I have searched stackoverflow on this problem and did find a few topics, but I feel like there isn\'t really a solid answer for me on this.
I have a form that users
1. I can find and replace all [?] and swap them out with [?] or an actual space.
This is a robust method, but it requires you to have a table of all the HTML entities (I assume the pasted input is coming from HTML) and to parse the pasted text for entity references.
2. I can place the code in question within a CDATA section.
In other words disable parsing for the whole section? Then you would have to parse it some other way. Could work.
3. I can include these entities within the XML file.
You mean include the entity definitions? I think this is an easy and robust way, if you don't mind making the XML file quite a bit bigger. You could have an "included" file (find one on the web) which is an external entity, which you reference from the top of your main XML file.
One downside is that the XML parser you use has to be one that processes external entities (which not all parsers are required to do). And it must correctly resolve the (possibly relative) URL of the external entity to something accessible. This is not too bad but it may increase constraints on your processing tools.
4. You could forbid non-XML in the pasted content. Among other things, this would disallow entity references that are not predefined in XML (the 5 that Tomalak mentioned) or defined in the content itself. However this may violate the requirements of the application, if users need to be able to paste HTML in there.
5. You could parse the pasted content as HTML into a DOM tree by setting someDiv.innerHTML = thePastedContent;
In other words, create a div somewhere (probably display=none, except for debugging). Say you then have a javascript variable myDiv that holds this div element, and another variable myField that holds the element that is your input text field. Then in javascript you do
myDiv.innerHTML = myField.value;
which takes the unparsed text from myField, parses it into an HTML DOM tree, and sticks it into myDiv as HTML content.
Then you would use some browser-based method for serializing (= "de-parsing") the DOM tree back into XML. See for example this question. Then you send the result to the server as XML.
Whether you want to do this fix in the browser or on the server (as @Hannes suggested) will depend on the size of the data, how quick the response has to be, how beefy your server is, and whether you care about hackers sending not-well-formed XML on purpose.