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phases/3-formula-pipeline/step3.md

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+# Step 3: formula-reference-links
+
+## Read First
+- /AGENTS.md
+- /PLAN.md
+- /PROGRESS.md
+- /docs/HARNESS.md
+- /docs/IMPLEMENTATION_PLAN.md
+- /docs/CONVERSION_POLICY.md
+- /phases/3-formula-pipeline/step2.md
+
+## Task
+Preserve formula numbering and body references as internal Markdown link targets when confidence is sufficient.
+
+Support common English and Korean reference patterns such as `Eq. (3)` and `식 (5)`.
+
+## Sprint Contract
+- Done means: formula anchors and reference rewrites are modeled and tested independently from final Markdown rendering.
+- Hard thresholds: low-confidence matches remain plain text; duplicate formula numbers do not create unstable anchors; references never point to missing anchors.
+- Files owned: `src/pdftomd/formulas.py`, reference model/tests, `PROGRESS.md`, phase index.
+- Dependencies: Steps 0 through 2.
+
+## Acceptance Criteria
+```powershell
+python scripts\validate_workspace.py
+.\venv\python.exe -m pytest tests
+```
+
+## Verification
+1. Run the acceptance commands.
+2. Confirm duplicate and missing reference cases are tested.
+3. Update `PROGRESS.md` and this phase index.
+
+## Do Not
+- Do not rewrite ambiguous references.
+- Do not render final Markdown chunks.
+- Do not remove the original formula number text.