fix(markdown): handle CRLF line endings in section heading parser

split('\n') on CRLF content leaves a trailing \r on each line, and the
heading regex /^(#{1,6})\s+(.+)$/ (anchored with $) fails to match
'## Heading\r' because $ matches before end-of-string, not before \r.
Result: Windows-authored markdown silently produces zero Section nodes.

Use split(/\r\n|\r|\n/) to normalize all line-ending conventions.

Pure additive — LF-only files produce identical output. CR-only (Mac OS
Classic) becomes tolerated as a side benefit at zero risk.

Adds integration test markdown-processor-crlf.test.ts covering LF
baseline, CRLF (the regression), CR-only, mixed, and startLine/endLine
correctness.

gitnexus/src/core/ingestion/markdown-processor.ts

@@ -36,7 +36,12 @@ export const processMarkdown = (
     // Skip if file node doesn't exist (shouldn't happen, structure-processor creates it)
     if (!graph.getNode(fileNodeId)) continue;
 
-    const lines = file.content.split('\n');
+    // Normalize CRLF/CR to LF before splitting so that line-end agnostic
+    // markdown files (Windows-authored, mixed) yield correct headings.
+    // Without this, `## Heading\r\n` produces `## Heading\r` after split,
+    // and the HEADING_RE regex (anchored with `$`) fails to match because
+    // `$` matches before end-of-string, not before `\r`.
+    const lines = file.content.split(/\r\n|\r|\n/);
 
     // --- Extract headings and build hierarchy ---
     // First pass: collect all heading positions so we can compute endLine spans

gitnexus/test/integration/markdown-processor-crlf.test.ts

@@ -0,0 +1,88 @@
+/**
+ * Regression test for CRLF-encoded markdown heading extraction.
+ *
+ * Files with CRLF line endings (Windows-authored markdown) previously
+ * produced zero Section nodes because `split('\n')` left a trailing `\r`
+ * on each line, and the heading regex `/^(#{1,6})\s+(.+)$/` (anchored
+ * with `$`) failed to match `## Heading\r` (since `$` matches before
+ * end-of-string, not before `\r`).
+ *
+ * Fix: split on `/\r\n|\r|\n/` so all line-ending conventions are
+ * normalized at split time. See markdown-processor.ts line 39.
+ */
+
+import { describe, it, expect } from 'vitest';
+import { processMarkdown } from '../../src/core/ingestion/markdown-processor.js';
+import { createKnowledgeGraph } from '../../src/core/graph/graph.js';
+import { generateId } from '../../src/lib/utils.js';
+import type { GraphNode } from 'gitnexus-shared';
+
+function setupGraphWithFile(filePath: string) {
+  const graph = createKnowledgeGraph();
+  const fileNode: GraphNode = {
+    id: generateId('File', filePath),
+    label: 'File',
+    properties: { name: filePath, filePath },
+  };
+  graph.addNode(fileNode);
+  return graph;
+}
+
+describe('markdown-processor CRLF tolerance', () => {
+  it('extracts headings from LF-encoded markdown (baseline)', () => {
+    const filePath = 'lf.md';
+    const graph = setupGraphWithFile(filePath);
+    const content = '# Title\nbody line 1\n## Sub\nbody line 2\n### SubSub\nmore\n';
+
+    const stats = processMarkdown(graph, [{ path: filePath, content }], new Set([filePath]));
+
+    expect(stats.sections).toBe(3);
+  });
+
+  it('extracts headings from CRLF-encoded markdown (the regression)', () => {
+    const filePath = 'crlf.md';
+    const graph = setupGraphWithFile(filePath);
+    const content = '# Title\r\nbody line 1\r\n## Sub\r\nbody line 2\r\n### SubSub\r\nmore\r\n';
+
+    const stats = processMarkdown(graph, [{ path: filePath, content }], new Set([filePath]));
+
+    // Pre-fix: this returned 0 because `## Sub\r` failed the heading regex.
+    expect(stats.sections).toBe(3);
+  });
+
+  it('extracts headings from CR-only-encoded markdown (old Mac OS Classic)', () => {
+    const filePath = 'cr.md';
+    const graph = setupGraphWithFile(filePath);
+    const content = '# Title\rbody line 1\r## Sub\rbody line 2\r';
+
+    const stats = processMarkdown(graph, [{ path: filePath, content }], new Set([filePath]));
+
+    expect(stats.sections).toBe(2);
+  });
+
+  it('extracts headings from mixed CRLF + LF markdown', () => {
+    const filePath = 'mixed.md';
+    const graph = setupGraphWithFile(filePath);
+    const content = '# LF Title\nbody\r\n## CRLF Sub\r\nmore\n### Trailing LF\nend\n';
+
+    const stats = processMarkdown(graph, [{ path: filePath, content }], new Set([filePath]));
+
+    expect(stats.sections).toBe(3);
+  });
+
+  it('reports correct startLine and endLine for CRLF content', () => {
+    const filePath = 'crlf-lines.md';
+    const graph = setupGraphWithFile(filePath);
+    // Lines 1, 3, 5 are headings (1-indexed)
+    const content = '# T\r\nbody\r\n## Sub\r\nmore\r\n### SubSub\r\ntail\r\n';
+
+    processMarkdown(graph, [{ path: filePath, content }], new Set([filePath]));
+
+    const sections = Array.from(graph.iterNodes()).filter((n) => n.label === 'Section');
+    const titleSection = sections.find((s) => s.properties.name === 'T');
+    const subSection = sections.find((s) => s.properties.name === 'Sub');
+
+    expect(titleSection?.properties.startLine).toBe(1);
+    expect(subSection?.properties.startLine).toBe(3);
+  });
+});