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flexmark-java extension for formatter
There is a newer version: 0.50.50
package com.vladsch.flexmark.formatter;

import com.vladsch.flexmark.html.HtmlRenderer;
import com.vladsch.flexmark.util.ast.*;
import com.vladsch.flexmark.util.format.options.ElementPlacement;
import com.vladsch.flexmark.util.format.options.ElementPlacementSort;
import com.vladsch.flexmark.util.options.DataHolder;
import com.vladsch.flexmark.util.options.DataKey;

import java.util.*;

import static com.vladsch.flexmark.formatter.RenderPurpose.TRANSLATION_SPANS;

public abstract class NodeRepositoryFormatter, B extends Node & ReferenceNode, N extends Node & ReferencingNode> implements PhasedNodeFormatter {
    public static final HashSet FORMATTING_PHASES = new HashSet(Arrays.asList(
            FormattingPhase.COLLECT,
            FormattingPhase.DOCUMENT_TOP,
            FormattingPhase.DOCUMENT_BOTTOM
    ));

    public Comparator getReferenceComparator() {
        return myComparator;
    }

    public abstract R getRepository(DataHolder options);
    public abstract ElementPlacement getReferencePlacement();
    public abstract ElementPlacementSort getReferenceSort();
    public abstract void renderReferenceBlock(B node, NodeFormatterContext context, MarkdownWriter markdown);

    protected final R referenceRepository;
    protected final List referenceList;
    protected final HashSet unusedReferences;
    protected final B lastReference;
    protected boolean recheckUndefinedReferences;
    protected boolean repositoryNodesDone;
    protected final Comparator myComparator;

    private NodeFormatterContext myContext;
    private Map referenceTranslationMap;
    private final DataKey> myReferenceMapKey;

    protected ElementPlacement getTranslationReferencePlacement() {
        if (myContext.isTransformingText()) {
            return ElementPlacement.AS_IS;
        } else {
            return getReferencePlacement();
        }
    }

    public String modifyTransformedReference(String transformedReferenceId, final NodeFormatterContext context) {
        return transformedReferenceId;
    }

    protected String transformReferenceId(final String nodeText, final NodeFormatterContext context) {
        if (context.isTransformingText()) {
            String transformed;

            switch (context.getRenderPurpose()) {
                case TRANSLATION_SPANS:
                case TRANSLATED_SPANS:
                    if (referenceTranslationMap != null) {
                        if (referenceTranslationMap.containsKey(nodeText)) {
                            transformed = referenceTranslationMap.get(nodeText);
                        } else {
                            transformed = context.transformNonTranslating(null, nodeText, null, null).toString();
                            referenceTranslationMap.put(nodeText, transformed);
                        }
                    } else {
                        transformed = context.transformNonTranslating(null, nodeText, null, null).toString();
                    }
                    return modifyTransformedReference(transformed, context);

                case TRANSLATED:
                    String untransformed = modifyTransformedReference(nodeText, context);
                    String s = context.transformNonTranslating(null, untransformed, null, null).toString();
                    return s;

                case FORMAT:
                default:
                    break;
            }
        }
        return nodeText;
    }

    public NodeRepositoryFormatter(DataHolder options, DataKey> referenceMapKey) {
        myReferenceMapKey = referenceMapKey;
        referenceRepository = getRepository(options);
        referenceList = referenceRepository.values();
        lastReference = referenceList.isEmpty() ? null : referenceList.get(referenceList.size() - 1);
        unusedReferences = new HashSet();
        this.recheckUndefinedReferences = HtmlRenderer.RECHECK_UNDEFINED_REFERENCES.getFrom(options);
        repositoryNodesDone = false;

        myComparator = new Comparator() {
            @Override
            public int compare(final B o1, final B o2) {
                return o1.compareTo(o2);
            }
        };
    }

    @Override
    public Set getFormattingPhases() {
        return FORMATTING_PHASES;
    }

    @Override
    public void renderDocument(final NodeFormatterContext context, final MarkdownWriter markdown, final Document document, final FormattingPhase phase) {
        // here non-rendered elements can be collected so that they are rendered in another part of the document
        myContext = context;

        if (context.isTransformingText() && myReferenceMapKey != null) {
            if (context.getRenderPurpose() == TRANSLATION_SPANS) {
                context.getTranslationStore().set(myReferenceMapKey, new HashMap());
            }
            referenceTranslationMap = context.getTranslationStore().get(myReferenceMapKey);
        }

        switch (phase) {
            case COLLECT:
                if (getTranslationReferencePlacement() != ElementPlacement.AS_IS && getReferenceSort() == ElementPlacementSort.SORT_UNUSED_LAST) {
                    // get all ref nodes and figure out which ones are unused
                    unusedReferences.addAll(referenceList);
                    final Iterable nodes = context.nodesOfType(getNodeClasses());
                    for (Node node: nodes) {
                        N referencingNode = lastReference == null ? null : lastReference.getReferencingNode(node);
                        if (referencingNode != null) {
                            B referenceBlock = referencingNode.getReferenceNode(referenceRepository);
                            if (referenceBlock != null) {
                                unusedReferences.remove(referenceBlock);
                            }
                        }
                    }
                }
                break;

            case DOCUMENT_TOP:
                if (getTranslationReferencePlacement() == ElementPlacement.DOCUMENT_TOP) {
                    // put all footnotes here
                    formatReferences(context, markdown);
                }
                break;

            case DOCUMENT_BOTTOM:
                if (getTranslationReferencePlacement() == ElementPlacement.DOCUMENT_BOTTOM) {
                    // put all footnotes here
                    formatReferences(context, markdown);
                }
                break;

            default:
                break;
        }
    }

    private void formatReferences(final NodeFormatterContext context, MarkdownWriter markdown) {
        ArrayList references = new ArrayList(referenceList);

        switch (getReferenceSort()) {
            case AS_IS:
                break;

            case SORT:
                Collections.sort(references, getReferenceComparator());
                break;

            case SORT_UNUSED_LAST:
                ArrayList used = new ArrayList();
                ArrayList unused = new ArrayList();
                for (B footnote: references) {
                    if (unusedReferences.contains(footnote)) {
                        unused.add(footnote);
                    } else {
                        used.add(footnote);
                    }
                }
                Collections.sort(used, getReferenceComparator());
                Collections.sort(unused, getReferenceComparator());
                references.clear();
                references.addAll(used);
                references.addAll(unused);
                break;
        }

        markdown.blankLine();
        for (B reference: references) {
            renderReferenceBlock(reference, context, markdown);
        }
        markdown.blankLine();
        repositoryNodesDone = true;
    }

    protected void renderReference(B node, NodeFormatterContext context, MarkdownWriter markdown) {
        if (!repositoryNodesDone) {
            switch (getTranslationReferencePlacement()) {
                case AS_IS:
                    renderReferenceBlock(node, context, markdown);
                    if (node.getNext() == null || node.getNext().getClass() != node.getClass()) {
                        markdown.blankLine();
                    }
                    break;

                case GROUP_WITH_FIRST:
                    // must be the first since we are here
                    formatReferences(context, markdown);
                    break;

                case GROUP_WITH_LAST:
                    if (node == lastReference) {
                        formatReferences(context, markdown);
                    }
                    break;
            }
        }
    }
}