@oriro/orirocli 0.1.8 → 0.1.11

package/skills/graphify/export.py

@@ -0,0 +1,1408 @@
+# write graph to HTML, JSON, SVG, GraphML, Obsidian vault, and Neo4j Cypher
+from __future__ import annotations
+import hashlib
+import html as _html
+import json
+import math
+import os
+import re
+import shutil
+from collections import Counter
+from datetime import date
+from pathlib import Path
+import networkx as nx
+from networkx.readwrite import json_graph
+from graphify.security import sanitize_label
+from graphify.analyze import _node_community_map
+from graphify.build import edge_data
+
+
+# Artifacts worth preserving across rebuilds (non-regenerable without LLM or curation).
+_BACKUP_ARTIFACTS = [
+    "graph.json",
+    "GRAPH_REPORT.md",
+    ".graphify_labels.json",
+    ".graphify_analysis.json",
+    "manifest.json",
+    ".graphify_semantic_marker",
+    "cost.json",
+]
+
+
+def backup_if_protected(out_dir: Path) -> "Path | None":
+    """Snapshot graph artifacts to a dated subfolder before an overwrite.
+
+    Triggers when graph.json exists AND either:
+    - .graphify_semantic_marker is present (graph cost real LLM tokens), or
+    - .graphify_labels.json contains at least one non-default community label
+      (graph has been curated by a human or skill).
+
+    Returns the backup folder path, or None if no backup was taken.
+    Never raises — backup failure prints a warning but never blocks the write.
+    Set GRAPHIFY_NO_BACKUP=1 to disable.
+    """
+    if os.environ.get("GRAPHIFY_NO_BACKUP"):
+        return None
+    out = Path(out_dir)
+    if not (out / "graph.json").exists():
+        return None
+
+    is_semantic = (out / ".graphify_semantic_marker").exists()
+    is_curated = False
+    labels_file = out / ".graphify_labels.json"
+    if labels_file.exists():
+        try:
+            labels = json.loads(labels_file.read_text(encoding="utf-8"))
+            is_curated = any(v != f"Community {k}" for k, v in labels.items())
+        except Exception:
+            pass
+
+    if not is_semantic and not is_curated:
+        return None
+
+    reason = "+".join(filter(None, ["semantic" if is_semantic else "", "curated" if is_curated else ""]))
+    today = date.today().isoformat()
+    backup_dir = out / today
+    graph_src = out / "graph.json"
+
+    # Skip re-copying if today's backup already has identical graph.json content.
+    # If content differs (graph changed since the last backup today), overwrite
+    # the backup in place — one folder per day, always the latest pre-overwrite state.
+    if backup_dir.exists() and (backup_dir / "graph.json").exists():
+        src_hash = hashlib.sha256(graph_src.read_bytes()).hexdigest()
+        bak_hash = hashlib.sha256((backup_dir / "graph.json").read_bytes()).hexdigest()
+        if src_hash == bak_hash:
+            return backup_dir  # identical content, nothing to do
+
+    try:
+        backup_dir.mkdir(parents=True, exist_ok=True)
+        copied = 0
+        for name in _BACKUP_ARTIFACTS:
+            src = out / name
+            if src.exists():
+                try:
+                    shutil.copy2(src, backup_dir / name)
+                    copied += 1
+                except Exception:
+                    pass
+        if copied:
+            print(f"[graphify] backed up {reason} graph ({copied} files) -> {backup_dir.name}/")
+        return backup_dir
+    except Exception as exc:
+        import sys
+        print(f"[graphify] warning: backup failed ({exc}) - continuing with overwrite", file=sys.stderr)
+        return None
+
+def _obsidian_tag(name: str) -> str:
+    """Sanitize a community name for use as an Obsidian tag.
+
+    Obsidian tags only allow alphanumerics, hyphens, underscores, and slashes.
+    Spaces become underscores; everything else is stripped.
+    """
+    return re.sub(r"[^a-zA-Z0-9_\-/]", "", name.replace(" ", "_"))
+
+
+def _strip_diacritics(text: str) -> str:
+    import unicodedata
+    nfkd = unicodedata.normalize("NFKD", text)
+    return "".join(c for c in nfkd if not unicodedata.combining(c))
+
+
+def _yaml_str(s: str) -> str:
+    """Escape a value for safe embedding in a YAML double-quoted scalar (F-009).
+
+    See `graphify.ingest._yaml_str` for the full rationale; duplicated here to
+    avoid pulling the URL-fetching `ingest` module into export's dependency
+    graph. Handles backslash, double-quote, all line breaks (\\n, \\r,
+    U+2028, U+2029), tab, NUL, and other C0/DEL control characters that
+    would otherwise let a hostile `source_file` / `community` / etc. break
+    out of the YAML scalar and inject sibling keys.
+    """
+    if s is None:
+        return ""
+    out: list[str] = []
+    for ch in str(s):
+        cp = ord(ch)
+        if ch == "\\":
+            out.append("\\\\")
+        elif ch == '"':
+            out.append('\\"')
+        elif ch == "\n":
+            out.append("\\n")
+        elif ch == "\r":
+            out.append("\\r")
+        elif ch == "\t":
+            out.append("\\t")
+        elif ch == "\0":
+            out.append("\\0")
+        elif cp == 0x2028:
+            out.append("\\L")
+        elif cp == 0x2029:
+            out.append("\\P")
+        elif cp < 0x20 or cp == 0x7F:
+            out.append(f"\\x{cp:02x}")
+        else:
+            out.append(ch)
+    return "".join(out)
+
+
+COMMUNITY_COLORS = [
+    "#4E79A7", "#F28E2B", "#E15759", "#76B7B2", "#59A14F",
+    "#EDC948", "#B07AA1", "#FF9DA7", "#9C755F", "#BAB0AC",
+]
+
+MAX_NODES_FOR_VIZ = 5_000
+
+
+def _viz_node_limit() -> int:
+    """Return the effective viz node limit, honoring GRAPHIFY_VIZ_NODE_LIMIT env var.
+
+    Falls back to MAX_NODES_FOR_VIZ when the env var is unset, empty, or non-integer.
+    Set to 0 to disable HTML viz unconditionally (useful for CI runners).
+    """
+    import os
+    raw = os.environ.get("GRAPHIFY_VIZ_NODE_LIMIT")
+    if raw is None or not raw.strip():
+        return MAX_NODES_FOR_VIZ
+    try:
+        return int(raw)
+    except ValueError:
+        return MAX_NODES_FOR_VIZ
+
+
+def _html_styles() -> str:
+    return """<style>
+  * { box-sizing: border-box; margin: 0; padding: 0; }
+  body { background: #0f0f1a; color: #e0e0e0; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", sans-serif; display: flex; height: 100vh; overflow: hidden; }
+  #graph { flex: 1; }
+  #sidebar { width: 280px; background: #1a1a2e; border-left: 1px solid #2a2a4e; display: flex; flex-direction: column; overflow: hidden; }
+  #search-wrap { padding: 12px; border-bottom: 1px solid #2a2a4e; }
+  #search { width: 100%; background: #0f0f1a; border: 1px solid #3a3a5e; color: #e0e0e0; padding: 7px 10px; border-radius: 6px; font-size: 13px; outline: none; }
+  #search:focus { border-color: #4E79A7; }
+  #search-results { max-height: 140px; overflow-y: auto; padding: 4px 12px; border-bottom: 1px solid #2a2a4e; display: none; }
+  .search-item { padding: 4px 6px; cursor: pointer; border-radius: 4px; font-size: 12px; white-space: nowrap; overflow: hidden; text-overflow: ellipsis; }
+  .search-item:hover { background: #2a2a4e; }
+  #info-panel { padding: 14px; border-bottom: 1px solid #2a2a4e; min-height: 140px; }
+  #info-panel h3 { font-size: 13px; color: #aaa; margin-bottom: 8px; text-transform: uppercase; letter-spacing: 0.05em; }
+  #info-content { font-size: 13px; color: #ccc; line-height: 1.6; }
+  #info-content .field { margin-bottom: 5px; }
+  #info-content .field b { color: #e0e0e0; }
+  #info-content .empty { color: #555; font-style: italic; }
+  .neighbor-link { display: block; padding: 2px 6px; margin: 2px 0; border-radius: 3px; cursor: pointer; font-size: 12px; white-space: nowrap; overflow: hidden; text-overflow: ellipsis; border-left: 3px solid #333; }
+  .neighbor-link:hover { background: #2a2a4e; }
+  #neighbors-list { max-height: 160px; overflow-y: auto; margin-top: 4px; }
+  #legend-wrap { flex: 1; overflow-y: auto; padding: 12px; }
+  #legend-wrap h3 { font-size: 13px; color: #aaa; margin-bottom: 10px; text-transform: uppercase; letter-spacing: 0.05em; }
+  .legend-item { display: flex; align-items: center; gap: 8px; padding: 4px 0; cursor: pointer; border-radius: 4px; font-size: 12px; }
+  .legend-item:hover { background: #2a2a4e; padding-left: 4px; }
+  .legend-item.dimmed { opacity: 0.35; }
+  .legend-dot { width: 12px; height: 12px; border-radius: 50%; flex-shrink: 0; }
+  .legend-label { flex: 1; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
+  .legend-count { color: #666; font-size: 11px; }
+  #stats { padding: 10px 14px; border-top: 1px solid #2a2a4e; font-size: 11px; color: #555; }
+  #legend-controls { display: flex; align-items: center; gap: 8px; margin-bottom: 8px; padding: 4px 0; }
+  #legend-controls label { display: flex; align-items: center; gap: 6px; cursor: pointer; font-size: 12px; color: #aaa; user-select: none; }
+  #legend-controls label:hover { color: #e0e0e0; }
+  .legend-cb, #select-all-cb { appearance: none; -webkit-appearance: none; width: 14px; height: 14px; border: 1.5px solid #3a3a5e; border-radius: 3px; background: #0f0f1a; cursor: pointer; position: relative; flex-shrink: 0; }
+  .legend-cb:checked, #select-all-cb:checked { background: #4E79A7; border-color: #4E79A7; }
+  .legend-cb:checked::after, #select-all-cb:checked::after { content: ''; position: absolute; left: 3.5px; top: 1px; width: 4px; height: 7px; border: solid #fff; border-width: 0 2px 2px 0; transform: rotate(45deg); }
+  #select-all-cb:indeterminate { background: #4E79A7; border-color: #4E79A7; }
+  #select-all-cb:indeterminate::after { content: ''; position: absolute; left: 2px; top: 5px; width: 8px; height: 2px; background: #fff; border: none; transform: none; }
+</style>"""
+
+
+def _hyperedge_script(hyperedges_json: str) -> str:
+    return f"""<script>
+// Render hyperedges as shaded regions
+const hyperedges = {hyperedges_json};
+// afterDrawing passes ctx already transformed to network coordinate space.
+// Draw node positions raw — no manual pan/zoom/DPR math needed.
+network.on('afterDrawing', function(ctx) {{
+    hyperedges.forEach(h => {{
+        const positions = h.nodes
+            .map(nid => network.getPositions([nid])[nid])
+            .filter(p => p !== undefined);
+        if (positions.length < 2) return;
+        ctx.save();
+        ctx.globalAlpha = 0.12;
+        ctx.fillStyle = '#6366f1';
+        ctx.strokeStyle = '#6366f1';
+        ctx.lineWidth = 2;
+        ctx.beginPath();
+        // Centroid and expanded hull in network coordinates
+        const cx = positions.reduce((s, p) => s + p.x, 0) / positions.length;
+        const cy = positions.reduce((s, p) => s + p.y, 0) / positions.length;
+        const expanded = positions.map(p => ({{
+            x: cx + (p.x - cx) * 1.15,
+            y: cy + (p.y - cy) * 1.15
+        }}));
+        ctx.moveTo(expanded[0].x, expanded[0].y);
+        expanded.slice(1).forEach(p => ctx.lineTo(p.x, p.y));
+        ctx.closePath();
+        ctx.fill();
+        ctx.globalAlpha = 0.4;
+        ctx.stroke();
+        // Label
+        ctx.globalAlpha = 0.8;
+        ctx.fillStyle = '#4f46e5';
+        ctx.font = 'bold 11px sans-serif';
+        ctx.textAlign = 'center';
+        ctx.fillText(h.label, cx, cy - 5);
+        ctx.restore();
+    }});
+}});
+</script>"""
+
+
+def _html_script(nodes_json: str, edges_json: str, legend_json: str) -> str:
+    return f"""<script>
+const RAW_NODES = {nodes_json};
+const RAW_EDGES = {edges_json};
+const LEGEND = {legend_json};
+
+// HTML-escape helper — prevents XSS when injecting graph data into innerHTML
+function esc(s) {{
+  return String(s).replace(/&/g,'&amp;').replace(/</g,'&lt;').replace(/>/g,'&gt;').replace(/"/g,'&quot;').replace(/'/g,'&#39;');
+}}
+
+// Build vis datasets
+const nodesDS = new vis.DataSet(RAW_NODES.map(n => ({{
+  id: n.id, label: n.label, color: n.color, size: n.size,
+  font: n.font, title: n.title,
+  _community: n.community, _community_name: n.community_name,
+  _source_file: n.source_file, _file_type: n.file_type, _degree: n.degree,
+}})));
+
+const edgesDS = new vis.DataSet(RAW_EDGES.map((e, i) => ({{
+  id: i, from: e.from, to: e.to,
+  label: '',
+  title: e.title,
+  dashes: e.dashes,
+  width: e.width,
+  color: e.color,
+  arrows: {{ to: {{ enabled: true, scaleFactor: 0.5 }} }},
+}})));
+
+const container = document.getElementById('graph');
+const network = new vis.Network(container, {{ nodes: nodesDS, edges: edgesDS }}, {{
+  physics: {{
+    enabled: true,
+    solver: 'forceAtlas2Based',
+    forceAtlas2Based: {{
+      gravitationalConstant: -60,
+      centralGravity: 0.005,
+      springLength: 120,
+      springConstant: 0.08,
+      damping: 0.4,
+      avoidOverlap: 0.8,
+    }},
+    stabilization: {{ iterations: 200, fit: true }},
+  }},
+  interaction: {{
+    hover: true,
+    tooltipDelay: 100,
+    hideEdgesOnDrag: true,
+    navigationButtons: false,
+    keyboard: false,
+  }},
+  nodes: {{ shape: 'dot', borderWidth: 1.5 }},
+  edges: {{ smooth: {{ type: 'continuous', roundness: 0.2 }}, selectionWidth: 3 }},
+}});
+
+network.once('stabilizationIterationsDone', () => {{
+  network.setOptions({{ physics: {{ enabled: false }} }});
+}});
+
+function showInfo(nodeId) {{
+  const n = nodesDS.get(nodeId);
+  if (!n) return;
+  const neighborIds = network.getConnectedNodes(nodeId);
+  const neighborItems = neighborIds.map(nid => {{
+    const nb = nodesDS.get(nid);
+    const color = nb ? nb.color.background : '#555';
+    return `<span class="neighbor-link" style="border-left-color:${{esc(color)}}" onclick="focusNode(${{JSON.stringify(nid)}})">${{esc(nb ? nb.label : nid)}}</span>`;
+  }}).join('');
+  document.getElementById('info-content').innerHTML = `
+    <div class="field"><b>${{esc(n.label)}}</b></div>
+    <div class="field">Type: ${{esc(n._file_type || 'unknown')}}</div>
+    <div class="field">Community: ${{esc(n._community_name)}}</div>
+    <div class="field">Source: ${{esc(n._source_file || '-')}}</div>
+    <div class="field">Degree: ${{n._degree}}</div>
+    ${{neighborIds.length ? `<div class="field" style="margin-top:8px;color:#aaa;font-size:11px">Neighbors (${{neighborIds.length}})</div><div id="neighbors-list">${{neighborItems}}</div>` : ''}}
+  `;
+}}
+
+function focusNode(nodeId) {{
+  network.focus(nodeId, {{ scale: 1.4, animation: true }});
+  network.selectNodes([nodeId]);
+  showInfo(nodeId);
+}}
+
+// Track hovered node — hover detection is more reliable than click params
+let hoveredNodeId = null;
+network.on('hoverNode', params => {{
+  hoveredNodeId = params.node;
+  container.style.cursor = 'pointer';
+}});
+network.on('blurNode', () => {{
+  hoveredNodeId = null;
+  container.style.cursor = 'default';
+}});
+container.addEventListener('click', () => {{
+  if (hoveredNodeId !== null) {{
+    showInfo(hoveredNodeId);
+    network.selectNodes([hoveredNodeId]);
+  }}
+}});
+network.on('click', params => {{
+  if (params.nodes.length > 0) {{
+    showInfo(params.nodes[0]);
+  }} else if (hoveredNodeId === null) {{
+    document.getElementById('info-content').innerHTML = '<span class="empty">Click a node to inspect it</span>';
+  }}
+}});
+
+const searchInput = document.getElementById('search');
+const searchResults = document.getElementById('search-results');
+searchInput.addEventListener('input', () => {{
+  const q = searchInput.value.toLowerCase().trim();
+  searchResults.innerHTML = '';
+  if (!q) {{ searchResults.style.display = 'none'; return; }}
+  const matches = RAW_NODES.filter(n => n.label.toLowerCase().includes(q)).slice(0, 20);
+  if (!matches.length) {{ searchResults.style.display = 'none'; return; }}
+  searchResults.style.display = 'block';
+  matches.forEach(n => {{
+    const el = document.createElement('div');
+    el.className = 'search-item';
+    el.textContent = n.label;
+    el.style.borderLeft = `3px solid ${{n.color.background}}`;
+    el.style.paddingLeft = '8px';
+    el.onclick = () => {{
+      network.focus(n.id, {{ scale: 1.5, animation: true }});
+      network.selectNodes([n.id]);
+      showInfo(n.id);
+      searchResults.style.display = 'none';
+      searchInput.value = '';
+    }};
+    searchResults.appendChild(el);
+  }});
+}});
+document.addEventListener('click', e => {{
+  if (!searchResults.contains(e.target) && e.target !== searchInput)
+    searchResults.style.display = 'none';
+}});
+
+const hiddenCommunities = new Set();
+
+const selectAllCb = document.getElementById('select-all-cb');
+
+function updateSelectAllState() {{
+  const total = LEGEND.length;
+  const hidden = hiddenCommunities.size;
+  selectAllCb.checked = hidden === 0;
+  selectAllCb.indeterminate = hidden > 0 && hidden < total;
+}}
+
+function toggleAllCommunities(hide) {{
+  document.querySelectorAll('.legend-item').forEach(item => {{
+    hide ? item.classList.add('dimmed') : item.classList.remove('dimmed');
+  }});
+  document.querySelectorAll('.legend-cb').forEach(cb => {{
+    cb.checked = !hide;
+  }});
+  LEGEND.forEach(c => {{
+    if (hide) hiddenCommunities.add(c.cid); else hiddenCommunities.delete(c.cid);
+  }});
+  const updates = RAW_NODES.map(n => ({{ id: n.id, hidden: hide }}));
+  nodesDS.update(updates);
+  updateSelectAllState();
+}}
+
+const legendEl = document.getElementById('legend');
+LEGEND.forEach(c => {{
+  const item = document.createElement('div');
+  item.className = 'legend-item';
+  const cb = document.createElement('input');
+  cb.type = 'checkbox';
+  cb.className = 'legend-cb';
+  cb.checked = true;
+  cb.addEventListener('change', (e) => {{
+    e.stopPropagation();
+    if (cb.checked) {{
+      hiddenCommunities.delete(c.cid);
+      item.classList.remove('dimmed');
+    }} else {{
+      hiddenCommunities.add(c.cid);
+      item.classList.add('dimmed');
+    }}
+    const updates = RAW_NODES
+      .filter(n => n.community === c.cid)
+      .map(n => ({{ id: n.id, hidden: !cb.checked }}));
+    nodesDS.update(updates);
+    updateSelectAllState();
+  }});
+  item.innerHTML = `<div class="legend-dot" style="background:${{c.color}}"></div>
+    <span class="legend-label">${{c.label}}</span>
+    <span class="legend-count">${{c.count}}</span>`;
+  item.prepend(cb);
+  item.onclick = (e) => {{
+    if (e.target === cb) return;
+    cb.checked = !cb.checked;
+    cb.dispatchEvent(new Event('change'));
+  }};
+  legendEl.appendChild(item);
+}});
+</script>"""
+
+
+_CONFIDENCE_SCORE_DEFAULTS = {"EXTRACTED": 1.0, "INFERRED": 0.5, "AMBIGUOUS": 0.2}
+
+
+def attach_hyperedges(G: nx.Graph, hyperedges: list) -> None:
+    """Store hyperedges in the graph's metadata dict."""
+    existing = G.graph.get("hyperedges", [])
+    seen_ids = {h["id"] for h in existing}
+    for h in hyperedges:
+        if h.get("id") and h["id"] not in seen_ids:
+            existing.append(h)
+            seen_ids.add(h["id"])
+    G.graph["hyperedges"] = existing
+
+
+def _git_head() -> str | None:
+    """Return the current git HEAD commit hash, or None if not in a git repo."""
+    import subprocess as _sp
+    try:
+        r = _sp.run(["git", "rev-parse", "HEAD"], capture_output=True, text=True, timeout=3)
+        return r.stdout.strip() if r.returncode == 0 else None
+    except Exception:
+        return None
+
+
+def to_json(G: nx.Graph, communities: dict[int, list[str]], output_path: str, *, force: bool = False, built_at_commit: str | None = None) -> bool:
+    # Safety check: refuse to silently shrink an existing graph (#479)
+    existing_path = Path(output_path)
+    if not force and existing_path.exists():
+        try:
+            from graphify.security import check_graph_file_size_cap
+            check_graph_file_size_cap(existing_path)
+            existing_data = json.loads(existing_path.read_text(encoding="utf-8"))
+            existing_n = len(existing_data.get("nodes", []))
+            new_n = G.number_of_nodes()
+            if new_n < existing_n:
+                import sys as _sys
+                print(
+                    f"[graphify] WARNING: new graph has {new_n} nodes but existing "
+                    f"graph.json has {existing_n} (net -{existing_n - new_n}). "
+                    f"Refusing to overwrite. Possible causes: missing chunk files from "
+                    f"a previous session, or fuzzy dedup collapsed same-named symbols "
+                    f"across files during an --update on an already-current graph. "
+                    f"Run a full rebuild (/graphify .) to be safe, or pass force=True "
+                    f"only if you have verified the reduction is legitimate.",
+                    file=_sys.stderr,
+                )
+                return False
+        except Exception:
+            pass  # unreadable existing file — proceed with write
+
+    node_community = _node_community_map(communities)
+    try:
+        data = json_graph.node_link_data(G, edges="links")
+    except TypeError:
+        data = json_graph.node_link_data(G)
+    for node in data["nodes"]:
+        node["community"] = node_community.get(node["id"])
+        node["norm_label"] = _strip_diacritics(node.get("label", "")).lower()
+    for link in data["links"]:
+        if "confidence_score" not in link:
+            conf = link.get("confidence", "EXTRACTED")
+            link["confidence_score"] = _CONFIDENCE_SCORE_DEFAULTS.get(conf, 1.0)
+        # Restore original edge direction. Undirected NetworkX storage may
+        # canonicalize endpoint order, flipping `calls` and other directional
+        # edges in graph.json. The build path stashes the true endpoints in
+        # _src/_tgt for exactly this purpose (#563).
+        true_src = link.pop("_src", None)
+        true_tgt = link.pop("_tgt", None)
+        if true_src is not None and true_tgt is not None:
+            link["source"] = true_src
+            link["target"] = true_tgt
+    data["hyperedges"] = getattr(G, "graph", {}).get("hyperedges", [])
+    commit = built_at_commit if built_at_commit is not None else _git_head()
+    if commit:
+        data["built_at_commit"] = commit
+    with open(output_path, "w", encoding="utf-8") as f:  # nosec
+        json.dump(data, f, indent=2)
+    return True
+
+
+def prune_dangling_edges(graph_data: dict) -> tuple[dict, int]:
+    """Remove edges whose source or target node is not in the node set.
+
+    Returns the cleaned graph_data dict and the number of pruned edges.
+    """
+    node_ids = {n["id"] for n in graph_data["nodes"]}
+    links_key = "links" if "links" in graph_data else "edges"
+    before = len(graph_data[links_key])
+    graph_data[links_key] = [
+        e for e in graph_data[links_key]
+        if e["source"] in node_ids and e["target"] in node_ids
+    ]
+    return graph_data, before - len(graph_data[links_key])
+
+
+def _cypher_escape(s: str) -> str:
+    """Escape a string for safe embedding in a Cypher single-quoted literal.
+
+    Handles all characters that could prematurely terminate the literal or
+    inject control sequences:
+      - `\\` and `'` (literal terminators)
+      - newlines/CRs (would break the per-line statement framing)
+      - NUL/control bytes (defensive — Neo4j errors on raw NULs)
+
+    Also strips any leading/trailing whitespace that would let an attacker
+    break the `;`-terminated statement boundary used by `cypher-shell`.
+    Closing `}` and `)` are NOT special inside a single-quoted Cypher string,
+    so escaping the quote and backslash correctly is sufficient (a `}` inside
+    a properly-closed `'...'` literal is just a character) — but we previously
+    missed `\\n` / `\\r` which DO let a payload break out of the statement
+    line and inject a fresh MATCH/DELETE on the following line. See F-008.
+    """
+    # First normalise: drop NUL and other C0 control chars except tab.
+    s = "".join(ch for ch in s if ch >= " " or ch == "\t")
+    return (
+        s.replace("\\", "\\\\")
+         .replace("'", "\\'")
+         .replace("\n", "\\n")
+         .replace("\r", "\\r")
+    )
+
+
+# Restrict identifier-position values (labels and relationship types are NOT
+# quoted in Cypher and so cannot be safely escaped — they must be allowlisted).
+_CYPHER_IDENT_RE = re.compile(r"[^A-Za-z0-9_]")
+
+
+def _cypher_label(raw: str, fallback: str) -> str:
+    """Sanitise a value used in identifier position (node label / rel type).
+
+    Cypher does not provide a way to escape `:Foo` label syntax, so we must
+    strip everything except `[A-Za-z0-9_]` and require the result to start
+    with a letter; otherwise we fall back to a safe constant.
+    """
+    cleaned = _CYPHER_IDENT_RE.sub("", raw or "")
+    if not cleaned or not cleaned[0].isalpha():
+        return fallback
+    return cleaned
+
+
+def to_cypher(G: nx.Graph, output_path: str) -> None:
+    lines = ["// Neo4j Cypher import - generated by /graphify", ""]
+    for node_id, data in G.nodes(data=True):
+        label = _cypher_escape(data.get("label", node_id))
+        node_id_esc = _cypher_escape(node_id)
+        ftype = _cypher_label(
+            (data.get("file_type", "unknown") or "unknown").capitalize(),
+            "Entity",
+        )
+        lines.append(f"MERGE (n:{ftype} {{id: '{node_id_esc}', label: '{label}'}});")
+    lines.append("")
+    for u, v, data in G.edges(data=True):
+        rel = _cypher_label(
+            (data.get("relation", "RELATES_TO") or "RELATES_TO").upper(),
+            "RELATES_TO",
+        )
+        conf = _cypher_escape(data.get("confidence", "EXTRACTED"))
+        u_esc = _cypher_escape(u)
+        v_esc = _cypher_escape(v)
+        lines.append(
+            f"MATCH (a {{id: '{u_esc}'}}), (b {{id: '{v_esc}'}}) "
+            f"MERGE (a)-[:{rel} {{confidence: '{conf}'}}]->(b);"
+        )
+    with open(output_path, "w", encoding="utf-8") as f:  # nosec
+        f.write("\n".join(lines))
+
+
+def to_html(
+    G: nx.Graph,
+    communities: dict[int, list[str]],
+    output_path: str,
+    community_labels: dict[int, str] | None = None,
+    member_counts: dict[int, int] | None = None,
+    node_limit: int | None = None,
+) -> None:
+    """Generate an interactive vis.js HTML visualization of the graph.
+
+    Features: node size by degree, click-to-inspect panel, search box,
+    community filter, physics clustering by community, confidence-styled edges.
+    Raises ValueError if graph exceeds MAX_NODES_FOR_VIZ.
+
+    If member_counts is provided (aggregated community view), node sizes are
+    based on community member counts rather than graph degree.
+
+    If node_limit is set and the graph exceeds it, automatically builds an
+    aggregated community-level meta-graph instead of raising ValueError.
+    """
+    limit = node_limit if node_limit is not None else _viz_node_limit()
+    if G.number_of_nodes() > limit:
+        if node_limit is not None:
+            # Build aggregated community meta-graph
+            from collections import Counter as _Counter
+            import networkx as _nx
+            print(f"Graph has {G.number_of_nodes()} nodes (above {limit} limit). Building aggregated community view...")
+            node_to_community = {nid: cid for cid, members in communities.items() for nid in members}
+            meta = _nx.Graph()
+            for cid, members in communities.items():
+                meta.add_node(str(cid), label=(community_labels or {}).get(cid, f"Community {cid}"))
+            edge_counts = _Counter()
+            for u, v in G.edges():
+                cu, cv = node_to_community.get(u), node_to_community.get(v)
+                if cu is not None and cv is not None and cu != cv:
+                    edge_counts[(min(cu, cv), max(cu, cv))] += 1
+            for (cu, cv), w in edge_counts.items():
+                meta.add_edge(str(cu), str(cv), weight=w,
+                              relation=f"{w} cross-community edges", confidence="AGGREGATED")
+            if meta.number_of_nodes() <= 1:
+                print("Single community - aggregated view not useful. Skipping graph.html.")
+                return
+            meta_communities = {cid: [str(cid)] for cid in communities}
+            mc = {cid: len(members) for cid, members in communities.items()}
+            # Remap hyperedges from semantic node IDs to community IDs
+            raw_hyperedges = G.graph.get("hyperedges", [])
+            if raw_hyperedges:
+                remapped = []
+                for he in raw_hyperedges:
+                    he_members = he.get("nodes") or he.get("members") or []
+                    comm_ids, seen = [], set()
+                    for nid in he_members:
+                        c = node_to_community.get(nid)
+                        if c is None:
+                            continue
+                        s = str(c)
+                        if s in seen:
+                            continue
+                        seen.add(s)
+                        comm_ids.append(s)
+                    if len(comm_ids) < 2:
+                        continue
+                    remapped.append({
+                        "id": he.get("id", ""),
+                        "label": he.get("label") or he.get("relation", "").replace("_", " "),
+                        "nodes": comm_ids,
+                    })
+                meta.graph["hyperedges"] = remapped
+            to_html(meta, meta_communities, output_path,
+                    community_labels=community_labels, member_counts=mc)
+            print(f"graph.html written (aggregated: {meta.number_of_nodes()} community nodes, {meta.number_of_edges()} cross-community edges)")
+            print("Tip: run with --obsidian for full node-level detail.")
+            return
+        raise ValueError(
+            f"Graph has {G.number_of_nodes()} nodes - too large for HTML viz "
+            f"(limit: {limit}). Use --no-viz, raise GRAPHIFY_VIZ_NODE_LIMIT, "
+            f"or reduce input size."
+        )
+
+    node_community = _node_community_map(communities)
+    degree = dict(G.degree())
+    max_deg = max(degree.values(), default=1) or 1
+    max_mc = (max(member_counts.values(), default=1) or 1) if member_counts else 1
+
+    # Build nodes list for vis.js
+    vis_nodes = []
+    for node_id, data in G.nodes(data=True):
+        cid = node_community.get(node_id, 0)
+        color = COMMUNITY_COLORS[cid % len(COMMUNITY_COLORS)]
+        label = sanitize_label(data.get("label", node_id))
+        deg = degree.get(node_id, 1)
+        if member_counts:
+            mc = member_counts.get(cid, 1)
+            size = 10 + 30 * (mc / max_mc)
+            font_size = 12
+        else:
+            size = 10 + 30 * (deg / max_deg)
+            # Only show label for high-degree nodes by default; others show on hover
+            font_size = 12 if deg >= max_deg * 0.15 else 0
+        vis_nodes.append({
+            "id": node_id,
+            "label": label,
+            "color": {"background": color, "border": color, "highlight": {"background": "#ffffff", "border": color}},
+            "size": round(size, 1),
+            "font": {"size": font_size, "color": "#ffffff"},
+            "title": _html.escape(label),
+            "community": cid,
+            "community_name": sanitize_label((community_labels or {}).get(cid, f"Community {cid}")),
+            "source_file": sanitize_label(str(data.get("source_file") or "")),
+            "file_type": data.get("file_type", ""),
+            "degree": deg,
+        })
+
+    # Build edges list. Restore original edge direction from _src/_tgt
+    # (stashed by build.py for exactly this reason): undirected NetworkX
+    # canonicalizes endpoint order, which would otherwise flip the arrow
+    # for `calls` and `rationale_for` in the rendered graph (#563).
+    vis_edges = []
+    for u, v, data in G.edges(data=True):
+        confidence = data.get("confidence", "EXTRACTED")
+        relation = data.get("relation", "")
+        true_src = data.get("_src", u)
+        true_tgt = data.get("_tgt", v)
+        vis_edges.append({
+            "from": true_src,
+            "to": true_tgt,
+            "label": relation,
+            "title": _html.escape(f"{relation} [{confidence}]"),
+            "dashes": confidence != "EXTRACTED",
+            "width": 2 if confidence == "EXTRACTED" else 1,
+            "color": {"opacity": 0.7 if confidence == "EXTRACTED" else 0.35},
+            "confidence": confidence,
+        })
+
+    # Build community legend data
+    legend_data = []
+    for cid in sorted((community_labels or {}).keys()):
+        color = COMMUNITY_COLORS[cid % len(COMMUNITY_COLORS)]
+        lbl = _html.escape(sanitize_label((community_labels or {}).get(cid, f"Community {cid}")))
+        n = member_counts.get(cid, len(communities.get(cid, []))) if member_counts else len(communities.get(cid, []))
+        legend_data.append({"cid": cid, "color": color, "label": lbl, "count": n})
+
+    # Escape </script> sequences so embedded JSON cannot break out of the script tag
+    def _js_safe(obj) -> str:
+        return json.dumps(obj).replace("</", "<\\/")
+
+    nodes_json = _js_safe(vis_nodes)
+    edges_json = _js_safe(vis_edges)
+    legend_json = _js_safe(legend_data)
+    hyperedges_json = _js_safe(getattr(G, "graph", {}).get("hyperedges", []))
+    title = _html.escape(sanitize_label(str(output_path)))
+    stats = f"{G.number_of_nodes()} nodes &middot; {G.number_of_edges()} edges &middot; {len(communities)} communities"
+
+    html = f"""<!DOCTYPE html>
+<html lang="en">
+<head>
+<meta charset="UTF-8">
+<title>graphify - {title}</title>
+<script src="https://unpkg.com/vis-network@9.1.6/standalone/umd/vis-network.min.js"
+        integrity="sha384-Ux6phic9PEHJ38YtrijhkzyJ8yQlH8i/+buBR8s3mAZOJrP1gwyvAcIYl3GWtpX1"
+        crossorigin="anonymous"></script>
+{_html_styles()}
+</head>
+<body>
+<div id="graph"></div>
+<div id="sidebar">
+  <div id="search-wrap">
+    <input id="search" type="text" placeholder="Search nodes..." autocomplete="off">
+    <div id="search-results"></div>
+  </div>
+  <div id="info-panel">
+    <h3>Node Info</h3>
+    <div id="info-content"><span class="empty">Click a node to inspect it</span></div>
+  </div>
+  <div id="legend-wrap">
+    <h3>Communities</h3>
+    <div id="legend-controls">
+      <label><input type="checkbox" id="select-all-cb" checked onchange="toggleAllCommunities(!this.checked)">Select All</label>
+    </div>
+    <div id="legend"></div>
+  </div>
+  <div id="stats">{stats}</div>
+</div>
+{_html_script(nodes_json, edges_json, legend_json)}
+{_hyperedge_script(hyperedges_json)}
+</body>
+</html>"""
+
+    Path(output_path).write_text(html, encoding="utf-8")  # nosec
+
+
+# Keep backward-compatible alias - skill.md calls generate_html
+generate_html = to_html
+
+
+def _cap_filename(s: str, limit: int = 200) -> str:
+    """Cap a filename stem to ``limit`` UTF-8 bytes so it stays under the 255-byte
+    filesystem limit even after the ``.md`` extension and dedup suffix are added
+    (#1094). The cap is on BYTES, not chars, because a label of multibyte
+    characters (CJK, accented) can exceed 255 bytes well under 255 chars. When
+    truncation happens, an 8-char hash of the full label is appended so two
+    distinct labels sharing a long prefix produce distinct, deterministic
+    filenames instead of colliding."""
+    b = s.encode("utf-8")
+    if len(b) <= limit:
+        return s
+    digest = hashlib.sha1(s.encode("utf-8")).hexdigest()[:8]  # nosec - not security
+    keep = limit - 9  # "_" + 8 hex chars
+    truncated = b[:keep].decode("utf-8", "ignore")  # "ignore" drops a split trailing char
+    return f"{truncated}_{digest}"
+
+
+def to_obsidian(
+    G: nx.Graph,
+    communities: dict[int, list[str]],
+    output_dir: str,
+    community_labels: dict[int, str] | None = None,
+    cohesion: dict[int, float] | None = None,
+) -> int:
+    """Export graph as an Obsidian vault - one .md file per node with [[wikilinks]],
+    plus one _COMMUNITY_name.md overview note per community (sorted to top by underscore prefix).
+
+    Open the output directory as a vault in Obsidian to get an interactive
+    graph view with community colors and full-text search over node metadata.
+
+    Returns the number of node notes + community notes written.
+    """
+    out = Path(output_dir)
+    out.mkdir(parents=True, exist_ok=True)
+
+    node_community = _node_community_map(communities)
+
+    # Map node_id → safe filename so wikilinks stay consistent.
+    # Deduplicate: if two nodes produce the same filename, append a numeric suffix.
+    def safe_name(label: str) -> str:
+        cleaned = re.sub(r'[\\/*?:"<>|#^[\]]', "", label.replace("\r\n", " ").replace("\r", " ").replace("\n", " ")).strip()
+        # Strip trailing .md/.mdx/.markdown so "CLAUDE.md" doesn't become "CLAUDE.md.md"
+        cleaned = re.sub(r"\.(md|mdx|qmd|markdown)$", "", cleaned, flags=re.IGNORECASE)
+        return _cap_filename(cleaned) if cleaned else "unnamed"
+
+    node_filename: dict[str, str] = {}
+    seen_names: dict[str, int] = {}
+    for node_id, data in G.nodes(data=True):
+        base = safe_name(data.get("label", node_id))
+        if base in seen_names:
+            seen_names[base] += 1
+            node_filename[node_id] = f"{base}_{seen_names[base]}"
+        else:
+            seen_names[base] = 0
+            node_filename[node_id] = base
+
+    # Helper: compute dominant confidence for a node across all its edges
+    def _dominant_confidence(node_id: str) -> str:
+        confs = []
+        for u, v, edata in G.edges(node_id, data=True):
+            confs.append(edata.get("confidence", "EXTRACTED"))
+        if not confs:
+            return "EXTRACTED"
+        return Counter(confs).most_common(1)[0][0]
+
+    # Map file_type → graphify tag
+    _FTYPE_TAG = {
+        "code": "graphify/code",
+        "document": "graphify/document",
+        "paper": "graphify/paper",
+        "image": "graphify/image",
+    }
+
+    # Write one .md file per node
+    for node_id, data in G.nodes(data=True):
+        label = data.get("label", node_id)
+        cid = node_community.get(node_id)
+        community_name = (
+            community_labels.get(cid, f"Community {cid}")
+            if community_labels and cid is not None
+            else f"Community {cid}"
+        )
+
+        # Build tags for this node
+        ftype = data.get("file_type", "")
+        ftype_tag = _FTYPE_TAG.get(ftype, f"graphify/{ftype}" if ftype else "graphify/document")
+        dom_conf = _dominant_confidence(node_id)
+        conf_tag = f"graphify/{dom_conf}"
+        comm_tag = f"community/{_obsidian_tag(community_name)}"
+        node_tags = [ftype_tag, conf_tag, comm_tag]
+
+        lines: list[str] = []
+
+        # YAML frontmatter - readable in Obsidian's properties panel.
+        # All scalars pass through _yaml_str so a hostile source_file or
+        # community label cannot break out and inject sibling keys (F-009).
+        lines += [
+            "---",
+            f'source_file: "{_yaml_str(data.get("source_file", ""))}"',
+            f'type: "{_yaml_str(ftype)}"',
+            f'community: "{_yaml_str(community_name)}"',
+        ]
+        if data.get("source_location"):
+            lines.append(f'location: "{_yaml_str(str(data["source_location"]))}"')
+        # Add tags list to frontmatter
+        lines.append("tags:")
+        for tag in node_tags:
+            lines.append(f"  - {tag}")
+        lines += ["---", "", f"# {label}", ""]
+
+        # Outgoing edges as wikilinks
+        neighbors = list(G.neighbors(node_id))
+        if neighbors:
+            lines.append("## Connections")
+            for neighbor in sorted(neighbors, key=lambda n: G.nodes[n].get("label", n)):
+                edata = edge_data(G, node_id, neighbor)
+                neighbor_label = node_filename[neighbor]
+                relation = edata.get("relation", "")
+                confidence = edata.get("confidence", "EXTRACTED")
+                lines.append(f"- [[{neighbor_label}]] - `{relation}` [{confidence}]")
+            lines.append("")
+
+        # Inline tags at bottom of note body (for Obsidian tag panel)
+        inline_tags = " ".join(f"#{t}" for t in node_tags)
+        lines.append(inline_tags)
+
+        fname = node_filename[node_id] + ".md"
+        (out / fname).write_text("\n".join(lines), encoding="utf-8")  # nosec
+
+    # Write one _COMMUNITY_name.md overview note per community
+    # Build inter-community edge counts for "Connections to other communities"
+    inter_community_edges: dict[int, dict[int, int]] = {}
+    for cid in communities:
+        inter_community_edges[cid] = {}
+    for u, v in G.edges():
+        cu = node_community.get(u)
+        cv = node_community.get(v)
+        if cu is not None and cv is not None and cu != cv:
+            inter_community_edges.setdefault(cu, {})
+            inter_community_edges.setdefault(cv, {})
+            inter_community_edges[cu][cv] = inter_community_edges[cu].get(cv, 0) + 1
+            inter_community_edges[cv][cu] = inter_community_edges[cv].get(cu, 0) + 1
+
+    # Precompute per-node community reach (number of distinct communities a node connects to)
+    def _community_reach(node_id: str) -> int:
+        neighbor_cids = {
+            node_community[nb]
+            for nb in G.neighbors(node_id)
+            if nb in node_community and node_community[nb] != node_community.get(node_id)
+        }
+        return len(neighbor_cids)
+
+    community_notes_written = 0
+    for cid, members in communities.items():
+        community_name = (
+            community_labels.get(cid, f"Community {cid}")
+            if community_labels and cid is not None
+            else f"Community {cid}"
+        )
+        n_members = len(members)
+        coh_value = cohesion.get(cid) if cohesion else None
+
+        lines: list[str] = []
+
+        # YAML frontmatter
+        lines.append("---")
+        lines.append("type: community")
+        if coh_value is not None:
+            lines.append(f"cohesion: {coh_value:.2f}")
+        lines.append(f"members: {n_members}")
+        lines.append("---")
+        lines.append("")
+        lines.append(f"# {community_name}")
+        lines.append("")
+
+        # Cohesion + member count summary
+        if coh_value is not None:
+            cohesion_desc = (
+                "tightly connected" if coh_value >= 0.7
+                else "moderately connected" if coh_value >= 0.4
+                else "loosely connected"
+            )
+            lines.append(f"**Cohesion:** {coh_value:.2f} - {cohesion_desc}")
+        lines.append(f"**Members:** {n_members} nodes")
+        lines.append("")
+
+        # Members section
+        lines.append("## Members")
+        for node_id in sorted(members, key=lambda n: G.nodes[n].get("label", n)):
+            data = G.nodes[node_id]
+            node_label = node_filename[node_id]
+            ftype = data.get("file_type", "")
+            source = data.get("source_file", "")
+            entry = f"- [[{node_label}]]"
+            if ftype:
+                entry += f" - {ftype}"
+            if source:
+                entry += f" - {source}"
+            lines.append(entry)
+        lines.append("")
+
+        # Dataview live query (improvement 2)
+        comm_tag_name = _obsidian_tag(community_name)
+        lines.append("## Live Query (requires Dataview plugin)")
+        lines.append("")
+        lines.append("```dataview")
+        lines.append(f"TABLE source_file, type FROM #community/{comm_tag_name}")
+        lines.append("SORT file.name ASC")
+        lines.append("```")
+        lines.append("")
+
+        # Connections to other communities
+        cross = inter_community_edges.get(cid, {})
+        if cross:
+            lines.append("## Connections to other communities")
+            for other_cid, edge_count in sorted(cross.items(), key=lambda x: -x[1]):
+                other_name = (
+                    community_labels.get(other_cid, f"Community {other_cid}")
+                    if community_labels and other_cid is not None
+                    else f"Community {other_cid}"
+                )
+                other_safe = safe_name(other_name)
+                lines.append(f"- {edge_count} edge{'s' if edge_count != 1 else ''} to [[_COMMUNITY_{other_safe}]]")
+            lines.append("")
+
+        # Top bridge nodes - highest degree nodes that connect to other communities
+        bridge_nodes = [
+            (node_id, G.degree(node_id), _community_reach(node_id))
+            for node_id in members
+            if _community_reach(node_id) > 0
+        ]
+        bridge_nodes.sort(key=lambda x: (-x[2], -x[1]))
+        top_bridges = bridge_nodes[:5]
+        if top_bridges:
+            lines.append("## Top bridge nodes")
+            for node_id, degree, reach in top_bridges:
+                node_label = node_filename[node_id]
+                lines.append(
+                    f"- [[{node_label}]] - degree {degree}, connects to {reach} "
+                    f"{'community' if reach == 1 else 'communities'}"
+                )
+
+        community_safe = safe_name(community_name)
+        fname = f"_COMMUNITY_{community_safe}.md"
+        (out / fname).write_text("\n".join(lines), encoding="utf-8")  # nosec
+        community_notes_written += 1
+
+    # Improvement 4: write .obsidian/graph.json to color nodes by community in graph view
+    obsidian_dir = out / ".obsidian"
+    obsidian_dir.mkdir(exist_ok=True)
+    graph_config = {
+        "colorGroups": [
+            {
+                "query": f"tag:#community/{label.replace(' ', '_')}",
+                "color": {"a": 1, "rgb": int(COMMUNITY_COLORS[cid % len(COMMUNITY_COLORS)].lstrip('#'), 16)}
+            }
+            for cid, label in sorted((community_labels or {}).items())
+        ]
+    }
+    (obsidian_dir / "graph.json").write_text(json.dumps(graph_config, indent=2), encoding="utf-8")  # nosec
+
+    return G.number_of_nodes() + community_notes_written
+
+
+def to_canvas(
+    G: nx.Graph,
+    communities: dict[int, list[str]],
+    output_path: str,
+    community_labels: dict[int, str] | None = None,
+    node_filenames: dict[str, str] | None = None,
+) -> None:
+    """Export graph as an Obsidian Canvas file - communities as groups, nodes as cards.
+
+    Generates a structured layout: communities arranged in a grid, nodes within
+    each community arranged in rows. Edges shown between connected nodes.
+    Opens in Obsidian as an infinite canvas with community groupings visible.
+    """
+    # Obsidian canvas color codes (cycle through for communities)
+    CANVAS_COLORS = ["1", "2", "3", "4", "5", "6"]  # red, orange, yellow, green, cyan, purple
+
+    def safe_name(label: str) -> str:
+        cleaned = re.sub(r'[\\/*?:"<>|#^[\]]', "", label.replace("\r\n", " ").replace("\r", " ").replace("\n", " ")).strip()
+        cleaned = re.sub(r"\.(md|mdx|qmd|markdown)$", "", cleaned, flags=re.IGNORECASE)
+        return _cap_filename(cleaned) if cleaned else "unnamed"
+
+    # Build node_filenames if not provided (same dedup logic as to_obsidian)
+    if node_filenames is None:
+        node_filenames = {}
+        seen_names: dict[str, int] = {}
+        for node_id, data in G.nodes(data=True):
+            base = safe_name(data.get("label", node_id))
+            if base in seen_names:
+                seen_names[base] += 1
+                node_filenames[node_id] = f"{base}_{seen_names[base]}"
+            else:
+                seen_names[base] = 0
+                node_filenames[node_id] = base
+
+    num_communities = len(communities)
+    cols = math.ceil(math.sqrt(num_communities)) if num_communities > 0 else 1
+    rows = math.ceil(num_communities / cols) if num_communities > 0 else 1
+
+    canvas_nodes: list[dict] = []
+    canvas_edges: list[dict] = []
+
+    # Lay out communities in a grid
+    gap = 80
+    group_x_offsets: list[int] = []
+    group_y_offsets: list[int] = []
+
+    # Precompute group sizes so we can calculate offsets
+    sorted_cids = sorted(communities.keys())
+    group_sizes: dict[int, tuple[int, int]] = {}
+    for cid in sorted_cids:
+        members = communities[cid]
+        n = len(members)
+        w = max(600, 220 * math.ceil(math.sqrt(n)) if n > 0 else 600)
+        h = max(400, 100 * math.ceil(n / 3) + 120 if n > 0 else 400)
+        group_sizes[cid] = (w, h)
+
+    # Compute cumulative row heights and col widths for grid placement
+    # Each grid cell uses the max width/height in its col/row
+    col_widths: list[int] = []
+    row_heights: list[int] = []
+    for col_idx in range(cols):
+        max_w = 0
+        for row_idx in range(rows):
+            linear = row_idx * cols + col_idx
+            if linear < len(sorted_cids):
+                cid = sorted_cids[linear]
+                w, _ = group_sizes[cid]
+                max_w = max(max_w, w)
+        col_widths.append(max_w)
+
+    for row_idx in range(rows):
+        max_h = 0
+        for col_idx in range(cols):
+            linear = row_idx * cols + col_idx
+            if linear < len(sorted_cids):
+                cid = sorted_cids[linear]
+                _, h = group_sizes[cid]
+                max_h = max(max_h, h)
+        row_heights.append(max_h)
+
+    # Map from cid → (group_x, group_y, group_w, group_h)
+    group_layout: dict[int, tuple[int, int, int, int]] = {}
+    for idx, cid in enumerate(sorted_cids):
+        col_idx = idx % cols
+        row_idx = idx // cols
+        gx = sum(col_widths[:col_idx]) + col_idx * gap
+        gy = sum(row_heights[:row_idx]) + row_idx * gap
+        gw, gh = group_sizes[cid]
+        group_layout[cid] = (gx, gy, gw, gh)
+
+    # Build set of all node_ids in canvas for edge filtering
+    all_canvas_nodes: set[str] = set()
+    for members in communities.values():
+        all_canvas_nodes.update(members)
+
+    # Generate group and node canvas entries
+    for idx, cid in enumerate(sorted_cids):
+        members = communities[cid]
+        community_name = (
+            community_labels.get(cid, f"Community {cid}")
+            if community_labels and cid is not None
+            else f"Community {cid}"
+        )
+        gx, gy, gw, gh = group_layout[cid]
+        canvas_color = CANVAS_COLORS[idx % len(CANVAS_COLORS)]
+
+        # Group node
+        canvas_nodes.append({
+            "id": f"g{cid}",
+            "type": "group",
+            "label": community_name,
+            "x": gx,
+            "y": gy,
+            "width": gw,
+            "height": gh,
+            "color": canvas_color,
+        })
+
+        # Node cards inside the group - rows of 3
+        sorted_members = sorted(members, key=lambda n: G.nodes[n].get("label", n))
+        for m_idx, node_id in enumerate(sorted_members):
+            col = m_idx % 3
+            row = m_idx // 3
+            nx_x = gx + 20 + col * (180 + 20)
+            nx_y = gy + 80 + row * (60 + 20)
+            fname = node_filenames.get(node_id, safe_name(G.nodes[node_id].get("label", node_id)))
+            canvas_nodes.append({
+                "id": f"n_{node_id}",
+                "type": "file",
+                "file": f"{fname}.md",
+                "x": nx_x,
+                "y": nx_y,
+                "width": 180,
+                "height": 60,
+            })
+
+    # Generate edges - only between nodes both in canvas, cap at 200 highest-weight
+    all_edges_weighted: list[tuple[float, str, str, str]] = []
+    for u, v, edata in G.edges(data=True):
+        if u in all_canvas_nodes and v in all_canvas_nodes:
+            weight = edata.get("weight", 1.0)
+            relation = edata.get("relation", "")
+            conf = edata.get("confidence", "EXTRACTED")
+            label = f"{relation} [{conf}]" if relation else f"[{conf}]"
+            all_edges_weighted.append((weight, u, v, label))
+
+    all_edges_weighted.sort(key=lambda x: -x[0])
+    for weight, u, v, label in all_edges_weighted[:200]:
+        canvas_edges.append({
+            "id": f"e_{u}_{v}",
+            "fromNode": f"n_{u}",
+            "toNode": f"n_{v}",
+            "label": label,
+        })
+
+    canvas_data = {"nodes": canvas_nodes, "edges": canvas_edges}
+    Path(output_path).write_text(json.dumps(canvas_data, indent=2), encoding="utf-8")  # nosec
+
+
+def push_to_neo4j(
+    G: nx.Graph,
+    uri: str,
+    user: str,
+    password: str,
+    communities: dict[int, list[str]] | None = None,
+) -> dict[str, int]:
+    """Push graph directly to a running Neo4j instance via the Python driver.
+
+    Requires: pip install neo4j
+
+    Uses MERGE so re-running is safe - nodes and edges are upserted, not duplicated.
+    Returns a dict with counts of nodes and edges pushed.
+    """
+    try:
+        from neo4j import GraphDatabase
+    except ImportError as e:
+        raise ImportError(
+            "neo4j driver not installed. Run: pip install neo4j"
+        ) from e
+
+    node_community = _node_community_map(communities) if communities else {}
+
+    def _safe_rel(relation: str) -> str:
+        return re.sub(r"[^A-Z0-9_]", "_", relation.upper().replace(" ", "_").replace("-", "_")) or "RELATED_TO"
+
+    def _safe_label(label: str) -> str:
+        """Sanitize a Neo4j node label to prevent Cypher injection."""
+        sanitized = re.sub(r"[^A-Za-z0-9_]", "", label)
+        return sanitized if sanitized else "Entity"
+
+    driver = GraphDatabase.driver(uri, auth=(user, password))
+    nodes_pushed = 0
+    edges_pushed = 0
+
+    with driver.session() as session:
+        for node_id, data in G.nodes(data=True):
+            props = {
+                k: v for k, v in data.items()
+                if isinstance(v, (str, int, float, bool)) and not k.startswith("_")
+            }
+            props["id"] = node_id
+            cid = node_community.get(node_id)
+            if cid is not None:
+                props["community"] = cid
+            ftype = _safe_label(data.get("file_type", "Entity").capitalize())
+            session.run(
+                f"MERGE (n:{ftype} {{id: $id}}) SET n += $props",
+                id=node_id,
+                props=props,
+            )
+            nodes_pushed += 1
+
+        for u, v, data in G.edges(data=True):
+            rel = _safe_rel(data.get("relation", "RELATED_TO"))
+            props = {
+                k: v for k, v in data.items()
+                if isinstance(v, (str, int, float, bool)) and not k.startswith("_")
+            }
+            session.run(
+                f"MATCH (a {{id: $src}}), (b {{id: $tgt}}) "
+                f"MERGE (a)-[r:{rel}]->(b) SET r += $props",
+                src=u,
+                tgt=v,
+                props=props,
+            )
+            edges_pushed += 1
+
+    driver.close()
+    return {"nodes": nodes_pushed, "edges": edges_pushed}
+
+
+def to_graphml(
+    G: nx.Graph,
+    communities: dict[int, list[str]],
+    output_path: str,
+) -> None:
+    """Export graph as GraphML - opens in Gephi, yEd, and any GraphML-compatible tool.
+
+    Community IDs are written as a node attribute so Gephi can colour by community.
+    Edge confidence (EXTRACTED/INFERRED/AMBIGUOUS) is preserved as an edge attribute.
+    """
+    H = G.copy()
+    node_community = _node_community_map(communities)
+    for node_id in H.nodes():
+        H.nodes[node_id]["community"] = node_community.get(node_id, -1)
+    # Drop internal markers (e.g. the AST-provenance "_origin" tag, #1116, and
+    # the "_src"/"_tgt" direction markers) — they are persistence/runtime details,
+    # not graph data, and should not leak into the exported file.
+    for _, attrs in H.nodes(data=True):
+        for k in [k for k in attrs if k.startswith("_")]:
+            del attrs[k]
+    for _, _, attrs in H.edges(data=True):
+        for k in [k for k in attrs if k.startswith("_")]:
+            del attrs[k]
+    nx.write_graphml(H, output_path)
+
+
+def to_svg(
+    G: nx.Graph,
+    communities: dict[int, list[str]],
+    output_path: str,
+    community_labels: dict[int, str] | None = None,
+    figsize: tuple[int, int] = (20, 14),
+) -> None:
+    """Export graph as an SVG file using matplotlib + spring layout.
+
+    Lightweight and embeddable - works in Obsidian notes, Notion, GitHub READMEs,
+    and any markdown renderer. No JavaScript required.
+
+    Node size scales with degree. Community colors match the HTML output.
+    """
+    try:
+        import matplotlib
+        matplotlib.use("Agg")
+        import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
+    except ImportError as e:
+        raise ImportError("matplotlib not installed. Run: pip install matplotlib") from e
+
+    node_community = _node_community_map(communities)
+
+    fig, ax = plt.subplots(figsize=figsize, facecolor="#1a1a2e")
+    ax.set_facecolor("#1a1a2e")
+    ax.axis("off")
+
+    pos = nx.spring_layout(G, seed=42, k=2.0 / (G.number_of_nodes() ** 0.5 + 1))
+
+    degree = dict(G.degree())
+    max_deg = max(degree.values(), default=1) or 1
+
+    node_colors = [COMMUNITY_COLORS[node_community.get(n, 0) % len(COMMUNITY_COLORS)] for n in G.nodes()]
+    node_sizes = [300 + 1200 * (degree.get(n, 1) / max_deg) for n in G.nodes()]
+
+    # Draw edges - dashed for non-EXTRACTED
+    for u, v, data in G.edges(data=True):
+        conf = data.get("confidence", "EXTRACTED")
+        style = "solid" if conf == "EXTRACTED" else "dashed"
+        alpha = 0.6 if conf == "EXTRACTED" else 0.3
+        x0, y0 = pos[u]
+        x1, y1 = pos[v]
+        ax.plot([x0, x1], [y0, y1], color="#aaaaaa", linewidth=0.8,
+                linestyle=style, alpha=alpha, zorder=1)
+
+    nx.draw_networkx_nodes(G, pos, ax=ax, node_color=node_colors,
+                           node_size=node_sizes, alpha=0.9)
+    nx.draw_networkx_labels(G, pos, ax=ax,
+                            labels={n: G.nodes[n].get("label", n) for n in G.nodes()},
+                            font_size=7, font_color="white")
+
+    # Legend
+    if community_labels:
+        patches = [
+            mpatches.Patch(
+                color=COMMUNITY_COLORS[cid % len(COMMUNITY_COLORS)],
+                label=f"{label} ({len(communities.get(cid, []))})",
+            )
+            for cid, label in sorted(community_labels.items())
+        ]
+        ax.legend(handles=patches, loc="upper left", framealpha=0.7,
+                  facecolor="#2a2a4e", labelcolor="white", fontsize=8)
+
+    plt.tight_layout()
+    plt.savefig(output_path, format="svg", bbox_inches="tight",
+                facecolor=fig.get_facecolor())
+    plt.close(fig)