I don't remember writing any doc about custom plugins. One of the reason is that every time I started thinking about an example of a custom plugin, the use case was better handled using an existing plugin. I wrote a page about custom parsers if that's any help. A plugin is a parser + a configurator.
I don't know how @replies#123 is supposed to work, can you break it down for me please? I assume that 123 is the ID of the post, but what's the replies part?
About @mentions, the simplest way would be to use the Preg plugin to match them. Then you have to retrieve the user ID. The simplest way is to use a tag filter to add the user ID to each tag during parsing. That means it'll perform one query per username mentioned. If you're concerned about a malicious user mentioning thousands of usernames, you can set a limit to the number of mentions in a post. Here's a working example that matches /@(?\w+)/ and creates a tag named MENTION for each mention.
If you really want to run only one query to retrieve all user IDs, you could preload user IDs before parsing, or implement your own parser that would preload all IDs before creating any tags. The downside is that it would query IDs for things that look like mentions but are not. For example, things in inline code such as @mention.
Alternatively, you could not add any ID during parsing and inject them after parsing in the XML. You wouldn't query IDs for inline code and such. On the other hand, it's more complicated.
