Upload a file using file_get_contents

First of all, the first rule of multipart Content-Type is to define a boundary that will be used as a delimiter between each part (because as the name says, it can have multiple parts). The boundary can be any string that is not contained in the content body. I will usually use a timestamp:

define('MULTIPART_BOUNDARY', '--------------------------'.microtime(true));

Once your boundary is defined, you must send it with the Content-Type header to tell the webserver what delimiter to expect:

$header="Content-Type: multipart/form-data; boundary=".MULTIPART_BOUNDARY;

Once that is done, you must build a proper content body that matches the HTTP specification and the header you sent. As you know, when POSTing a file from a form, you will usually have a form field name. We’ll define it:

// equivalent to <input type="file" name="uploaded_file"/>
define('FORM_FIELD', 'uploaded_file'); 

Then we build the content body:

$filename = "/path/to/uploaded/file.zip";
$file_contents = file_get_contents($filename);    

$content =  "--".MULTIPART_BOUNDARY."\r\n".
            "Content-Disposition: form-data; name=\"".FORM_FIELD."\"; filename=\"".basename($filename)."\"\r\n".
            "Content-Type: application/zip\r\n\r\n".
            $file_contents."\r\n";

// add some POST fields to the request too: $_POST['foo'] = 'bar'
$content .= "--".MULTIPART_BOUNDARY."\r\n".
            "Content-Disposition: form-data; name=\"foo\"\r\n\r\n".
            "bar\r\n";

// signal end of request (note the trailing "--")
$content .= "--".MULTIPART_BOUNDARY."--\r\n";

As you can see, we’re sending the Content-Disposition header with the form-data disposition, along with the name parameter (the form field name) and the filename parameter (the original filename). It is also important to send the Content-Type header with the proper MIME type, if you want to correctly populate the $_FILES[]['type'] thingy.

If you had multiple files to upload, you just repeat the process with the $content bit, with of course, a different FORM_FIELD for each file.

Now, build the context:

$context = stream_context_create(array(
    'http' => array(
          'method' => 'POST',
          'header' => $header,
          'content' => $content,
    )
));

And execute:

file_get_contents('http://url/to/upload/handler', false, $context);

NOTE: There is no need to encode your binary file before sending it. HTTP can handle binary just fine.