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How to use Markdown with links in JSF?

I am developing an JSF web application and would like to introduce a lot of documentation to be visible directly in the web application. Technically I would like to use Markdown language and made already first experimence with.
I am currently playing around with flexmark Java library to render e. g. HTML strings from a markdown document. Also this seems to work fine. But what to do with links to other md files?
If I do have my markdown part: See also [here](Background.md)
Then this will be rendered correct to HTML with a link like: See also here.
But how should I tell my web server to react on this link and update the document part of the page with the rendered md file?
I would need to manually find such links in the generated HTML and change them to a kind of JavaScript call, telling my server to render the panel using the other md file.
Or should I create an IFrame so that within this frame, I could follow the link to e. g. a web servlet, rendering the md files to new HTML?
But this all feels a bit clumbsy to me. Am I missing a more easy solution?

Ok, no other answers, so I answer on my own.
The comment about primefaces extension with localized is interesting, but too far away from my focus and some features did not really match to my requirements.
Therefore I stayed with a pure markdown library and made the rest on my own.
With the links it was much more easy than expected! Within JavaScript you can very easily detect all links of the page (document.links), iterate over them and just set an onclick function (see here).

Safe API to transform HTML (Java)

I'd like to take a web page and add some tags to its head. Specifically, a CSS link and a JavaScript link. I need to do this programatically for a wide variety of web pages. Now, I could hack this out with a regex or two, but I'd like to use something more robust.
What's a good way to inject or transform HTML? I'm using Scala, but anything Java or JVM will work.

You can use jsoup.
An example for modifying content in html is here

Java UI markup alternative to HTML?

I'm trying to use Java to develop a piece of software, but I've run into the issue of UI elements parsing HTML beyond the way I want them to.
The Java JEditorPane seems to be only able to be marked up by HTML or something that is essentially HTML underneath. I want the user to be able to type and see HTML tags, not have them formatted into markup, but still have something like the tags colored red and standard text not.
Is there a method of marking up Java's UIs without HTML? (I don't mind using an extra library, but if it can be avoided that'd be great.)

I haven't used it, but RSyntaxTextArea seems to achieve what you want. The intro says
RSyntaxTextArea is a syntax highlighting text component for Java
Swing.
and
Syntax highlighting for over 30 programming languages
Example usage and source code at github.

Reading HTML+JavaScript using Java

I can read the HTML contents via http (for example, http://www.foo.com) using Java (with URL and BufferedReader classes). However, a couple of them contain JavaScript. My current app cannot process JavaScript.
What's the best way to read HTML content with JavaScript using Java?
I am open using other languages if it is easier.
Thanks in advance for your help.
UPDATE - Clarification:
A couple HTML contents are generated dynamically using JavaScript. I can see the result (in pure HTML after the JavaScript processing) when viewing them on a browser.
On the other hand, when my Java app retrieves the HTML contents, it says that there is no JavaScript on my app.
Ideally, I want to be able to get the same result as on the browser using my Java app.
Thanks for everyone's response.

HtmlUnit has good JavaScript support and it should (almost) parse the HTML as a web browser.
http://htmlunit.sourceforge.net/
http://htmlunit.sourceforge.net/javascript.html

Cobra (http://lobobrowser.org/cobra/getting-started.jsp) will fit your needs

For just HTML parsing you can use HTMLParser (org.htmlparser). However from the way you described your problem, it seems you need a browser, because executing is totally different than just parsing. Cheers.

With no doubt you need to use Java html parser:
Java Open Source HTML Parsers
Which Html Parser is best?
HTML/XML Parser for Java
HTML PARSER in java [closed]

server-side css selectors

I am creating a tool that will check dynamically generated XHTML and validate it against expected contents.
I need to confirm the structure is correct and that specific attributes exist/match. There may be other attributes which I'm not interested in, so a direct string comparison is not suitable.
One way of validating this is with XPath, and I have implemented this already, but I would also like something less verbose - I want to be able to use CSS Selectors, like I can with jQuery, but on the server - within CFML code - as opposed to on the client.
Is there a CFML or Java library that allows me to use CSS Selectors against an XHTML string?

I've just released an open source project which is a W3C CSS Selectors Level 3 implementation in Java. Please give it a try. I was looking for the same thing and decided to implement my own engine. It's inspired by the code in WebKit etc.
http://github.com/chrsan/css-selectors/tree

I don't know of a Java library itself, but there is a Ruby library called Hpricot that does exactly what you're looking for. In conjunction with the Ruby implementation on the Java platform, JRuby, it should be relatively straightforward to call Ruby methods from your Java code (using BSF, JSR-222 Scripting APIs, or an internal API).
Are you using Coldfusion 8? Coldfusion 8, being based on Java 6, supports JSR-222 Scripting APIs "javax.scripting".
Take a look at this blog entry on embedding PHP within CFML. You should be able to do the same with Ruby. There is ZIP file example code linked from this blog posting, and if you crack open the CFML, you'll see a good example of embedding Ruby within CFML.
Although it might take a bit of work to make all the pieces work together, but with a bit of investment, it should give you the robust parsing/CSS selector querying that you're looking for.

Hpricot is definetly a fantastic solution if the JRuby-route is open to you.
Wrt. XPath being the "correct" way to access XML documents... sorry but this is rubbish. There are numerous ways to access elements of an XML document: DOM traversal, XPath, XQuery, CSS selectors to name a few. XPath is certainly popular but CSS selectors are very very powerful, assuming your XML document has HTML semantics.

If you can use PHP within your CFML (as mentioned above), you could take advantage of this excellent "jQuery for PHP" library, phpQuery
Full CSS selector support, manipulation functions, traversing, etc. It should work great for what you need.
Hope it helps.

There is a theoretical difference between the server and client. To a web browser, the document is a living DOM hierarchy. To your server code it's merely an XML document of whatever type. XPath is the "correct" way to access elements of an XML document.
So unless you have a serious performance problem with your current XPath solution, or it doesn't actually work correctly, I suggest you stick with it. Trying something too clever brings the risk of breaking something that's working.
If you find the XPath to be too verbose and ugly to leave sitting around, or want more power to re-use the tool in different cases, or just can't resist trying to do something clever, then you could try writing a utility that compiles a given CSS selector into an XPath. You could then call this in one line whenever you needed.

it may be easier to use cQuery.com - cQuery.com is an API based 'Content Query Engine' to extract content from live websites by using CSS.
You can using it programatically in you application.