To get code blocks with syntax highlighting embedded happily in a list, embed the markup lines that come before and after the code block to the appropriate level of indenting for an additional paragraph, then proceed as normal. For example:

1. lorem ipsum

  ```ruby
resources :dolor
  ```

   1. sit amet

      ```ruby
resources :elit
      ```

   1. sed do

1. eiusmod

indents each code block to the appropriate depth and maintains the integrity of the indexes.

It's relevant and useful to include the name of the file that a code block should go in

Not always. Many questions give a short block of text as an example of where they're having the problem, and answers respond with an amended version of the code block. It doesn't matter what the name of the file is (it really could be anything with an appropriate extension). The code might not even be for a file! Most regexes, for example, can be used in almost any language, but where I find myself using them most often is in the search box of my IDE. Furthermore, not everything that finds itself in a code block is even code (e.g. error messages).

Needless to say, you don't need to provide a file name (or even a context) for every block of code. So we're back to the start: People will still assume they don't need to include the file name when it would be helpful to do so. Or maybe people will include a file name in contexts where they don't need to, making the post noisier.

Lastly, I prefer regular markdown formatting (if not plain text) over your suggestion, both aesthetically and formatting-wise — your suggested format is much too tricky for the vast majority of people to use.