Develop Reference

How do you run a server-side script without it being sent to the browser at all?

I understand that the title is a little confusing, but essentially I want to make my website run a php file on the server side that uses arguments from the html e.g
document.getElementById("example").value;
So I'd like to run it on the server but not have it linked to the html file. Is this possible?

I suggest you create PHP scripts on server side and reach them with XMLHttpRequest (tutorial here) or AJAX with Jquery for example.
PHP scripts you need, don't have to generate any HTML code : they just would process data.
In your JS, you get your values from the page, then you send your data to the server.

Javascript: Save uploaded file

I would like to save uploaded file using javascript, in my linux server. The code I wrote is:
if (uploadInput.files.length == 0) {
console.log("No file is uploaded. ");
} else {
console.log("File uploaded.");
var file = uploadInput.files[0];
}
Now I would like to save that file as "files/upload.csv". Can anyone please advise, how can I do it?
Thanks in advance

What I'm going to do is walk you through the logic, instead of providing code. There is just not enough information here on what you want to do to provide actual code and the sample you provided is a very small part of what the actual solution would need to include.
I'm assuming the code you wrote above is meant to run on a website visitor's browser (client-side). Client-side code can't save to a server. What it can do, is send the file contents to the server. But then you'd need something on the server side to process that file contents and actually save it to the server-side files directory.
One method to send the file contents from the client to the server is to use AJAX - you can do this with native javascript, but I would recommend looking into a library such as Jquery, which makes it a lot easier. See http://api.jquery.com/jquery.ajax/ This AJAX code will need a communication point on the server to send the file contents to. From your profile it seems you're familiar with PHP. You could make a php file on the server (say receivefilecontents.php) that takes in input from that client-side AJAX call, and then saves it to a server directory - you could also do this in Python, Java or a number of other languages.

How to send a javascript file (with several functions in it) from the server to the client side?

I need to have the functionality in the server side in order to hide the implementetion to the final user.
I didn't find a topic with this kind of solution.
I have a .js file with functions I use within the html5 file.
The js files are "called" in the html by using the script tag, but through the url the user can track them and see the .js file content. I don't want this to happen.
$getScript() does the job, but again the url can be cathched, thus the file content too. Much the same with $ajax function.
Everything work ok, but I want to hide the js content.
The .js file is something like this:
var x, x,....
function A(){...}
function B(){...}
and so on, I use A(), B() functions in the html.
Which is the best approach to get the content file from the server without doing the url visible?
Server: nodejs. (I send some json files through socket.io correctly, but I don't know how to achieve this other issue.
Thanks in advance, best!

If you are sending sensitive information to the client then you are doing it wrong. No matter if the client has the URL to the script, they will still be able to find it if they are determined as long as it is sent to their computer.
Find a different way to accomplish what you are trying to do without sending sensitive information to the client. It is not safe.

Passing Value from C++ to Javascript

i have a c++ file which reads values from a sensor and I want to display those values on a website dynamically. So Im looking for a way to pass these values(integers) from my cpp file to an javascript which displays them on the site.
My first, simple try was to write the values into a js file as variables every second from my cpp script. The Js then uses this file as a source and displays its variables on the site:
cpp:
fprintf(file, "var mx=%d, my=%d, mz=%d, ax=%d, ay=%d, az=%d, gx=%d, gy=%d, gz=%d;\n",
imu.raw_m[0], imu.raw_m[1], imu.raw_m[2], // M = Magnetometer
imu.raw_a[0], imu.raw_a[1], imu.raw_a[2], // A = Accelerometer
imu.raw_g[0], imu.raw_g[1], imu.raw_g[2] // G = Gyroscope
);
html/js:
<script src="./imu.js" type="text/javascript"></script>
The Problem now is of course, that I need to refresh the page all the time, because the imu.js file is cached by the website.
I'd rather have a way to directly pass to integers from the cpp file to the js script. I read something about json or Googles V8 script. But I'd like to hear your suggestions first.
By the way, Im running this on a raspi, if this is important.
Thanks for your help
EDIT:
I'm goning to try it with a mysql database, in which my cpp file writes the data from the sensor with Connector/c++ from http://dev.mysql.com/doc/connector-cpp/en/ and my website reads them.

You could compile your C++ code into a Node.js plugin, you can then register a JavaScript function with your plugin which the C++ calls when it updates the value. That way you can pass values directly from C++ into Javascript in a managed and controlled way.
Node.js has the added benefit of being able to host your webpage and do all the Websocket and HTTP stuff that can be a pain in C++.

You do not have to refresh if your script is smart about how to access the data file! In case you do have a webserver at hand: Take care that your data file is accessible by your webserver and then let your script request the file via ajax (link to w3schools)

I'm doing something similar on a BeagleBone Black. With websocketd you can turn pretty much any program into a websocket endpoint and then send data via stdin and stdout commands. This would be a particularly good solution for you since websockets are designed to handle information that's constantly changing.

Using JS to include remote PHP file

I am wondering if it is possible to use JS (jQuery) to make a $.post from any website on any domain, to a script on my server?
The reason for this question, is because I do not want to give out my PHP files to the client (and I dont want to spend money on ionCube or the likes), so making the request to my server would not give out my source.
My prefered way would be to simply include a JS file, like
<script src="http://MySite.com/MyScript.js"></script>
and have a function in there that does the Post to my PHP script, however due to the same-origin policy, I cannot do a POST request to a remote server.
I could of course make a proxy.php and make the request to it, but I am trying to keep it in a way so the client only have to include a small snippet into their HTML code, in order to use my app.
Is there a (less painfull) way to do this?

Instead of using Javascript, why not give your client a PHP file that calls file_get_html() against your code on your server? It would have the same effect, without worrying about the client-side Javascript.
This would function similarly to a remote PHP include, but it is executed on your server and received as HTML.
You could also use cURL in PHP to call your remote PHP script, returning the output as HTML, and parsing out the bits you need.
file_get_html() is component of Simple HTML DOM