Thanks everyone, the env vars worked perfectly well.

I got it to almost work doing reinterpretation of the AST.
There is just one tiny thing that doesn't seem to work, and that is adding 
a citation to a Listing.

I am going to copy-paste the filter and the example. Hopefully, someone who 
knows more Pandoc
internals can help me understand what is going on, and possibly, how to fix 
it.

Thanks


```Haskell filter
module Main where

import Text.Pandoc.JSON
import System.IO.Error (catchIOError)
import System.Environment (getEnv)
import Text.Pandoc
import Data.Text (Text, pack)
import qualified Data.Map as M

writeMd :: Pandoc -> PandocIO Text
writeMd p = writeMarkdown def p

readMd :: Text -> PandocIO Pandoc
readMd t = readMarkdown def t

removeFenceNotes :: Block -> Block
removeFenceNotes cb@(CodeBlock (_, _, namevals) _) =
  case lookup "note" namevals of
       Just _     -> Div ("", [], []) []
       Nothing    -> cb
removeFenceNotes x = x

reinterpretation :: Block -> IO [Block]
reinterpretation cb@(CodeBlock (_, _, namevals) text) =
  case lookup "note" namevals of
    Just _ -> do
      p <- runIOorExplode $ readMd (pack text)
      textMd <- runIOorExplode $ writeMd p
      p' <- runIOorExplode $ readMd textMd
      case p' of
        Pandoc _ b -> return b
    Nothing -> return [cb]
reinterpretation x = return [x]

main = do
  v <- catchIOError (getEnv "FILTERING_MODE") (\_ -> return "")
  case v of
    "WITH_COMMENTS" -> toJSONFilter reinterpretation
    "NO_COMMENTS"  -> toJSONFilter removeFenceNotes -- disable comments
    _ -> return ()
```

I call Pandoc with the following command:

```
FILTERING_MODE=WITH_COMMENTS pandoc -s -f markdown -F filters -F 
pandoc-crossref meta.yaml -o test.pdf TEST.md
```

and the TEST.md file looks as follows:

```
# Capabilities status

```{#lst:maybeLinearSupport .encore
    caption="Support for `Maybe`'s do not fully work with `linear` types."}

subord class Two
  var x: int
  def init(): unit
    this.x = 5
  end
end

linear class One: Id
  var sub: Two
  def init(): unit
    this.sub = new Two()
  end
  def x(): int
    this.sub.x
  end
  def setX(x: int): unit
    this.sub.x = x
  end
end

-- this function does not compile. I cannot get it to
-- compile in any possible way

fun moo(var m: Maybe[One]): One
  match consume m with
    case Nothing => consume new One()
    case Just(z) => consume(z)
  end
end

```


In @lst:maybeLinearSupport, if `One` is `read`, then the function `moo` who 
receives
a `Maybe[One]` works. The distinction between a `read Maybe[One]` and a 
`linear Maybe[One]`
prevents us from reusing this function, i.e., the annotations of `var` and 
`val`
are different and the function cannot be polymorphic on its *mode*.

~~~{note=""}
linearity seems to be more related to a property of the object rather than
a mode by itself. this means, @lst:maybeLinearSupport can declare a 
function that
we know does not use any linear and we could declare another function that 
may
be `read`, `local` or any other mode that has to be treated *linearly*.
what are the implications of this?
~~~

```

The end result contains the notes without the code block scope and also 
contain the
all markdown items well-formatted, i.e., bold, italics, etc. The only thing 
that didn't work
was reading the reference `@lst:maybeLinearSupport`, which is printed as it 
looks, instead
of referencing the figure.

Thanks.



On Tuesday, October 2, 2018 at 11:39:41 PM UTC+2, Kolen Cheung wrote:
>
> c.f. the thread in 
> https://groups.google.com/d/msg/pandoc-discuss/LIAfgkZKUiE/_KfI3VI6EgAJ about 
> filter arg. In short env. var. is the way to go right now. 
>

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