@oriro/orirocli 0.1.9 → 0.1.12

package/skills/graphify/export.py

@@ -1,1408 +0,0 @@
-# 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)