indirect_call edges from module-top-level code keep absolute-path-derived source id (id_remap skips raw_calls)

[phhktb]

Summary

Running the full extraction pipeline on a ~420-file JS/TS project, graphify.diagnostics.diagnose_extraction reports 586 dangling-endpoint edges. I traced the indirect_call subset (58 edges, all with a missing source) to a concrete bug in the id-remap pass in extract.py.

Confirmed bug: id_remap is applied to all_nodes/all_edges but never to all_raw_calls

• extractors/engine.py:2342 creates a whole-file "module" node: file_nid = _make_id(str(path)), i.e. an id derived directly from the (often absolute) filesystem path.
• That file_nid is used as scope_nid/caller_nid for indirect_call edges emitted from module-top-level code (calls not inside any function), e.g. via _emit_indirect_ref(ident, file_nid, js_module_bound, "collection") around engine.py:4468-4502. These go through raw_calls (all_raw_calls) for cross-file resolution.
• extract.py:4661-4753 builds an id_remap dict that maps exactly this absolute-path-derived id (_make_id(str(path)) / _make_id(str(path.resolve()))) to the canonical relative form _file_node_id(rel) — this is the fix for graph.json edge endpoints still leak absolute-path-derived file ids #502.
• extract.py:4754-4762 applies id_remap to all_nodes and all_edges only:

  if id_remap:
      for n in all_nodes:
          if n.get("id") in id_remap:
              n["id"] = id_remap[n["id"]]
      for e in all_edges:
          if e.get("source") in id_remap:
              e["source"] = id_remap[e["source"]]
          if e.get("target") in id_remap:
              e["target"] = id_remap[e["target"]]

  all_raw_calls is never touched by this loop.
• The other remap (sym_remap, built from prefix_remap) does patch raw_calls[caller_nid] (extract.py:4820-4823), but sym_remap is keyed off _file_node_id(path) (the relative-form prefix), which never matches the absolute-form file_nid. So neither remap pass fixes raw_calls[caller_nid] for this id shape.
• Net effect: when a raw_calls entry with caller_nid = file_nid (absolute-derived) is later resolved into a real indirect_call edge, its source keeps the stale absolute-path id — which matches no node in all_nodes (those were remapped), so it dangles.

Example (Windows, absolute input paths)

indirect_call: c_users_x_documents_github_myproj_src_index_js -> src_obfuscators_nonvm_obfuscatewithoutvm_obfuscatewithoutvm
  (source_file=src/index.js, source_location=L47)

Expected source id: src_index (matches the canonical file-node id used everywhere else).

Secondary observation (not root-caused, flagging for investigation)

Also saw ~50 dangling edges where an imports edge targets a barrel/re-export index.js file's re-exported symbol id instead of the file where the symbol is actually defined, e.g.:

imports: src_obfuscators_nonvm_nonvmbackenddefinition -> src_obfuscators_shared_backend_index_createbackendadapter

createBackendAdapter is defined in a sibling file under shared/backend/ and re-exported through index.js. There's existing re_exports/edge_alias_candidates repoint logic around extract.py:4824-4858 that looks like it's meant to handle exactly this shape, but I haven't traced why it doesn't catch this case — didn't want to guess, so flagging separately from the confirmed bug above.

Environment

• graphify (graphifyy) installed via uv tool install
• OS: Windows 11
• Corpus: ~422 JS/TS files, extracted via graphify.extract.extract(code_files, cache_root=Path('.')) with absolute Path inputs from graphify.detect.detect()
• Detected via: graphify.diagnostics.diagnose_extraction(extraction, directed=False, root='.')

[safishamsi]

Fixed in v0.9.29. id_remap is now applied to raw_calls caller_nid, so module-top-level indirect_call sources canonicalize to the real file node instead of an absolute-path-derived id; a general backstop also rewrites any remaining absolute-derived id/endpoint. https://github.com/Graphify-Labs/graphify/releases/tag/v0.9.29