@oriro/orirocli 0.1.11 → 0.1.12

package/skills/graphify/benchmark.py

@@ -1,155 +0,0 @@
-"""Token-reduction benchmark - measures how much context graphify saves vs naive full-corpus approach."""
-from __future__ import annotations
-import json
-import sys
-from pathlib import Path
-import networkx as nx
-from networkx.readwrite import json_graph
-
-from graphify.build import edge_data
-from graphify.serve import _query_terms
-
-
-_CHARS_PER_TOKEN = 4  # standard approximation
-
-
-def _safe(unicode_char: str, ascii_fallback: str) -> str:
-    """Return unicode_char if stdout can encode it, else ascii_fallback.
-
-    Windows consoles often default to cp1252 which cannot encode box-drawing
-    or arrow glyphs; printing them raises UnicodeEncodeError mid-output.
-    """
-    encoding = getattr(sys.stdout, "encoding", None) or ""
-    try:
-        unicode_char.encode(encoding)
-        return unicode_char
-    except (UnicodeEncodeError, LookupError):
-        return ascii_fallback
-
-
-def _hr(width: int = 50) -> str:
-    """Horizontal rule that survives non-UTF-8 stdout (e.g. Windows cp1252 console)."""
-    return _safe("─", "-") * width
-
-
-def _estimate_tokens(text: str) -> int:
-    return max(1, len(text) // _CHARS_PER_TOKEN)
-
-
-def _query_subgraph_tokens(G: nx.Graph, question: str, depth: int = 3) -> int:
-    """Run BFS from best-matching nodes and return estimated tokens in the subgraph context."""
-    terms = _query_terms(question)
-    scored = []
-    for nid, data in G.nodes(data=True):
-        label = data.get("label", "").lower()
-        score = sum(1 for t in terms if t in label)
-        if score > 0:
-            scored.append((score, nid))
-    scored.sort(reverse=True)
-    start_nodes = [nid for _, nid in scored[:3]]
-    if not start_nodes:
-        return 0
-
-    visited: set[str] = set(start_nodes)
-    frontier = set(start_nodes)
-    edges_seen: list[tuple] = []
-    for _ in range(depth):
-        next_frontier: set[str] = set()
-        for n in frontier:
-            for neighbor in G.neighbors(n):
-                if neighbor not in visited:
-                    next_frontier.add(neighbor)
-                    edges_seen.append((n, neighbor))
-        visited.update(next_frontier)
-        frontier = next_frontier
-
-    lines = []
-    for nid in visited:
-        d = G.nodes[nid]
-        lines.append(f"NODE {d.get('label', nid)} src={d.get('source_file', '')} loc={d.get('source_location', '')}")
-    for u, v in edges_seen:
-        if u in visited and v in visited:
-            d = edge_data(G, u, v)
-            lines.append(f"EDGE {G.nodes[u].get('label', u)} --{d.get('relation', '')}--> {G.nodes[v].get('label', v)}")
-
-    return _estimate_tokens("\n".join(lines))
-
-
-_SAMPLE_QUESTIONS = [
-    "how does authentication work",
-    "what is the main entry point",
-    "how are errors handled",
-    "what connects the data layer to the api",
-    "what are the core abstractions",
-]
-
-
-def run_benchmark(
-    graph_path: str = "graphify-out/graph.json",
-    corpus_words: int | None = None,
-    questions: list[str] | None = None,
-) -> dict:
-    """Measure token reduction: corpus tokens vs graphify query tokens.
-
-    Args:
-        graph_path: path to the built graph
-        corpus_words: total word count from detect() output; if None, estimated from graph
-        questions: list of questions to benchmark; defaults to _SAMPLE_QUESTIONS
-
-    Returns dict with: corpus_tokens, avg_query_tokens, reduction_ratio, per_question
-    """
-    from graphify.security import check_graph_file_size_cap
-    check_graph_file_size_cap(Path(graph_path))
-    data = json.loads(Path(graph_path).read_text(encoding="utf-8"))
-    try:
-        G = json_graph.node_link_graph(data, edges="links")
-    except TypeError:
-        G = json_graph.node_link_graph(data)
-
-    if corpus_words is None:
-        # Rough estimate: each node label is ~3 words, plus source context
-        corpus_words = G.number_of_nodes() * 50
-
-    corpus_tokens = corpus_words * 100 // 75  # words → tokens (100 words ≈ 133 tokens)
-
-    qs = questions or _SAMPLE_QUESTIONS
-    per_question = []
-    for q in qs:
-        qt = _query_subgraph_tokens(G, q)
-        if qt > 0:
-            per_question.append({"question": q, "query_tokens": qt, "reduction": round(corpus_tokens / qt, 1)})
-
-    if not per_question:
-        return {"error": "No matching nodes found for sample questions. Build the graph first."}
-
-    avg_query_tokens = sum(p["query_tokens"] for p in per_question) // len(per_question)
-    reduction_ratio = round(corpus_tokens / avg_query_tokens, 1) if avg_query_tokens > 0 else 0
-
-    return {
-        "corpus_tokens": corpus_tokens,
-        "corpus_words": corpus_words,
-        "nodes": G.number_of_nodes(),
-        "edges": G.number_of_edges(),
-        "avg_query_tokens": avg_query_tokens,
-        "reduction_ratio": reduction_ratio,
-        "per_question": per_question,
-    }
-
-
-def print_benchmark(result: dict) -> None:
-    """Print a human-readable benchmark report."""
-    if "error" in result:
-        print(f"Benchmark error: {result['error']}")
-        return
-
-    print(f"\ngraphify token reduction benchmark")
-    print(_hr(50))
-    arrow = _safe("→", "->")
-    print(f"  Corpus:          {result['corpus_words']:,} words {arrow} ~{result['corpus_tokens']:,} tokens (naive)")
-    print(f"  Graph:           {result['nodes']:,} nodes, {result['edges']:,} edges")
-    print(f"  Avg query cost:  ~{result['avg_query_tokens']:,} tokens")
-    print(f"  Reduction:       {result['reduction_ratio']}x fewer tokens per query")
-    print(f"\n  Per question:")
-    for p in result["per_question"]:
-        print(f"    [{p['reduction']}x] {p['question'][:55]}")
-    print()

package/skills/graphify/build.py

@@ -1,487 +0,0 @@
-# assemble node+edge dicts into a NetworkX graph, preserving edge direction
-#
-# Node deduplication — three layers:
-#
-# 1. Within a file (AST): each extractor tracks a `seen_ids` set. A node ID is
-#    emitted at most once per file, so duplicate class/function definitions in
-#    the same source file are collapsed to the first occurrence.
-#
-# 2. Between files (build): NetworkX G.add_node() is idempotent — calling it
-#    twice with the same ID overwrites the attributes with the second call's
-#    values. Nodes are added in extraction order (AST first, then semantic),
-#    so if the same entity is extracted by both passes the semantic node
-#    silently overwrites the AST node. This is intentional: semantic nodes
-#    carry richer labels and cross-file context, while AST nodes have precise
-#    source_location. If you need to change the priority, reorder extractions
-#    passed to build().
-#
-# 3. Semantic merge (skill): before calling build(), the skill merges cached
-#    and new semantic results using an explicit `seen` set keyed on node["id"],
-#    so duplicates across cache hits and new extractions are resolved there
-#    before any graph construction happens.
-#
-from __future__ import annotations
-import json
-import os
-import re
-import sys
-import unicodedata
-from pathlib import Path
-import networkx as nx
-from .validate import validate_extraction
-
-
-# Synonym mapper for known invalid file_type values that LLM subagents commonly
-# emit. Keeps semantic intent close (markdown→document, tool→code) and falls
-# back to "concept" for any other invalid value (see #840).
-_FILE_TYPE_SYNONYMS = {
-    "markdown": "document",
-    "text": "document",
-    "tool": "code",
-    "library": "code",
-    "pattern": "concept",
-    "principle": "concept",
-    "constraint": "concept",
-    "tech": "concept",
-    "technology": "concept",
-    "data-source": "concept",
-    "data_source": "concept",
-    "gotcha": "concept",
-    "framework": "concept",
-}
-
-
-def _normalize_id(s: str) -> str:
-    r"""Normalize an ID string the same way extract._make_id does.
-
-    Used to reconcile edge endpoints when the LLM generates IDs with slightly
-    different punctuation or casing than the AST extractor. Must stay in sync
-    with extract._make_id — NFKC normalization, \w with re.UNICODE, underscore
-    collapse, and casefold must all match (#811).
-    """
-    s = unicodedata.normalize("NFKC", s)
-    cleaned = re.sub(r"[^\w]+", "_", s, flags=re.UNICODE)
-    cleaned = re.sub(r"_+", "_", cleaned)
-    return cleaned.strip("_").casefold()
-
-
-def _norm_source_file(p: str | None, root: str | None = None) -> str | None:
-    """Normalize path separators and relativize absolute paths.
-
-    Converts backslashes to forward slashes (Windows compatibility) and, when
-    root is provided, strips the absolute prefix from paths produced by semantic
-    subagents so source_file is always repo-relative (fixes #932).
-    """
-    if not p:
-        return p
-    p = p.replace("\\", "/")
-    if root and os.path.isabs(p):
-        try:
-            p = Path(p).relative_to(root).as_posix()
-        except ValueError:
-            pass
-    return p
-
-
-def edge_data(G: nx.Graph, u: str, v: str) -> dict:
-    """Return one edge attribute dict for (u, v), tolerating MultiGraph.
-
-    For MultiGraph/MultiDiGraph there can be multiple parallel edges;
-    this returns the first one (sufficient for callers that only need
-    relation/confidence for rendering). Fixes #796.
-    """
-    raw = G[u][v]
-    if isinstance(G, (nx.MultiGraph, nx.MultiDiGraph)):
-        return next(iter(raw.values()), {})
-    return raw
-
-
-def edge_datas(G: nx.Graph, u: str, v: str) -> list[dict]:
-    """Return every edge attribute dict for (u, v); always a list."""
-    raw = G[u][v]
-    if isinstance(G, (nx.MultiGraph, nx.MultiDiGraph)):
-        return list(raw.values())
-    return [raw]
-
-
-def build_from_json(extraction: dict, *, directed: bool = False, root: str | Path | None = None) -> nx.Graph:
-    """Build a NetworkX graph from an extraction dict.
-
-    directed=True produces a DiGraph that preserves edge direction (source→target).
-    directed=False (default) produces an undirected Graph for backward compatibility.
-    root: if given, absolute source_file paths from semantic subagents are made
-        relative to root so all nodes share a consistent path key (#932).
-    """
-    _root = str(Path(root).resolve()) if root else None
-    # NetworkX <= 3.1 serialised edges as "links"; remap to "edges" for compatibility.
-    if "edges" not in extraction and "links" in extraction:
-        extraction = dict(extraction, edges=extraction["links"])
-
-    # Canonicalize legacy node/edge schema before validation.
-    for node in extraction.get("nodes", []):
-        if not isinstance(node, dict):
-            continue
-        if "source" in node and "source_file" not in node:
-            # Count edges that reference this node so the warning is actionable (#479)
-            node_id = node.get("id", "?")
-            affected_edges = sum(
-                1 for e in extraction.get("edges", [])
-                if e.get("source") == node_id or e.get("target") == node_id
-            )
-            print(
-                f"[graphify] WARNING: node '{node_id}' uses field 'source' instead of "
-                f"'source_file' — {affected_edges} edge(s) may be misrouted. "
-                f"Rename the field to 'source_file' to silence this warning.",
-                file=sys.stderr,
-            )
-            node["source_file"] = node.pop("source")
-        # Default missing/None file_type to "concept" so legacy graph.json
-        # entries (and stub nodes preserved by `_rebuild_code` from older
-        # graphify versions that didn't always populate file_type) don't
-        # trigger spurious "invalid file_type 'None'" validator warnings (#660).
-        if node.get("file_type") in (None, ""):
-            node["file_type"] = "concept"
-        ft = node.get("file_type", "")
-        if ft and ft not in {"code", "document", "paper", "image", "rationale", "concept"}:
-            node["file_type"] = _FILE_TYPE_SYNONYMS.get(ft, "concept")
-
-    errors = validate_extraction(extraction)
-    # Dangling edges (stdlib/external imports) are expected - only warn about real schema errors.
-    real_errors = [e for e in errors if "does not match any node id" not in e]
-    if real_errors:
-        print(f"[graphify] Extraction warning ({len(real_errors)} issues): {real_errors[0]}", file=sys.stderr)
-    G: nx.Graph = nx.DiGraph() if directed else nx.Graph()
-    for node in extraction.get("nodes", []):
-        if "source_file" in node:
-            node["source_file"] = _norm_source_file(node["source_file"], _root)
-        G.add_node(node["id"], **{k: v for k, v in node.items() if k != "id"})
-    node_set = set(G.nodes())
-
-    # #1145: merge semantic ghost-duplicate nodes into AST nodes.
-    # When AST and semantic extractors emit different IDs for the same symbol
-    # (one has source_location=L<n>, the other has source_location=None), find
-    # pairs that share (source_file basename, label) and collapse the semantic
-    # copy into the AST copy so edges re-point to a single node.
-    # Two passes: first collect all AST (located) nodes, then find ghosts.
-    _loc_nodes: dict[tuple[str, str], str] = {}   # (basename, label) -> AST node id
-    _noloc_nodes: dict[tuple[str, str], str] = {}  # (basename, label) -> semantic node id
-    for nid in node_set:
-        attrs = G.nodes[nid]
-        label = str(attrs.get("label", "")).strip()
-        sf = str(attrs.get("source_file", ""))
-        basename = Path(sf).name if sf else ""
-        if not label or not basename:
-            continue
-        if attrs.get("source_location"):
-            _loc_nodes[(basename, label)] = nid
-    for nid in node_set:
-        attrs = G.nodes[nid]
-        label = str(attrs.get("label", "")).strip()
-        sf = str(attrs.get("source_file", ""))
-        basename = Path(sf).name if sf else ""
-        if not label or not basename or attrs.get("source_location"):
-            continue
-        key = (basename, label)
-        if key in _loc_nodes and _loc_nodes[key] != nid:
-            _noloc_nodes[key] = nid
-    # For every ghost that has an AST counterpart, record a remap.
-    _ghost_remap: dict[str, str] = {}  # ghost_id -> canonical_id
-    for key, sem_id in _noloc_nodes.items():
-        ast_id = _loc_nodes.get(key)
-        if ast_id is not None:
-            _ghost_remap[sem_id] = ast_id
-    # Remove ghost nodes from the graph; edges will be re-pointed via norm_to_id.
-    for ghost_id in _ghost_remap:
-        G.remove_node(ghost_id)
-        node_set.discard(ghost_id)
-
-    # Normalized ID map: lets edges survive when the LLM generates IDs with
-    # slightly different casing or punctuation than the AST extractor.
-    # e.g. "Session_ValidateToken" maps to "session_validatetoken".
-    norm_to_id: dict[str, str] = {_normalize_id(nid): nid for nid in node_set}
-    # Also map ghost IDs to their canonical AST replacements.
-    for ghost_id, canonical_id in _ghost_remap.items():
-        norm_to_id[_normalize_id(ghost_id)] = canonical_id
-        norm_to_id[ghost_id] = canonical_id
-    # Iterate edges in a deterministic order. The graph is undirected and stores
-    # direction in _src/_tgt; when two edges collapse onto the same node pair the
-    # last write wins, so an unstable iteration order flips _src/_tgt run-to-run
-    # and makes the serialized graph churn. Sorting fixes the last-write outcome.
-    for edge in sorted(
-        extraction.get("edges", []),
-        key=lambda e: (
-            str(e.get("source", e.get("from", ""))),
-            str(e.get("target", e.get("to", ""))),
-            str(e.get("relation", "")),
-        ),
-    ):
-        if "source" not in edge and "from" in edge:
-            edge["source"] = edge["from"]
-        if "target" not in edge and "to" in edge:
-            edge["target"] = edge["to"]
-        if "source" not in edge or "target" not in edge:
-            continue
-        src, tgt = edge["source"], edge["target"]
-        # Remap mismatched IDs via normalization before dropping the edge.
-        if src not in node_set:
-            src = norm_to_id.get(_normalize_id(src), src)
-        if tgt not in node_set:
-            tgt = norm_to_id.get(_normalize_id(tgt), tgt)
-        if src not in node_set or tgt not in node_set:
-            continue  # skip edges to external/stdlib nodes - expected, not an error
-        attrs = {k: v for k, v in edge.items() if k not in ("source", "target")}
-        if "source_file" in attrs:
-            attrs["source_file"] = _norm_source_file(attrs["source_file"], _root)
-        # Drop cross-language INFERRED `calls` edges — same short names (render,
-        # parse, etc.) appear across language boundaries in multi-language chunks,
-        # producing phantom edges that don't represent real call relationships.
-        if attrs.get("relation") == "calls" and attrs.get("confidence") == "INFERRED":
-            _LANG_FAMILY: dict[str, str] = {
-                ".py": "py", ".pyi": "py",
-                ".js": "js", ".mjs": "js", ".cjs": "js", ".jsx": "js",
-                ".ts": "js", ".tsx": "js",
-                ".go": "go", ".rs": "rs",
-                ".java": "jvm", ".kt": "jvm", ".scala": "jvm", ".groovy": "jvm",
-                ".c": "c", ".h": "c", ".cc": "cpp", ".cpp": "cpp", ".hpp": "cpp",
-                ".rb": "rb", ".php": "php", ".cs": "cs", ".swift": "swift", ".lua": "lua",
-            }
-            src_ext = Path(G.nodes[src].get("source_file") or "").suffix.lower()
-            tgt_ext = Path(G.nodes[tgt].get("source_file") or "").suffix.lower()
-            if src_ext and tgt_ext and _LANG_FAMILY.get(src_ext) != _LANG_FAMILY.get(tgt_ext):
-                continue
-        # Preserve original edge direction - undirected graphs lose it otherwise,
-        # causing display functions to show edges backwards.
-        attrs["_src"] = src
-        attrs["_tgt"] = tgt
-        # When the graph is undirected and the same node pair appears twice with
-        # the same relation but opposite directions (e.g. a `calls` b and b `calls` a),
-        # nx.Graph collapses them into one edge. The deterministic sort above means
-        # the lexicographically-later direction would systematically overwrite the
-        # earlier one's _src/_tgt, silently flipping the surviving edge's caller
-        # and callee. First-seen direction wins instead — drop the redundant
-        # reverse-direction duplicate so the original direction is preserved (#1061).
-        if not G.is_directed() and G.has_edge(src, tgt):
-            existing = edge_data(G, src, tgt)
-            if existing.get("relation") == attrs.get("relation") and (
-                existing.get("_src") == tgt and existing.get("_tgt") == src
-            ):
-                continue
-        G.add_edge(src, tgt, **attrs)
-    hyperedges = extraction.get("hyperedges", [])
-    if hyperedges:
-        G.graph["hyperedges"] = hyperedges
-    return G
-
-
-def build(
-    extractions: list[dict],
-    *,
-    directed: bool = False,
-    dedup: bool = True,
-    dedup_llm_backend: str | None = None,
-    root: str | Path | None = None,
-) -> nx.Graph:
-    """Merge multiple extraction results into one graph.
-
-    directed=True produces a DiGraph that preserves edge direction (source→target).
-    directed=False (default) produces an undirected Graph for backward compatibility.
-    dedup=True (default) runs entity deduplication before building the graph.
-    dedup_llm_backend: if set (e.g. "gemini", "claude", or "kimi"), uses LLM to resolve
-        ambiguous pairs in the 75–92 Jaro-Winkler score zone.
-    root: if given, absolute source_file paths are made relative to root (#932).
-
-    Extractions are merged in order. For nodes with the same ID, the last
-    extraction's attributes win (NetworkX add_node overwrites). Pass AST
-    results before semantic results so semantic labels take precedence, or
-    reverse the order if you prefer AST source_location precision to win.
-    """
-    from graphify.dedup import deduplicate_entities
-    combined: dict = {"nodes": [], "edges": [], "hyperedges": [], "input_tokens": 0, "output_tokens": 0}
-    for ext in extractions:
-        combined["nodes"].extend(ext.get("nodes", []))
-        combined["edges"].extend(ext.get("edges", []))
-        combined["hyperedges"].extend(ext.get("hyperedges", []))
-        combined["input_tokens"] += ext.get("input_tokens", 0)
-        combined["output_tokens"] += ext.get("output_tokens", 0)
-    if dedup and combined["nodes"]:
-        combined["nodes"], combined["edges"] = deduplicate_entities(
-            combined["nodes"], combined["edges"], communities={},
-            dedup_llm_backend=dedup_llm_backend,
-        )
-    return build_from_json(combined, directed=directed, root=root)
-
-
-def _norm_label(label: str) -> str:
-    """Canonical dedup key — Unicode-aware, preserves CJK/word characters."""
-    label = unicodedata.normalize("NFKC", label)
-    return re.sub(r"[\W_ ]+", " ", label.casefold(), flags=re.UNICODE).strip()
-
-
-def deduplicate_by_label(nodes: list[dict], edges: list[dict]) -> tuple[list[dict], list[dict]]:
-    """Merge nodes that share a normalised label, rewriting edge references.
-
-    Prefers IDs without chunk suffixes (_c\\d+) and shorter IDs when tied.
-    Drops self-loops created by the merge. Called in build() automatically.
-    """
-    _CHUNK_SUFFIX = re.compile(r"_c\d+$")
-    canonical: dict[str, dict] = {}  # norm_label -> surviving node
-    remap: dict[str, str] = {}       # old_id -> surviving_id
-
-    for node in nodes:
-        key = _norm_label(node.get("label", node.get("id", "")))
-        if not key:
-            continue
-        existing = canonical.get(key)
-        if existing is None:
-            canonical[key] = node
-        else:
-            has_suffix = bool(_CHUNK_SUFFIX.search(node["id"]))
-            existing_has_suffix = bool(_CHUNK_SUFFIX.search(existing["id"]))
-            if has_suffix and not existing_has_suffix:
-                remap[node["id"]] = existing["id"]
-            elif existing_has_suffix and not has_suffix:
-                remap[existing["id"]] = node["id"]
-                canonical[key] = node
-            elif len(node["id"]) < len(existing["id"]):
-                remap[existing["id"]] = node["id"]
-                canonical[key] = node
-            else:
-                remap[node["id"]] = existing["id"]
-
-    if not remap:
-        return nodes, edges
-
-    print(f"[graphify] Deduplicated {len(remap)} duplicate node(s) by label.", file=sys.stderr)
-    deduped_nodes = list(canonical.values())
-    deduped_edges = []
-    for edge in edges:
-        e = dict(edge)
-        e["source"] = remap.get(e["source"], e["source"])
-        e["target"] = remap.get(e["target"], e["target"])
-        if e["source"] != e["target"]:
-            deduped_edges.append(e)
-    return deduped_nodes, deduped_edges
-
-
-def build_merge(
-    new_chunks: list[dict],
-    graph_path: str | Path = "graphify-out/graph.json",
-    prune_sources: list[str] | None = None,
-    *,
-    directed: bool = False,
-    dedup: bool = True,
-    dedup_llm_backend: str | None = None,
-    root: str | Path | None = None,
-) -> nx.Graph:
-    """Load existing graph.json, merge new chunks into it, and save back.
-
-    Never replaces - only grows (or prunes deleted-file nodes via prune_sources).
-    Safe to call repeatedly: existing nodes and edges are preserved.
-    root: if given, absolute source_file paths in new_chunks are made relative (#932).
-    """
-    graph_path = Path(graph_path)
-    if graph_path.exists():
-        # Read JSON directly instead of going through node_link_graph().
-        # The latter rebuilds an undirected nx.Graph and then enumerating
-        # edges() yields endpoints based on node insertion order, which
-        # silently flips directional edges (e.g. `calls`) when the callee
-        # was inserted before the caller. The _src/_tgt direction-preserving
-        # attrs are popped before saving in export.py, so going through the
-        # NetworkX round-trip loses direction permanently (#760).
-        from graphify.security import check_graph_file_size_cap
-        check_graph_file_size_cap(graph_path)
-        data = json.loads(graph_path.read_text(encoding="utf-8"))
-        links_key = "links" if "links" in data else "edges"
-        existing_nodes = list(data.get("nodes", []))
-        existing_edges = list(data.get(links_key, []))
-        base = [{"nodes": existing_nodes, "edges": existing_edges}]
-    else:
-        existing_nodes = []
-        base = []
-
-    all_chunks = base + list(new_chunks)
-    G = build(all_chunks, directed=directed, dedup=dedup, dedup_llm_backend=dedup_llm_backend, root=root)
-
-    # Prune nodes and edges from deleted source files
-    if prune_sources:
-        # Build a set containing both the raw form (matches nodes that kept
-        # absolute source_file) and the normalised relative form (matches nodes
-        # that were relativised by _norm_source_file at build time).
-        # .resolve() handles symlinked roots and redundant ".." / "./" segments
-        # so Path.relative_to() succeeds even when the scan root is a symlink.
-        # (#1007: manifest absolute paths vs graph relative source_file mismatch)
-        _root_str = str(Path(root).resolve()) if root is not None else None
-        prune_set: set[str] = set()
-        for p in prune_sources:
-            if not p:
-                continue
-            prune_set.add(p)
-            norm = _norm_source_file(p, _root_str)
-            if norm:
-                prune_set.add(norm)
-        to_remove = [
-            n for n, d in G.nodes(data=True)
-            if d.get("source_file") in prune_set
-        ]
-        G.remove_nodes_from(to_remove)
-        n_files = len(prune_sources)
-        n_nodes = len(to_remove)
-        if n_nodes:
-            print(
-                f"[graphify] Pruned {n_nodes} node(s) from {n_files} deleted source file(s).",
-                file=sys.stderr,
-            )
-
-        edges_to_remove = [
-            (u, v) for u, v, d in G.edges(data=True)
-            if d.get("source_file") in prune_set
-        ]
-        if edges_to_remove:
-            G.remove_edges_from(edges_to_remove)
-            print(
-                f"[graphify] Pruned {len(edges_to_remove)} edge(s) from deleted source file(s).",
-                file=sys.stderr,
-            )
-
-        if not n_nodes and not edges_to_remove:
-            print(
-                f"[graphify] {n_files} source file(s) deleted since last run — "
-                f"no matching nodes or edges in graph, already clean.",
-                file=sys.stderr,
-            )
-
-    # Safety check: refuse to shrink the graph silently (#479)
-    # Skip when dedup or prune_sources is active — shrinkage is intentional there.
-    if graph_path.exists() and not dedup and not prune_sources:
-        existing_n = len(existing_nodes)
-        new_n = G.number_of_nodes()
-        if new_n < existing_n:
-            raise ValueError(
-                f"graphify: build_merge would shrink graph from {existing_n} → {new_n} nodes. "
-                f"Pass prune_sources explicitly if you intend to remove nodes."
-            )
-
-    return G
-
-
-def prefix_graph_for_global(G: nx.Graph, repo_tag: str) -> nx.Graph:
-    """Return a copy of G with all node IDs prefixed with repo_tag::.
-
-    Labels are preserved unchanged (for display). A 'local_id' attribute
-    is added to each node so the original ID can be recovered. Edges are
-    rewritten to match the new prefixed IDs. The 'repo' attribute is set
-    on every node.
-    """
-    relabel = {n: f"{repo_tag}::{n}" for n in G.nodes}
-    H = nx.relabel_nodes(G, relabel, copy=True)
-    for node, data in H.nodes(data=True):
-        data["repo"] = repo_tag
-        data.setdefault("local_id", node.split("::", 1)[1])
-    return H
-
-
-def prune_repo_from_graph(G: nx.Graph, repo_tag: str) -> int:
-    """Remove all nodes tagged with repo_tag from G in-place. Returns count removed."""
-    to_remove = [n for n, d in G.nodes(data=True) if d.get("repo") == repo_tag]
-    G.remove_nodes_from(to_remove)
-    return len(to_remove)