import live www.sillylaird.ca webrootHEADmain

2 files changed, 915 insertions, 0 deletions

diff --git a/.agents/skills/obsidian-literature-workflow/scripts/build_literature_canvas.py b/.agents/skills/obsidian-literature-workflow/scripts/build_literature_canvas.py
new file mode 100644
index 0000000..c1fc27d
--- /dev/null
+++ b/.agents/skills/obsidian-literature-workflow/scripts/build_literature_canvas.py
@@ -0,0 +1,644 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import argparse
+import hashlib
+import json
+import re
+import sys
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+WIKILINK_RE = re.compile(r"\[\[([^\]|#]+)(?:#[^\]|]+)?(?:\|[^\]]+)?\]\]")
+LIST_KEYS = {
+    "authors",
+    "keywords",
+    "concepts",
+    "methods",
+    "related_papers",
+    "linked_knowledge",
+    "paper_relationships",
+    "linked_papers",
+    "argument_claims",
+    "argument_methods",
+    "argument_gaps",
+    "linked_claims",
+    "linked_methods",
+    "linked_gaps",
+    "claim_method_links",
+    "method_gap_links",
+}
+PAPER_LIMIT = 48
+KNOWLEDGE_LIMIT = 18
+KNOWLEDGE_COLUMNS = 3
+NODE_WIDTH = 300
+NODE_HEIGHT = 180
+ARG_NODE_WIDTH = 280
+ARG_NODE_HEIGHT = 120
+X_GAP = 80
+Y_GAP = 70
+GROUP_X_GAP = 180
+GROUP_Y_GAP = 180
+ARG_GROUP_X_GAP = 200
+PAPER_RELATION_LIMIT = 2
+PAPER_CLAIM_LIMIT = 1
+PAPER_METHOD_LIMIT = 1
+PAPER_RELATION_LIMIT = 1
+SUBFIELD_ORDER = (
+    "speech-transfer-constraints",
+    "alignment-and-domain-adaptation",
+    "geometry-and-representation",
+    "subject-aware-adaptation",
+    "other",
+)
+SUBFIELD_LABELS = {
+    "speech-transfer-constraints": "Speech-specific transfer constraints",
+    "alignment-and-domain-adaptation": "Alignment and domain adaptation",
+    "geometry-and-representation": "Geometry and representation",
+    "subject-aware-adaptation": "Subject-aware adaptation",
+    "other": "Other papers",
+}
+SUBFIELD_COLORS = {
+    "speech-transfer-constraints": "6",
+    "alignment-and-domain-adaptation": "2",
+    "geometry-and-representation": "5",
+    "subject-aware-adaptation": "3",
+    "other": "1",
+}
+SUBFIELD_COLUMNS = 2
+
+
+@dataclass(frozen=True)
+class NoteRecord:
+    title: str
+    note_relpath: str
+    vault_relpath: str
+    file_name: str
+    related_papers: tuple[str, ...]
+    linked_knowledge: tuple[str, ...]
+    paper_relationships: tuple[tuple[str, str], ...]
+    linked_papers: tuple[str, ...]
+    claim_refs: tuple[str, ...]
+    method_refs: tuple[str, ...]
+    gap_refs: tuple[str, ...]
+    claim_method_links: tuple[tuple[str, str, str], ...]
+    method_gap_links: tuple[tuple[str, str, str], ...]
+    wikilinks: tuple[str, ...]
+    subfield: str
+    canvas_visibility: str
+
+
+def load_project_kb_module() -> Any:
+    script_dir = Path(__file__).resolve().parents[2] / "obsidian-project-memory" / "scripts"
+    sys.path.insert(0, str(script_dir))
+    import project_kb  # type: ignore
+
+    return project_kb
+
+
+def parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        description="Build a default literature canvas for the bound Obsidian project."
+    )
+    parser.add_argument("--cwd", default=".")
+    parser.add_argument("--project-id", default="")
+    parser.add_argument("--output", default="Maps/literature.canvas")
+    return parser.parse_args()
+
+
+def parse_frontmatter(text: str) -> dict[str, Any]:
+    if not text.startswith("---\n"):
+        return {}
+    end = text.find("\n---\n", 4)
+    if end == -1:
+        return {}
+    lines = text[4:end].splitlines()
+    data: dict[str, Any] = {}
+    current_key: str | None = None
+    for raw_line in lines:
+        if not raw_line.strip():
+            continue
+        if raw_line.startswith("  - ") or raw_line.startswith("- "):
+            if current_key and current_key in LIST_KEYS:
+                data.setdefault(current_key, []).append(
+                    raw_line.split("- ", 1)[1].strip().strip('"')
+                )
+            continue
+        if ":" not in raw_line:
+            current_key = None
+            continue
+        key, value = raw_line.split(":", 1)
+        key = key.strip()
+        value = value.strip()
+        current_key = key
+        if not value:
+            if key in LIST_KEYS:
+                data[key] = []
+            else:
+                data[key] = ""
+            continue
+        data[key] = value.strip('"')
+    return data
+
+
+def body_without_frontmatter(text: str) -> str:
+    if not text.startswith("---\n"):
+        return text
+    end = text.find("\n---\n", 4)
+    if end == -1:
+        return text
+    return text[end + 5 :]
+
+
+def normalize_note_target(value: str) -> str:
+    cleaned = value.strip()
+    if cleaned.endswith(".md"):
+        cleaned = cleaned[:-3]
+    if cleaned.startswith("./"):
+        cleaned = cleaned[2:]
+    return cleaned
+
+
+def parse_relationship_entries(values: list[str]) -> tuple[tuple[str, str], ...]:
+    parsed: list[tuple[str, str]] = []
+    for raw in values:
+        cleaned = raw.strip()
+        if not cleaned:
+            continue
+        if "::" in cleaned:
+            target, label = cleaned.split("::", 1)
+        else:
+            target, label = cleaned, "related"
+        parsed.append((normalize_note_target(target), label.strip() or "related"))
+    return tuple(parsed)
+
+
+def parse_triple_entries(values: list[str]) -> tuple[tuple[str, str, str], ...]:
+    parsed: list[tuple[str, str, str]] = []
+    for raw in values:
+        cleaned = raw.strip()
+        if not cleaned:
+            continue
+        parts = [part.strip() for part in cleaned.split("::")]
+        if len(parts) == 2:
+            parsed.append((parts[0], parts[1], "relates"))
+        elif len(parts) >= 3:
+            parsed.append((parts[0], parts[1], parts[2] or "relates"))
+    return tuple(parsed)
+
+
+def parse_plain_labels(values: list[str]) -> tuple[str, ...]:
+    labels = []
+    for raw in values:
+        cleaned = raw.strip()
+        if cleaned and cleaned not in labels:
+            labels.append(cleaned)
+    return tuple(labels)
+
+
+def extract_wikilinks(text: str) -> tuple[str, ...]:
+    seen: list[str] = []
+    for match in WIKILINK_RE.findall(text):
+        target = normalize_note_target(match)
+        if target not in seen:
+            seen.append(target)
+    return tuple(seen)
+
+
+def note_id(prefix: str, value: str) -> str:
+    digest = hashlib.sha1(f"{prefix}:{value}".encode("utf-8")).hexdigest()
+    return digest[:16]
+
+
+def file_node(note: NoteRecord, x: int, y: int, color: str) -> dict[str, Any]:
+    return {
+        "id": note_id("node", note.note_relpath),
+        "type": "file",
+        "x": x,
+        "y": y,
+        "width": NODE_WIDTH,
+        "height": NODE_HEIGHT,
+        "file": note.vault_relpath,
+        "color": color,
+    }
+
+
+def text_node(node_key: str, text: str, x: int, y: int, width: int, height: int) -> dict[str, Any]:
+    return {
+        "id": note_id("text", node_key),
+        "type": "text",
+        "x": x,
+        "y": y,
+        "width": width,
+        "height": height,
+        "text": text,
+        "color": "5",
+    }
+
+
+def group_node(node_key: str, label: str, x: int, y: int, width: int, height: int, color: str) -> dict[str, Any]:
+    return {
+        "id": note_id("group", node_key),
+        "type": "group",
+        "x": x,
+        "y": y,
+        "width": width,
+        "height": height,
+        "label": label,
+        "color": color,
+    }
+
+
+def edge_id(source: str, target: str, label: str) -> str:
+    digest = hashlib.sha1(f"{source}:{target}:{label}".encode("utf-8")).hexdigest()
+    return digest[:16]
+
+
+def make_edge(from_node: str, to_node: str, label: str) -> dict[str, Any]:
+    return {
+        "id": edge_id(from_node, to_node, label),
+        "fromNode": from_node,
+        "fromSide": "bottom",
+        "toNode": to_node,
+        "toSide": "top",
+        "toEnd": "arrow",
+        "label": label,
+    }
+
+
+def collect_notes(folder: Path, folder_name: str, vault_root: Path, limit: int) -> list[NoteRecord]:
+    notes: list[NoteRecord] = []
+    if not folder.exists():
+        return notes
+    for path in sorted(folder.glob("*.md"))[:limit]:
+        text = path.read_text(encoding="utf-8")
+        frontmatter = parse_frontmatter(text)
+        body = body_without_frontmatter(text)
+        title = str(frontmatter.get("title") or path.stem.replace("-", " "))
+        notes.append(
+            NoteRecord(
+                title=title,
+                note_relpath=f"{folder_name}/{path.name}",
+                vault_relpath=str(path.relative_to(vault_root)).replace("\\", "/"),
+                file_name=path.name,
+                related_papers=tuple(
+                    normalize_note_target(v) for v in frontmatter.get("related_papers", [])
+                ),
+                linked_knowledge=tuple(
+                    normalize_note_target(v) for v in frontmatter.get("linked_knowledge", [])
+                ),
+                paper_relationships=parse_relationship_entries(
+                    list(frontmatter.get("paper_relationships", []))
+                ),
+                linked_papers=tuple(
+                    normalize_note_target(v) for v in frontmatter.get("linked_papers", [])
+                ),
+                claim_refs=parse_plain_labels(
+                    list(frontmatter.get("argument_claims", []))
+                    + list(frontmatter.get("linked_claims", []))
+                ),
+                method_refs=parse_plain_labels(
+                    list(frontmatter.get("argument_methods", []))
+                    + list(frontmatter.get("linked_methods", []))
+                ),
+                gap_refs=parse_plain_labels(
+                    list(frontmatter.get("argument_gaps", []))
+                    + list(frontmatter.get("linked_gaps", []))
+                ),
+                claim_method_links=parse_triple_entries(
+                    list(frontmatter.get("claim_method_links", []))
+                ),
+                method_gap_links=parse_triple_entries(
+                    list(frontmatter.get("method_gap_links", []))
+                ),
+                wikilinks=extract_wikilinks(body),
+                subfield=str(frontmatter.get("subfield") or "other"),
+                canvas_visibility=str(frontmatter.get("canvas_visibility") or "show"),
+            )
+        )
+    return notes
+
+
+def looks_like_literature_knowledge(note: NoteRecord) -> bool:
+    key = note.note_relpath.lower()
+    if any(token in key for token in ("literature", "paper", "method", "survey", "gap", "related")):
+        return True
+    return any(target.startswith("Papers/") for target in note.wikilinks)
+
+
+def select_knowledge_notes(
+    all_knowledge: list[NoteRecord], papers: list[NoteRecord]
+) -> list[NoteRecord]:
+    requested = set()
+    for note in papers:
+        requested.update(note.linked_knowledge)
+        requested.update(target for target in note.wikilinks if target.startswith("Knowledge/"))
+
+    selected: list[NoteRecord] = []
+    seen: set[str] = set()
+    for note in all_knowledge:
+        note_key = note.note_relpath[:-3]
+        if note_key in requested:
+            selected.append(note)
+            seen.add(note_key)
+
+    if selected:
+        return selected[:KNOWLEDGE_LIMIT]
+
+    for note in all_knowledge:
+        note_key = note.note_relpath[:-3]
+        if note_key in seen:
+            continue
+        if looks_like_literature_knowledge(note):
+            selected.append(note)
+            seen.add(note_key)
+        if len(selected) >= KNOWLEDGE_LIMIT:
+            break
+
+    return selected[:KNOWLEDGE_LIMIT]
+
+
+def layout_grid(index: int, columns: int, x0: int, y0: int) -> tuple[int, int]:
+    col = index % columns
+    row = index // columns
+    x = x0 + col * (NODE_WIDTH + X_GAP)
+    y = y0 + row * (NODE_HEIGHT + Y_GAP)
+    return x, y
+
+
+def compute_group_dimensions(item_count: int, columns: int) -> tuple[int, int]:
+    rows = max(1, (max(item_count, 1) - 1) // columns + 1)
+    width = columns * NODE_WIDTH + (columns - 1) * X_GAP + 120
+    height = rows * NODE_HEIGHT + (rows - 1) * Y_GAP + 140
+    return width, height
+
+
+def compute_argument_group_dimensions(item_count: int, columns: int) -> tuple[int, int]:
+    rows = max(1, (max(item_count, 1) - 1) // columns + 1)
+    width = columns * ARG_NODE_WIDTH + (columns - 1) * X_GAP + 120
+    height = rows * ARG_NODE_HEIGHT + (rows - 1) * Y_GAP + 140
+    return width, height
+
+
+def argument_node(kind: str, label: str, x: int, y: int) -> dict[str, Any]:
+    return {
+        "id": note_id(kind, label),
+        "type": "text",
+        "x": x,
+        "y": y,
+        "width": ARG_NODE_WIDTH,
+        "height": ARG_NODE_HEIGHT,
+        "text": label,
+        "color": {"claim": "4", "method": "2", "gap": "6"}.get(kind, "5"),
+    }
+
+
+def render_canvas(project_title: str, papers: list[NoteRecord], knowledge: list[NoteRecord]) -> dict[str, Any]:
+    nodes: list[dict[str, Any]] = []
+    edges: list[dict[str, Any]] = []
+    node_lookup: dict[str, str] = {}
+    claim_lookup: dict[str, str] = {}
+    method_lookup: dict[str, str] = {}
+    gap_lookup: dict[str, str] = {}
+
+    knowledge_rows = max(1, (max(len(knowledge), 1) - 1) // KNOWLEDGE_COLUMNS + 1)
+    knowledge_group_width = KNOWLEDGE_COLUMNS * NODE_WIDTH + (KNOWLEDGE_COLUMNS - 1) * X_GAP + 120
+    knowledge_group_height = knowledge_rows * NODE_HEIGHT + (knowledge_rows - 1) * Y_GAP + 140
+    knowledge_y = 220
+    argument_y = knowledge_y + knowledge_group_height + 180
+
+    nodes.append(
+        text_node(
+            "literature-summary",
+            (
+                f"# Literature Canvas\\n\\n"
+                f"Project: {project_title}\\n\\n"
+                f"- This is an argument map with `paper + claim + method + gap`.\\n"
+                f"- The graph is intentionally thinned: each paper only keeps its most important claim / method links.\\n"
+                f"- Papers are grouped by subfield and spaced out to reduce crossing lines."
+            ),
+            0,
+            0,
+            1080,
+            150,
+        )
+    )
+    nodes.append(group_node("knowledge-group", "Knowledge", -40, knowledge_y - 40, knowledge_group_width, knowledge_group_height, "4"))
+
+    for idx, note in enumerate(knowledge):
+        x, y = layout_grid(idx, KNOWLEDGE_COLUMNS, 20, knowledge_y)
+        node = file_node(note, x, y, "4")
+        nodes.append(node)
+        node_lookup[note.note_relpath[:-3]] = node["id"]
+
+    claim_labels: list[str] = []
+    method_labels: list[str] = []
+    gap_labels: list[str] = []
+    for note in (*papers, *knowledge):
+        for label in note.claim_refs:
+            if label not in claim_labels:
+                claim_labels.append(label)
+        for label in note.method_refs:
+            if label not in method_labels:
+                method_labels.append(label)
+        for label in note.gap_refs:
+            if label not in gap_labels:
+                gap_labels.append(label)
+
+    claim_group_width, claim_group_height = compute_argument_group_dimensions(len(claim_labels), 2)
+    method_group_width, method_group_height = compute_argument_group_dimensions(len(method_labels), 2)
+    gap_group_width, gap_group_height = compute_argument_group_dimensions(len(gap_labels), 2)
+    argument_row_height = max(claim_group_height, method_group_height, gap_group_height)
+
+    argument_groups = [
+        ("claim", "Claims", claim_labels, -40, argument_y, claim_group_width, claim_group_height, "4"),
+        ("method", "Methods", method_labels, -40 + claim_group_width + ARG_GROUP_X_GAP, argument_y, method_group_width, method_group_height, "2"),
+        ("gap", "Gaps", gap_labels, -40 + claim_group_width + ARG_GROUP_X_GAP + method_group_width + ARG_GROUP_X_GAP, argument_y, gap_group_width, gap_group_height, "6"),
+    ]
+    for kind, label, labels, group_x, group_y, group_width, group_height, color in argument_groups:
+        nodes.append(group_node(f"{kind}-group", label, group_x, group_y, group_width, group_height, color))
+        for idx, arg_label in enumerate(labels):
+            x, y = layout_grid(idx, 2, group_x + 60, group_y + 40)
+            node = argument_node(kind, arg_label, x, y)
+            nodes.append(node)
+            if kind == "claim":
+                claim_lookup[arg_label] = node["id"]
+            elif kind == "method":
+                method_lookup[arg_label] = node["id"]
+            else:
+                gap_lookup[arg_label] = node["id"]
+
+    paper_y = argument_y + argument_row_height + 180
+
+    grouped_papers: dict[str, list[NoteRecord]] = {}
+    for note in papers:
+        grouped_papers.setdefault(note.subfield or "other", []).append(note)
+
+    active_groups = [key for key in SUBFIELD_ORDER if grouped_papers.get(key)]
+    if not active_groups:
+        active_groups = ["other"]
+        grouped_papers["other"] = list(papers)
+
+    group_layout_meta: list[tuple[str, int, int, int, int]] = []
+    for idx, subfield in enumerate(active_groups):
+        notes_in_group = grouped_papers[subfield]
+        group_width, group_height = compute_group_dimensions(len(notes_in_group), 2)
+        col = idx % SUBFIELD_COLUMNS
+        row = idx // SUBFIELD_COLUMNS
+        group_x = -40 + col * (group_width + GROUP_X_GAP)
+        group_y = paper_y + row * (group_height + GROUP_Y_GAP)
+        group_layout_meta.append((subfield, group_x, group_y, group_width, group_height))
+        nodes.append(
+            group_node(
+                f"paper-group-{subfield}",
+                SUBFIELD_LABELS.get(subfield, subfield.replace("-", " ").title()),
+                group_x,
+                group_y,
+                group_width,
+                group_height,
+                SUBFIELD_COLORS.get(subfield, "2"),
+            )
+        )
+
+        for note_idx, note in enumerate(notes_in_group):
+            x, y = layout_grid(note_idx, 2, group_x + 60, group_y + 40)
+            node = file_node(note, x, y, SUBFIELD_COLORS.get(subfield, "2"))
+            nodes.append(node)
+            node_lookup[note.note_relpath[:-3]] = node["id"]
+
+    seen_edges: set[tuple[str, str, str]] = set()
+    for note in papers:
+        source = node_lookup.get(note.note_relpath[:-3])
+        if not source:
+            continue
+        explicit_relationships = list(note.paper_relationships)
+        if not explicit_relationships:
+            explicit_relationships = [(target, "related") for target in note.related_papers]
+        for target, label in explicit_relationships[:PAPER_RELATION_LIMIT]:
+            target_node = node_lookup.get(target)
+            if not target_node:
+                continue
+            marker = (source, target_node, label)
+            if marker not in seen_edges:
+                edges.append(make_edge(source, target_node, label))
+                seen_edges.add(marker)
+        for claim in note.claim_refs[:PAPER_CLAIM_LIMIT]:
+            target_node = claim_lookup.get(claim)
+            if not target_node:
+                continue
+            marker = (source, target_node, "supports")
+            if marker not in seen_edges:
+                edges.append(make_edge(source, target_node, "supports"))
+                seen_edges.add(marker)
+        for method in note.method_refs[:PAPER_METHOD_LIMIT]:
+            target_node = method_lookup.get(method)
+            if not target_node:
+                continue
+            marker = (source, target_node, "uses")
+            if marker not in seen_edges:
+                edges.append(make_edge(source, target_node, "uses"))
+                seen_edges.add(marker)
+    for note in knowledge:
+        source = node_lookup.get(note.note_relpath[:-3])
+        if not source:
+            continue
+        for target in note.linked_papers:
+            target_node = node_lookup.get(target)
+            if not target_node:
+                continue
+            marker = (source, target_node, "summarizes")
+            if marker not in seen_edges:
+                edges.append(make_edge(source, target_node, "summarizes"))
+                seen_edges.add(marker)
+        for claim in note.claim_refs:
+            target_node = claim_lookup.get(claim)
+            if not target_node:
+                continue
+            marker = (source, target_node, "summarizes")
+            if marker not in seen_edges:
+                edges.append(make_edge(source, target_node, "summarizes"))
+                seen_edges.add(marker)
+        for method in note.method_refs:
+            target_node = method_lookup.get(method)
+            if not target_node:
+                continue
+            marker = (source, target_node, "summarizes")
+            if marker not in seen_edges:
+                edges.append(make_edge(source, target_node, "summarizes"))
+                seen_edges.add(marker)
+        for gap in note.gap_refs:
+            target_node = gap_lookup.get(gap)
+            if not target_node:
+                continue
+            marker = (source, target_node, "summarizes")
+            if marker not in seen_edges:
+                edges.append(make_edge(source, target_node, "summarizes"))
+                seen_edges.add(marker)
+        for claim, method, label in note.claim_method_links:
+            source_node = claim_lookup.get(claim)
+            target_node = method_lookup.get(method)
+            if not source_node or not target_node:
+                continue
+            marker = (source_node, target_node, label)
+            if marker not in seen_edges:
+                edges.append(make_edge(source_node, target_node, label))
+                seen_edges.add(marker)
+        for method, gap, label in note.method_gap_links:
+            source_node = method_lookup.get(method)
+            target_node = gap_lookup.get(gap)
+            if not source_node or not target_node:
+                continue
+            marker = (source_node, target_node, label)
+            if marker not in seen_edges:
+                edges.append(make_edge(source_node, target_node, label))
+                seen_edges.add(marker)
+        for target in note.wikilinks:
+            if not target.startswith("Knowledge/"):
+                continue
+            target_node = node_lookup.get(target)
+            if not target_node:
+                continue
+            marker = (source, target_node, "relates")
+            if marker not in seen_edges:
+                edges.append(make_edge(source, target_node, "relates"))
+                seen_edges.add(marker)
+
+    return {"nodes": nodes, "edges": edges}
+
+
+def main() -> None:
+    args = parse_args()
+    project_kb = load_project_kb_module()
+    repo_root = project_kb.find_repo_root(Path(args.cwd).resolve())
+    binding = project_kb.resolve_binding(repo_root, args.project_id or None)
+
+    papers = [
+        note
+        for note in collect_notes(binding.project_root / "Papers", "Papers", binding.vault_path, PAPER_LIMIT)
+        if note.canvas_visibility != "hidden"
+    ]
+    all_knowledge = collect_notes(
+        binding.project_root / "Knowledge", "Knowledge", binding.vault_path, KNOWLEDGE_LIMIT * 3
+    )
+    knowledge = select_knowledge_notes(all_knowledge, papers)
+    canvas = render_canvas(project_kb.titleize_slug(binding.project_id), papers, knowledge)
+
+    output_path = binding.project_root / args.output
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    output_path.write_text(json.dumps(canvas, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
+    print(
+        json.dumps(
+            {
+                "project_id": binding.project_id,
+                "output": str(output_path),
+                "paper_count": len(papers),
+                "knowledge_count": len(knowledge),
+            },
+            ensure_ascii=False,
+        )
+    )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/.agents/skills/obsidian-literature-workflow/scripts/build_literature_graph.py b/.agents/skills/obsidian-literature-workflow/scripts/build_literature_graph.py
new file mode 100755
index 0000000..cfa1ec1
--- /dev/null
+++ b/.agents/skills/obsidian-literature-workflow/scripts/build_literature_graph.py
@@ -0,0 +1,271 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import argparse
+import re
+import sys
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+PAPER_LIMIT = 48
+EDGE_LIMIT = 160
+WIKILINK_RE = re.compile(r"\[\[([^\]|#]+)(?:#[^\]|]+)?(?:\|[^\]]+)?\]\]")
+LIST_KEYS = {
+    'authors', 'keywords', 'concepts', 'methods',
+    'related_papers', 'linked_experiments', 'linked_results'
+}
+
+
+@dataclass(frozen=True)
+class PaperNote:
+    title: str
+    note_relpath: str
+    file_name: str
+    concepts: tuple[str, ...]
+    methods: tuple[str, ...]
+    related_papers: tuple[str, ...]
+    linked_experiments: tuple[str, ...]
+    linked_results: tuple[str, ...]
+    wikilinks: tuple[str, ...]
+
+
+def load_project_kb_module() -> Any:
+    script_dir = Path(__file__).resolve().parents[2] / 'obsidian-project-memory' / 'scripts'
+    sys.path.insert(0, str(script_dir))
+    import project_kb  # type: ignore
+    return project_kb
+
+
+def parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser(description='Build a literature graph note for the bound Obsidian project.')
+    parser.add_argument('--cwd', default='.')
+    parser.add_argument('--project-id', default='')
+    parser.add_argument('--output', default='Knowledge/Literature-Map.md')
+    return parser.parse_args()
+
+
+def parse_frontmatter(text: str) -> dict[str, Any]:
+    if not text.startswith('---\n'):
+        return {}
+    end = text.find('\n---\n', 4)
+    if end == -1:
+        return {}
+    lines = text[4:end].splitlines()
+    data: dict[str, Any] = {}
+    current_key: str | None = None
+    for raw_line in lines:
+        if not raw_line.strip():
+            continue
+        if raw_line.startswith('  - ') or raw_line.startswith('- '):
+            if current_key and current_key in LIST_KEYS:
+                data.setdefault(current_key, []).append(raw_line.split('- ', 1)[1].strip().strip('"'))
+            continue
+        if ':' not in raw_line:
+            current_key = None
+            continue
+        key, value = raw_line.split(':', 1)
+        key = key.strip()
+        value = value.strip()
+        current_key = key
+        if not value:
+            if key in LIST_KEYS:
+                data[key] = []
+            else:
+                data[key] = ''
+            continue
+        data[key] = value.strip('"')
+    return data
+
+
+def body_without_frontmatter(text: str) -> str:
+    if not text.startswith('---\n'):
+        return text
+    end = text.find('\n---\n', 4)
+    if end == -1:
+        return text
+    return text[end + 5:]
+
+
+def normalize_note_target(value: str) -> str:
+    cleaned = value.strip()
+    if cleaned.endswith('.md'):
+        cleaned = cleaned[:-3]
+    if cleaned.startswith('./'):
+        cleaned = cleaned[2:]
+    return cleaned
+
+
+def mermaid_id(prefix: str, value: str) -> str:
+    slug = re.sub(r'[^a-zA-Z0-9]+', '_', value).strip('_').lower()
+    if not slug:
+        slug = 'node'
+    return f'{prefix}_{slug[:48]}'
+
+
+def extract_wikilinks(text: str) -> tuple[str, ...]:
+    seen: list[str] = []
+    for match in WIKILINK_RE.findall(text):
+        target = normalize_note_target(match)
+        if target not in seen:
+            seen.append(target)
+    return tuple(seen)
+
+
+def collect_paper_notes(project_root: Path) -> list[PaperNote]:
+    papers_dir = project_root / 'Papers'
+    notes: list[PaperNote] = []
+    if not papers_dir.exists():
+        return notes
+    for path in sorted(papers_dir.glob('*.md'))[:PAPER_LIMIT]:
+        text = path.read_text(encoding='utf-8')
+        frontmatter = parse_frontmatter(text)
+        body = body_without_frontmatter(text)
+        title = str(frontmatter.get('title') or path.stem.replace('-', ' '))
+        notes.append(
+            PaperNote(
+                title=title,
+                note_relpath=f'Papers/{path.name}',
+                file_name=path.name,
+                concepts=tuple(frontmatter.get('concepts', [])),
+                methods=tuple(frontmatter.get('methods', [])),
+                related_papers=tuple(normalize_note_target(v) for v in frontmatter.get('related_papers', [])),
+                linked_experiments=tuple(normalize_note_target(v) for v in frontmatter.get('linked_experiments', [])),
+                linked_results=tuple(normalize_note_target(v) for v in frontmatter.get('linked_results', [])),
+                wikilinks=extract_wikilinks(body),
+            )
+        )
+    return notes
+
+
+def render_mermaid(notes: list[PaperNote]) -> str:
+    lines: list[str] = ['graph LR']
+    paper_index = {note.note_relpath[:-3]: note for note in notes}
+    seen_edges: set[tuple[str, str, str]] = set()
+
+    for note in notes:
+        paper_node = mermaid_id('paper', note.file_name)
+        lines.append(f'    {paper_node}["{note.title}"]')
+
+        for concept in note.concepts:
+            concept_node = mermaid_id('concept', concept)
+            lines.append(f'    {concept_node}(("{concept}"))')
+            edge = (paper_node, concept_node, 'concept')
+            if edge not in seen_edges and len(seen_edges) < EDGE_LIMIT:
+                lines.append(f'    {paper_node} -->|concept| {concept_node}')
+                seen_edges.add(edge)
+
+        for method in note.methods:
+            method_node = mermaid_id('method', method)
+            lines.append(f'    {method_node}{{"{method}"}}')
+            edge = (paper_node, method_node, 'method')
+            if edge not in seen_edges and len(seen_edges) < EDGE_LIMIT:
+                lines.append(f'    {paper_node} -->|method| {method_node}')
+                seen_edges.add(edge)
+
+        related_targets = set(note.related_papers)
+        related_targets.update(target for target in note.wikilinks if target.startswith('Papers/'))
+        for target in sorted(related_targets):
+            target_note = paper_index.get(target)
+            if not target_note:
+                continue
+            target_node = mermaid_id('paper', target_note.file_name)
+            edge = (paper_node, target_node, 'related')
+            if edge not in seen_edges and len(seen_edges) < EDGE_LIMIT:
+                lines.append(f'    {paper_node} -->|related| {target_node}')
+                seen_edges.add(edge)
+
+        for experiment in note.linked_experiments:
+            exp_node = mermaid_id('experiment', experiment)
+            label = experiment.split('/')[-1]
+            lines.append(f'    {exp_node}["{label}"]')
+            edge = (paper_node, exp_node, 'experiment')
+            if edge not in seen_edges and len(seen_edges) < EDGE_LIMIT:
+                lines.append(f'    {paper_node} -->|experiment| {exp_node}')
+                seen_edges.add(edge)
+
+        for result in note.linked_results:
+            result_node = mermaid_id('result', result)
+            label = result.split('/')[-1]
+            lines.append(f'    {result_node}["{label}"]')
+            edge = (paper_node, result_node, 'result')
+            if edge not in seen_edges and len(seen_edges) < EDGE_LIMIT:
+                lines.append(f'    {paper_node} -->|result| {result_node}')
+                seen_edges.add(edge)
+
+    deduped: list[str] = []
+    seen_lines: set[str] = set()
+    for line in lines:
+        if line not in seen_lines:
+            deduped.append(line)
+            seen_lines.add(line)
+    return '\n'.join(deduped)
+
+
+def render_map_note(project_id: str, notes: list[PaperNote], mermaid_graph: str, updated: str) -> str:
+    paper_bullets = '\n'.join(f'- [[{note.note_relpath[:-3]}]]' for note in notes) or '- No paper notes yet.'
+    concept_counts: dict[str, int] = {}
+    method_counts: dict[str, int] = {}
+    for note in notes:
+        for concept in note.concepts:
+            concept_counts[concept] = concept_counts.get(concept, 0) + 1
+        for method in note.methods:
+            method_counts[method] = method_counts.get(method, 0) + 1
+    concept_lines = '\n'.join(
+        f'- {name} ({count})' for name, count in sorted(concept_counts.items(), key=lambda kv: (-kv[1], kv[0]))[:12]
+    ) or '- No concept clusters recorded yet.'
+    method_lines = '\n'.join(
+        f'- {name} ({count})' for name, count in sorted(method_counts.items(), key=lambda kv: (-kv[1], kv[0]))[:12]
+    ) or '- No method clusters recorded yet.'
+
+    return f'''---
+type: knowledge
+title: Literature Map
+project: {project_id}
+updated: {updated}
+---
+
+# Literature Map
+
+## Purpose
+- Provide a lightweight literature knowledge map for the current project.
+- Help navigate paper notes, concept clusters, and downstream experiment/result hooks.
+
+## Paper notes included
+{paper_bullets}
+
+## Concept clusters
+{concept_lines}
+
+## Method clusters
+{method_lines}
+
+## Graph
+```mermaid
+{mermaid_graph}
+```
+
+## How to use
+- Open the linked paper notes above for detailed reading notes.
+- Use Obsidian backlinks/local graph on top of these wikilinks.
+- Refresh this note after a batch Zotero ingestion or major paper-note update.
+'''
+
+
+def main() -> None:
+    args = parse_args()
+    project_kb = load_project_kb_module()
+    repo_root = project_kb.find_repo_root(Path(args.cwd).resolve())
+    binding = project_kb.resolve_binding(repo_root, args.project_id or None)
+    notes = collect_paper_notes(binding.project_root)
+    output_rel = args.output if args.output.endswith('.md') else f'{args.output}.md'
+    output_path = binding.project_root / output_rel
+    mermaid_graph = render_mermaid(notes)
+    content = render_map_note(binding.project_id, notes, mermaid_graph, project_kb.now_iso())
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    output_path.write_text(content.rstrip() + '\n', encoding='utf-8')
+    print(output_path)
+
+
+if __name__ == '__main__':
+    main()