update AGENTS.md in terms of glossary links and cross references

Author: drbenvincent

AGENTS.md

@@ -22,7 +22,10 @@
 - **Structure**: Notebooks (how-to examples) go in `docs/source/notebooks/`, knowledgebase (educational content) goes in `docs/source/knowledgebase/`
 - **Notebook naming**: Use pattern `{method}_{model}.ipynb` (e.g., `did_pymc.ipynb`, `rd_skl.ipynb`), organized by causal method
 - **MyST directives**: Use `:::{note}` and other MyST features for callouts and formatting
-- **Glossary linking**: Use Sphinx `:term:` directives to link to glossary terms (defined in `glossary.rst`), typically on first mention in a file
+- **Glossary linking**: Link to glossary terms (defined in `glossary.rst`) on first mention in a file:
+  - In Markdown files (`.md`, `.ipynb`): Use MyST syntax `{term}glossary term``
+  - In RST files (`.rst`): Use Sphinx syntax `:term:`glossary term``
+- **Cross-references**: For other cross-references in Markdown files, use MyST role syntax with curly braces (e.g., `{doc}path/to/doc`, `{ref}label-name`)
 - **Citations**: Use `references.bib` for citations, cite sources in example notebooks where possible. Include reference section at bottom of notebooks using `:::{bibliography}` directive with `:filter: docname in docnames`
 - **API documentation**: Auto-generated from docstrings via Sphinx autodoc, no manual API docs needed
 - **Build**: Use `make html` to build documentation