gistfile1.txt

pandoc -F pandoc-citeproc -t markdown-citations << EOT

Foo [@doe1].
Bar [@doe2].
Foo [@doe1].
Remove this line to see the problem [@doe2].

# References

---
csl: modern-humanities-research-association.csl
# csl: chicago-fullnote-bibliography.csl
references:
- id: doe1
  type: book
  author:
  - family: Doe
    given: John
  title: First book
  publisher: Publisher
  publisher-place: Place
  issued:
    date-parts:
    - - 2006
- id: doe2
  type: book
  author:
  - family: Doe
    given: John
  title: Second book
  publisher: Publisher
  publisher-place: Place
  issued:
    date-parts:
    - - 2006
...
EOT