsg (id, text) {
    var Chats = Store.Chat.models;
    var contact = id;
    var message = text;
    for (chat in Chats) {
        if (isNaN(chat)) {
            continue;
        };
        var temp = {};
        temp.contact = Chats[chat].__x__formattedTitle;
        temp.id = Chats[chat].__x_id;
        if(temp.id.search(contact)!=-1 && temp.id.search('g.us')==-1 ){
            Chats[chat].sendMessage(message);
            return true
        }
    }    
}

Awesome. Good job.
But how do you integrate this code with an external service?
I wrote a python server that handles input messages and answers like a bot, later I wrote an ajax call in this code to make the remote call.
However, I keep having tons of problems regarding security.
I have already tried all possible workaround I can think of with no success yet.

How do you integrate this with external sources?

If anyone is having trouble trying to remove a message for everyone in a chat, I made a script for that:
Use: deleteMessage("5************-15********@g.us", "I will be deleted")

// The chat_id is in chat.__x_id._serialized; 
window.deleteMessage = function(chat_id, msg_str) {
    if (window.Store === undefined) {
        try {  // Often this cause the error "Cannot read property 'call' of undefined" but works anyway
            webpackJsonp([], {"bcihgfbdeb": (x, y, z) => window.Store = z('"bcihgfbdeb"')}, "bcihgfbdeb");
            webpackJsonp([], {"iaeeehaci": (x, y, z) => window.Store.Wap = z('"iaeeehaci"')}, "iaeeehaci");
        } catch (e) {}
    }
    Chats = Store.Chat.models
    for(chat in Chats) {
        if (isNaN(chat)) {
            continue;
        };
        temp_id = Chats[chat].__x_id._serialized;
        if(temp_id.search(chat_id) != -1){
            messages = Chats[chat].msgs.models
            for(message in messages) {
                temp_msg = messages[message]
                if(temp_msg.__x_text == msg_str && temp_msg.canRevoke()) {
                    temp_msg.sendRevoke(temp_msg)
                    return true;
                }
            }
        }
    }
}

Temp.id.search is not a function

Here is a quick fix for Store is not defined
Just run
if (window.Store === undefined) {
webpackJsonp([], {"bcihgfbdeb": (x, y, z) => window.Store = z('"bcihgfbdeb"')}, "bcihgfbdeb");
webpackJsonp([], {"iaeeehaci": (x, y, z) => window.Store.Wap = z('"iaeeehaci"')}, "iaeeehaci");
}
Credit @schgressive

A little update:

if (window.Store === undefined) {
    webpackJsonp([], { "bcihgfbdeb": (x, y, z) => window.Store = z('"bcihgfbdeb"') }, "bcihgfbdeb");
    webpackJsonp([], { "cbagcefdge": (x, y, z) => window.Store.Wap = z('"cbagcefdge"') }, "cbagcefdge");
  }

A better fix to find the Store Object:
https://github.com/Zibri/WhatsAppWebApi/blob/master/zstore.js

but the script errors out saying:
Uncaught TypeError: temp.id.search is not a function

Uncaught TypeError: temp.id.search is not a function
Change to temp.id = Chats[chat].__x_id.user;

And how to get received message event?

The sendMessage function in the Store.Chat.models[i].sendMessage has disappeared, has someone successfully fixed that?
The error
M433:1 Uncaught TypeError: Store.Chat.models[0].sendMessage is not a function

Store.Chat.models
Uncaught TypeError: Cannot read property 'models' of undefined