@neat.is/core 0.4.6 → 0.4.8

package/dist/index.cjs

@@ -1017,6 +1017,24 @@ function isFrontierNode(graph, nodeId) {
   const attrs = graph.getNodeAttributes(nodeId);
   return attrs.type === import_types.NodeType.FrontierNode;
 }
+function resolveOwningService(graph, nodeId) {
+  if (!graph.hasNode(nodeId)) return null;
+  const attrs = graph.getNodeAttributes(nodeId);
+  if (attrs.type === import_types.NodeType.ServiceNode) {
+    return { id: nodeId, svc: attrs };
+  }
+  if (attrs.type === import_types.NodeType.FileNode) {
+    for (const edgeId of graph.inboundEdges(nodeId)) {
+      const e = graph.getEdgeAttributes(edgeId);
+      if (e.type !== import_types.EdgeType.CONTAINS) continue;
+      const owner = graph.getNodeAttributes(e.source);
+      if (owner.type === import_types.NodeType.ServiceNode) {
+        return { id: e.source, svc: owner };
+      }
+    }
+  }
+  return null;
+}
 function bestEdgeBySource(graph, edgeIds) {
   const best = /* @__PURE__ */ new Map();
   for (const id of edgeIds) {
@@ -1123,9 +1141,9 @@ function databaseRootCauseShape(graph, origin, walk) {
   const candidatePairs = compatPairs().filter((p) => p.engine === targetDb.engine);
   if (candidatePairs.length === 0) return null;
   for (const id of walk.path) {
-    const attrs = graph.getNodeAttributes(id);
-    if (attrs.type !== import_types.NodeType.ServiceNode) continue;
-    const svc = attrs;
+    const owner = resolveOwningService(graph, id);
+    if (!owner) continue;
+    const { id: serviceId3, svc } = owner;
     const deps = svc.dependencies ?? {};
     for (const pair of candidatePairs) {
       const declared = deps[pair.driver];
@@ -1138,7 +1156,7 @@ function databaseRootCauseShape(graph, origin, walk) {
       );
       if (!result.compatible) {
         return {
-          rootCauseNode: id,
+          rootCauseNode: serviceId3,
           rootCauseReason: result.reason ?? "incompatible driver",
           ...result.minDriverVersion ? {
             fixRecommendation: `Upgrade ${svc.name} ${pair.driver} driver to >= ${result.minDriverVersion}`
@@ -1151,9 +1169,9 @@ function databaseRootCauseShape(graph, origin, walk) {
 }
 function serviceRootCauseShape(graph, _origin, walk) {
   for (const id of walk.path) {
-    const attrs = graph.getNodeAttributes(id);
-    if (attrs.type !== import_types.NodeType.ServiceNode) continue;
-    const svc = attrs;
+    const owner = resolveOwningService(graph, id);
+    if (!owner) continue;
+    const { id: serviceId3, svc } = owner;
     const deps = svc.dependencies ?? {};
     const serviceNodeEngine = svc.nodeEngine;
     for (const constraint of nodeEngineConstraints()) {
@@ -1162,7 +1180,7 @@ function serviceRootCauseShape(graph, _origin, walk) {
       const result = checkNodeEngineConstraint(constraint, declared, serviceNodeEngine);
       if (!result.compatible && result.reason) {
         return {
-          rootCauseNode: id,
+          rootCauseNode: serviceId3,
           rootCauseReason: result.reason,
           ...result.requiredNodeVersion ? {
             fixRecommendation: `Bump ${svc.name}'s engines.node to >= ${result.requiredNodeVersion}`
@@ -1177,7 +1195,7 @@ function serviceRootCauseShape(graph, _origin, walk) {
       const result = checkPackageConflict(conflict, declared, requiredDeclared);
       if (!result.compatible && result.reason) {
         return {
-          rootCauseNode: id,
+          rootCauseNode: serviceId3,
           rootCauseReason: result.reason,
           fixRecommendation: `Upgrade ${svc.name}'s ${conflict.requires.name} to >= ${conflict.requires.minVersion}`
         };
@@ -1186,9 +1204,15 @@ function serviceRootCauseShape(graph, _origin, walk) {
   }
   return null;
 }
+function fileRootCauseShape(graph, origin, walk) {
+  const owner = resolveOwningService(graph, origin.id);
+  if (!owner) return null;
+  return serviceRootCauseShape(graph, owner.svc, walk);
+}
 var rootCauseShapes = {
   [import_types.NodeType.DatabaseNode]: databaseRootCauseShape,
-  [import_types.NodeType.ServiceNode]: serviceRootCauseShape
+  [import_types.NodeType.ServiceNode]: serviceRootCauseShape,
+  [import_types.NodeType.FileNode]: fileRootCauseShape
 };
 function getRootCause(graph, errorNodeId, errorEvent) {
   if (!graph.hasNode(errorNodeId)) return null;
@@ -1673,6 +1697,86 @@ function hostFromUrl(u) {
 function pickAddress(span) {
   return pickAttr(span, "server.address", "net.peer.name", "net.host.name") ?? hostFromUrl(pickAttr(span, "url.full", "http.url"));
 }
+var CODE_FILEPATH_ATTR = "code.filepath";
+var CODE_LINENO_ATTR = "code.lineno";
+var CODE_FUNCTION_ATTR = "code.function";
+function toPosix(p) {
+  return p.split("\\").join("/");
+}
+function languageForExt(relPath) {
+  const dot = relPath.lastIndexOf(".");
+  if (dot === -1) return void 0;
+  switch (relPath.slice(dot).toLowerCase()) {
+    case ".py":
+      return "python";
+    case ".ts":
+    case ".tsx":
+      return "typescript";
+    case ".js":
+    case ".jsx":
+    case ".mjs":
+    case ".cjs":
+      return "javascript";
+    default:
+      return void 0;
+  }
+}
+function relPathForRuntimeFile(filepath, serviceNode) {
+  let p = toPosix(filepath).replace(/^file:\/\//, "");
+  const root = serviceNode?.repoPath;
+  if (root && root !== "." && root.length > 0) {
+    const rootPosix = toPosix(root);
+    const anchor = `/${rootPosix}/`;
+    const idx = p.lastIndexOf(anchor);
+    if (idx !== -1) return p.slice(idx + anchor.length);
+    const base = rootPosix.split("/").filter(Boolean).pop();
+    if (base) {
+      const baseAnchor = `/${base}/`;
+      const bidx = p.lastIndexOf(baseAnchor);
+      if (bidx !== -1) return p.slice(bidx + baseAnchor.length);
+    }
+  }
+  p = p.replace(/^[A-Za-z]:/, "").replace(/^\/+/, "");
+  return p.length > 0 ? p : null;
+}
+function callSiteFromSpan(span, serviceNode) {
+  const filepath = span.attributes[CODE_FILEPATH_ATTR];
+  if (typeof filepath !== "string" || filepath.length === 0) return null;
+  const relPath = relPathForRuntimeFile(filepath, serviceNode);
+  if (!relPath) return null;
+  const linenoRaw = span.attributes[CODE_LINENO_ATTR];
+  const line = typeof linenoRaw === "number" && Number.isFinite(linenoRaw) ? linenoRaw : void 0;
+  const fnRaw = span.attributes[CODE_FUNCTION_ATTR];
+  const fn = typeof fnRaw === "string" && fnRaw.length > 0 ? fnRaw : void 0;
+  return { relPath, ...line !== void 0 ? { line } : {}, ...fn ? { fn } : {} };
+}
+function ensureObservedFileNode(graph, serviceName, serviceNodeId, callSite) {
+  const fileNodeId = (0, import_types3.fileId)(serviceName, callSite.relPath);
+  if (!graph.hasNode(fileNodeId)) {
+    const language = languageForExt(callSite.relPath);
+    const node = {
+      id: fileNodeId,
+      type: import_types3.NodeType.FileNode,
+      service: serviceName,
+      path: callSite.relPath,
+      ...language ? { language } : {},
+      discoveredVia: "otel"
+    };
+    graph.addNode(fileNodeId, node);
+  }
+  const containsId = makeObservedEdgeId(import_types3.EdgeType.CONTAINS, serviceNodeId, fileNodeId);
+  if (!graph.hasEdge(containsId)) {
+    const edge = {
+      id: containsId,
+      source: serviceNodeId,
+      target: fileNodeId,
+      type: import_types3.EdgeType.CONTAINS,
+      provenance: import_types3.Provenance.OBSERVED
+    };
+    graph.addEdgeWithKey(containsId, serviceNodeId, fileNodeId, edge);
+  }
+  return fileNodeId;
+}
 function makeObservedEdgeId(type, source, target) {
   return (0, import_types3.observedEdgeId)(source, target, type);
 }
@@ -1915,6 +2019,9 @@ async function handleSpan(ctx, span) {
   const sourceId = ensureServiceNode(ctx.graph, span.service, env);
   const isError = span.statusCode === 2;
   cacheSpanService(span, nowMs);
+  const sourceServiceNode = ctx.graph.getNodeAttributes(sourceId);
+  const callSite = callSiteFromSpan(span, sourceServiceNode);
+  const observedSource = () => callSite ? ensureObservedFileNode(ctx.graph, span.service, sourceId, callSite) : sourceId;
   let affectedNode = sourceId;
   if (span.dbSystem) {
     const host = pickAddress(span);
@@ -1924,7 +2031,7 @@ async function handleSpan(ctx, span) {
       const result = upsertObservedEdge(
         ctx.graph,
         import_types3.EdgeType.CONNECTS_TO,
-        sourceId,
+        observedSource(),
         targetId,
         ts,
         isError
@@ -1940,7 +2047,7 @@ async function handleSpan(ctx, span) {
         upsertObservedEdge(
           ctx.graph,
           import_types3.EdgeType.CALLS,
-          sourceId,
+          observedSource(),
           targetId,
           ts,
           isError
@@ -1952,7 +2059,7 @@ async function handleSpan(ctx, span) {
         upsertObservedEdge(
           ctx.graph,
           import_types3.EdgeType.CALLS,
-          sourceId,
+          observedSource(),
           frontierNodeId,
           ts,
           isError
@@ -3583,7 +3690,7 @@ async function addConfigNodes(graph, services, scanPath) {
 
 // src/extract/calls/index.ts
 init_cjs_shims();
-var import_types14 = require("@neat.is/types");
+var import_types15 = require("@neat.is/types");
 
 // src/extract/calls/http.ts
 init_cjs_shims();
@@ -3591,12 +3698,13 @@ var import_node_path20 = __toESM(require("path"), 1);
 var import_tree_sitter = __toESM(require("tree-sitter"), 1);
 var import_tree_sitter_javascript = __toESM(require("tree-sitter-javascript"), 1);
 var import_tree_sitter_python = __toESM(require("tree-sitter-python"), 1);
-var import_types9 = require("@neat.is/types");
+var import_types10 = require("@neat.is/types");
 
 // src/extract/calls/shared.ts
 init_cjs_shims();
 var import_node_fs13 = require("fs");
 var import_node_path19 = __toESM(require("path"), 1);
+var import_types9 = require("@neat.is/types");
 async function walkSourceFiles(dir) {
   const out = [];
   async function walk(current) {
@@ -3636,6 +3744,58 @@ function snippet(text, line) {
   const lines = text.split("\n");
   return (lines[line - 1] ?? "").trim();
 }
+function toPosix2(p) {
+  return p.split("\\").join("/");
+}
+function languageForPath(relPath) {
+  switch (import_node_path19.default.extname(relPath).toLowerCase()) {
+    case ".py":
+      return "python";
+    case ".ts":
+    case ".tsx":
+      return "typescript";
+    case ".js":
+    case ".jsx":
+    case ".mjs":
+    case ".cjs":
+      return "javascript";
+    default:
+      return void 0;
+  }
+}
+function ensureFileNode(graph, serviceName, serviceNodeId, relPath) {
+  let nodesAdded = 0;
+  let edgesAdded = 0;
+  const fileNodeId = (0, import_types9.fileId)(serviceName, relPath);
+  if (!graph.hasNode(fileNodeId)) {
+    const language = languageForPath(relPath);
+    const node = {
+      id: fileNodeId,
+      type: import_types9.NodeType.FileNode,
+      service: serviceName,
+      path: relPath,
+      ...language ? { language } : {},
+      discoveredVia: "static"
+    };
+    graph.addNode(fileNodeId, node);
+    nodesAdded++;
+  }
+  const containsId = (0, import_types9.extractedEdgeId)(serviceNodeId, fileNodeId, import_types9.EdgeType.CONTAINS);
+  if (!graph.hasEdge(containsId)) {
+    const edge = {
+      id: containsId,
+      source: serviceNodeId,
+      target: fileNodeId,
+      type: import_types9.EdgeType.CONTAINS,
+      provenance: import_types9.Provenance.EXTRACTED,
+      confidence: (0, import_types9.confidenceForExtracted)("structural"),
+      evidence: { file: relPath }
+    };
+    graph.addEdgeWithKey(containsId, serviceNodeId, fileNodeId, edge);
+    edgesAdded++;
+  }
+  return { fileNodeId, nodesAdded, edgesAdded };
+}
 
 // src/extract/calls/http.ts
 var STRING_LITERAL_NODE_TYPES = /* @__PURE__ */ new Set(["string_fragment", "string_content"]);
@@ -3669,16 +3829,16 @@ function callsFromSource(source, parser, knownHosts) {
   const tree = parser.parse(source);
   const literals = [];
   collectStringLiterals(tree.rootNode, literals);
-  const targets = /* @__PURE__ */ new Set();
+  const out = [];
   for (const lit of literals) {
     if (isInsideJsxExternalLink(lit.node)) continue;
     for (const host of knownHosts) {
       if (urlMatchesHost(lit.text, host)) {
-        targets.add(host);
+        out.push({ host, line: lit.node.startPosition.row + 1 });
       }
     }
   }
-  return targets;
+  return out;
 }
 function makeJsParser() {
   const p = new import_tree_sitter.default();
@@ -3701,71 +3861,78 @@ async function addHttpCallEdges(graph, services) {
     hostToNodeId.set(import_node_path20.default.basename(service.dir), service.node.id);
     hostToNodeId.set(service.pkg.name, service.node.id);
   }
+  let nodesAdded = 0;
   let edgesAdded = 0;
   for (const service of services) {
     const files = await loadSourceFiles(service.dir);
-    const seenTargets = /* @__PURE__ */ new Map();
+    const seen = /* @__PURE__ */ new Set();
     for (const file of files) {
       if (isTestPath(file.path)) continue;
       const parser = import_node_path20.default.extname(file.path) === ".py" ? pyParser : jsParser;
-      let targets;
+      let sites;
       try {
-        targets = callsFromSource(file.content, parser, knownHosts);
+        sites = callsFromSource(file.content, parser, knownHosts);
       } catch (err) {
         recordExtractionError("http call extraction", file.path, err);
         continue;
       }
-      for (const t of targets) {
-        const targetId = hostToNodeId.get(t);
+      if (sites.length === 0) continue;
+      const relFile = toPosix2(import_node_path20.default.relative(service.dir, file.path));
+      for (const site of sites) {
+        const targetId = hostToNodeId.get(site.host);
         if (!targetId || targetId === service.node.id) continue;
-        if (!seenTargets.has(targetId)) {
-          seenTargets.set(targetId, { file: file.path, host: t });
+        const dedupKey = `${relFile}|${targetId}`;
+        if (seen.has(dedupKey)) continue;
+        seen.add(dedupKey);
+        const confidence = (0, import_types10.confidenceForExtracted)("hostname-shape-match");
+        const ev = {
+          file: relFile,
+          line: site.line,
+          snippet: snippet(file.content, site.line)
+        };
+        const { fileNodeId, nodesAdded: n, edgesAdded: e } = ensureFileNode(
+          graph,
+          service.pkg.name,
+          service.node.id,
+          relFile
+        );
+        nodesAdded += n;
+        edgesAdded += e;
+        if (!(0, import_types10.passesExtractedFloor)(confidence)) {
+          noteExtractedDropped({
+            source: fileNodeId,
+            target: targetId,
+            type: import_types10.EdgeType.CALLS,
+            confidence,
+            confidenceKind: "hostname-shape-match",
+            evidence: ev
+          });
+          continue;
+        }
+        const edgeId = (0, import_types4.extractedEdgeId)(fileNodeId, targetId, import_types10.EdgeType.CALLS);
+        if (!graph.hasEdge(edgeId)) {
+          const edge = {
+            id: edgeId,
+            source: fileNodeId,
+            target: targetId,
+            type: import_types10.EdgeType.CALLS,
+            provenance: import_types10.Provenance.EXTRACTED,
+            confidence,
+            evidence: ev
+          };
+          graph.addEdgeWithKey(edgeId, fileNodeId, targetId, edge);
+          edgesAdded++;
         }
-      }
-    }
-    for (const [targetId, evidenceFile] of seenTargets) {
-      const fileContent = files.find((f) => f.path === evidenceFile.file)?.content ?? "";
-      const line = lineOf(fileContent, `//${evidenceFile.host}`);
-      const confidence = (0, import_types9.confidenceForExtracted)("hostname-shape-match");
-      const ev = {
-        file: import_node_path20.default.relative(service.dir, evidenceFile.file),
-        line,
-        snippet: snippet(fileContent, line)
-      };
-      const edgeId = (0, import_types4.extractedEdgeId)(service.node.id, targetId, import_types9.EdgeType.CALLS);
-      if (!(0, import_types9.passesExtractedFloor)(confidence)) {
-        noteExtractedDropped({
-          source: service.node.id,
-          target: targetId,
-          type: import_types9.EdgeType.CALLS,
-          confidence,
-          confidenceKind: "hostname-shape-match",
-          evidence: ev
-        });
-        continue;
-      }
-      const edge = {
-        id: edgeId,
-        source: service.node.id,
-        target: targetId,
-        type: import_types9.EdgeType.CALLS,
-        provenance: import_types9.Provenance.EXTRACTED,
-        confidence,
-        evidence: ev
-      };
-      if (!graph.hasEdge(edge.id)) {
-        graph.addEdgeWithKey(edge.id, edge.source, edge.target, edge);
-        edgesAdded++;
       }
     }
   }
-  return edgesAdded;
+  return { nodesAdded, edgesAdded };
 }
 
 // src/extract/calls/kafka.ts
 init_cjs_shims();
 var import_node_path21 = __toESM(require("path"), 1);
-var import_types10 = require("@neat.is/types");
+var import_types11 = require("@neat.is/types");
 var PRODUCER_TOPIC_RE = /(?:producer|kafkaProducer)[\s\S]{0,40}?\.send\s*\(\s*\{[\s\S]{0,200}?topic\s*:\s*['"`]([^'"`]+)['"`]/g;
 var CONSUMER_TOPIC_RE = /(?:consumer|kafkaConsumer)[\s\S]{0,40}?\.(?:subscribe|run)\s*\(\s*\{[\s\S]{0,200}?topic[s]?\s*:\s*(?:\[\s*)?['"`]([^'"`]+)['"`]/g;
 function findAll(re, text) {
@@ -3786,7 +3953,7 @@ function kafkaEndpointsFromFile(file, serviceDir) {
     seen.add(key);
     const line = lineOf(file.content, topic);
     out.push({
-      infraId: (0, import_types10.infraId)("kafka-topic", topic),
+      infraId: (0, import_types11.infraId)("kafka-topic", topic),
       name: topic,
       kind: "kafka-topic",
       edgeType,
@@ -3809,7 +3976,7 @@ function kafkaEndpointsFromFile(file, serviceDir) {
 // src/extract/calls/redis.ts
 init_cjs_shims();
 var import_node_path22 = __toESM(require("path"), 1);
-var import_types11 = require("@neat.is/types");
+var import_types12 = require("@neat.is/types");
 var REDIS_URL_RE = /redis(?:s)?:\/\/(?:[^@'"`\s]+@)?([^:/'"`\s]+)(?::(\d+))?/g;
 function redisEndpointsFromFile(file, serviceDir) {
   const out = [];
@@ -3822,7 +3989,7 @@ function redisEndpointsFromFile(file, serviceDir) {
     seen.add(host);
     const line = lineOf(file.content, host);
     out.push({
-      infraId: (0, import_types11.infraId)("redis", host),
+      infraId: (0, import_types12.infraId)("redis", host),
       name: host,
       kind: "redis",
       edgeType: "CALLS",
@@ -3843,7 +4010,7 @@ function redisEndpointsFromFile(file, serviceDir) {
 // src/extract/calls/aws.ts
 init_cjs_shims();
 var import_node_path23 = __toESM(require("path"), 1);
-var import_types12 = require("@neat.is/types");
+var import_types13 = require("@neat.is/types");
 var S3_BUCKET_RE = /Bucket\s*:\s*['"`]([^'"`]+)['"`]/g;
 var DYNAMO_TABLE_RE = /TableName\s*:\s*['"`]([^'"`]+)['"`]/g;
 function hasMarker(text, markers) {
@@ -3867,7 +4034,7 @@ function awsEndpointsFromFile(file, serviceDir) {
     seen.add(key);
     const line = lineOf(file.content, name);
     out.push({
-      infraId: (0, import_types12.infraId)(kind, name),
+      infraId: (0, import_types13.infraId)(kind, name),
       name,
       kind,
       edgeType: "CALLS",
@@ -3902,7 +4069,7 @@ function awsEndpointsFromFile(file, serviceDir) {
 // src/extract/calls/grpc.ts
 init_cjs_shims();
 var import_node_path24 = __toESM(require("path"), 1);
-var import_types13 = require("@neat.is/types");
+var import_types14 = require("@neat.is/types");
 var GRPC_CLIENT_RE = /new\s+([A-Z][A-Za-z0-9_]*)Client\s*\(\s*['"`]?([^,'"`)]+)?/g;
 var AWS_SDK_IMPORT_RE = /(?:from\s+['"`]|require\(\s*['"`])@aws-sdk\/client-([a-z0-9-]+)['"`]/g;
 var GRPC_IMPORT_RE = /(?:from\s+['"`]|require\(\s*['"`])@grpc\/grpc-js['"`]|_grpc_pb['"`]/;
@@ -3950,7 +4117,7 @@ function grpcEndpointsFromFile(file, serviceDir) {
     const { kind } = classified;
     const line = lineOf(file.content, m[0]);
     out.push({
-      infraId: (0, import_types13.infraId)(kind, name),
+      infraId: (0, import_types14.infraId)(kind, name),
       name,
       kind,
       edgeType: "CALLS",
@@ -3972,11 +4139,11 @@ function grpcEndpointsFromFile(file, serviceDir) {
 function edgeTypeFromEndpoint(ep) {
   switch (ep.edgeType) {
     case "PUBLISHES_TO":
-      return import_types14.EdgeType.PUBLISHES_TO;
+      return import_types15.EdgeType.PUBLISHES_TO;
     case "CONSUMES_FROM":
-      return import_types14.EdgeType.CONSUMES_FROM;
+      return import_types15.EdgeType.CONSUMES_FROM;
     default:
-      return import_types14.EdgeType.CALLS;
+      return import_types15.EdgeType.CALLS;
   }
 }
 function isAwsKind(kind) {
@@ -4003,7 +4170,7 @@ async function addExternalEndpointEdges(graph, services) {
       if (!graph.hasNode(ep.infraId)) {
         const node = {
           id: ep.infraId,
-          type: import_types14.NodeType.InfraNode,
+          type: import_types15.NodeType.InfraNode,
           name: ep.name,
           // #238 — `aws-*` covers AWS-SDK client kinds (aws-s3, aws-dynamodb,
           // aws-cognito-identity-provider, …); `s3-` / `dynamodb-` cover the
@@ -4015,13 +4182,19 @@ async function addExternalEndpointEdges(graph, services) {
         nodesAdded++;
       }
       const edgeType = edgeTypeFromEndpoint(ep);
-      const edgeId = (0, import_types4.extractedEdgeId)(service.node.id, ep.infraId, edgeType);
-      if (seenEdges.has(edgeId)) continue;
-      seenEdges.add(edgeId);
-      const confidence = (0, import_types14.confidenceForExtracted)(ep.confidenceKind);
-      if (!(0, import_types14.passesExtractedFloor)(confidence)) {
+      const confidence = (0, import_types15.confidenceForExtracted)(ep.confidenceKind);
+      const relFile = toPosix2(ep.evidence.file);
+      const { fileNodeId, nodesAdded: n, edgesAdded: e } = ensureFileNode(
+        graph,
+        service.pkg.name,
+        service.node.id,
+        relFile
+      );
+      nodesAdded += n;
+      edgesAdded += e;
+      if (!(0, import_types15.passesExtractedFloor)(confidence)) {
         noteExtractedDropped({
-          source: service.node.id,
+          source: fileNodeId,
           target: ep.infraId,
           type: edgeType,
           confidence,
@@ -4030,13 +4203,16 @@ async function addExternalEndpointEdges(graph, services) {
         });
         continue;
       }
+      const edgeId = (0, import_types4.extractedEdgeId)(fileNodeId, ep.infraId, edgeType);
+      if (seenEdges.has(edgeId)) continue;
+      seenEdges.add(edgeId);
       if (!graph.hasEdge(edgeId)) {
         const edge = {
           id: edgeId,
-          source: service.node.id,
+          source: fileNodeId,
           target: ep.infraId,
           type: edgeType,
-          provenance: import_types14.Provenance.EXTRACTED,
+          provenance: import_types15.Provenance.EXTRACTED,
           confidence,
           evidence: ep.evidence
         };
@@ -4048,11 +4224,11 @@ async function addExternalEndpointEdges(graph, services) {
   return { nodesAdded, edgesAdded };
 }
 async function addCallEdges(graph, services) {
-  const httpEdges = await addHttpCallEdges(graph, services);
+  const http = await addHttpCallEdges(graph, services);
   const ext = await addExternalEndpointEdges(graph, services);
   return {
-    nodesAdded: ext.nodesAdded,
-    edgesAdded: httpEdges + ext.edgesAdded
+    nodesAdded: http.nodesAdded + ext.nodesAdded,
+    edgesAdded: http.edgesAdded + ext.edgesAdded
   };
 }
 
@@ -4062,15 +4238,15 @@ init_cjs_shims();
 // src/extract/infra/docker-compose.ts
 init_cjs_shims();
 var import_node_path25 = __toESM(require("path"), 1);
-var import_types16 = require("@neat.is/types");
+var import_types17 = require("@neat.is/types");
 
 // src/extract/infra/shared.ts
 init_cjs_shims();
-var import_types15 = require("@neat.is/types");
+var import_types16 = require("@neat.is/types");
 function makeInfraNode(kind, name, provider = "self", extras) {
   return {
-    id: (0, import_types15.infraId)(kind, name),
-    type: import_types15.NodeType.InfraNode,
+    id: (0, import_types16.infraId)(kind, name),
+    type: import_types16.NodeType.InfraNode,
     name,
     provider,
     kind,
@@ -4149,15 +4325,15 @@ async function addComposeInfra(graph, scanPath, services) {
     for (const dep of dependsOnList(svc.depends_on)) {
       const targetId = composeNameToNodeId.get(dep);
       if (!targetId) continue;
-      const edgeId = (0, import_types4.extractedEdgeId)(sourceId, targetId, import_types16.EdgeType.DEPENDS_ON);
+      const edgeId = (0, import_types4.extractedEdgeId)(sourceId, targetId, import_types17.EdgeType.DEPENDS_ON);
       if (graph.hasEdge(edgeId)) continue;
       const edge = {
         id: edgeId,
         source: sourceId,
         target: targetId,
-        type: import_types16.EdgeType.DEPENDS_ON,
-        provenance: import_types16.Provenance.EXTRACTED,
-        confidence: (0, import_types16.confidenceForExtracted)("structural"),
+        type: import_types17.EdgeType.DEPENDS_ON,
+        provenance: import_types17.Provenance.EXTRACTED,
+        confidence: (0, import_types17.confidenceForExtracted)("structural"),
         evidence: { file: evidenceFile }
       };
       graph.addEdgeWithKey(edgeId, edge.source, edge.target, edge);
@@ -4171,7 +4347,7 @@ async function addComposeInfra(graph, scanPath, services) {
 init_cjs_shims();
 var import_node_path26 = __toESM(require("path"), 1);
 var import_node_fs14 = require("fs");
-var import_types17 = require("@neat.is/types");
+var import_types18 = require("@neat.is/types");
 function runtimeImage(content) {
   const lines = content.split("\n");
   let last = null;
@@ -4210,15 +4386,15 @@ async function addDockerfileRuntimes(graph, services, scanPath) {
       graph.addNode(node.id, node);
       nodesAdded++;
     }
-    const edgeId = (0, import_types4.extractedEdgeId)(service.node.id, node.id, import_types17.EdgeType.RUNS_ON);
+    const edgeId = (0, import_types4.extractedEdgeId)(service.node.id, node.id, import_types18.EdgeType.RUNS_ON);
     if (!graph.hasEdge(edgeId)) {
       const edge = {
         id: edgeId,
         source: service.node.id,
         target: node.id,
-        type: import_types17.EdgeType.RUNS_ON,
-        provenance: import_types17.Provenance.EXTRACTED,
-        confidence: (0, import_types17.confidenceForExtracted)("structural"),
+        type: import_types18.EdgeType.RUNS_ON,
+        provenance: import_types18.Provenance.EXTRACTED,
+        confidence: (0, import_types18.confidenceForExtracted)("structural"),
         evidence: {
           file: import_node_path26.default.relative(scanPath, dockerfilePath).split(import_node_path26.default.sep).join("/")
         }
@@ -4346,13 +4522,24 @@ var import_node_path30 = __toESM(require("path"), 1);
 init_cjs_shims();
 var import_node_fs17 = require("fs");
 var import_node_path29 = __toESM(require("path"), 1);
-var import_types18 = require("@neat.is/types");
+var import_types19 = require("@neat.is/types");
+function dropOrphanedFileNodes(graph) {
+  const orphans = [];
+  graph.forEachNode((id, attrs) => {
+    if (attrs.type !== import_types19.NodeType.FileNode) return;
+    if (graph.inboundEdges(id).length === 0 && graph.outboundEdges(id).length === 0) {
+      orphans.push(id);
+    }
+  });
+  for (const id of orphans) graph.dropNode(id);
+  return orphans.length;
+}
 function retireExtractedEdgesByMissingFile(graph, scanPath, serviceDirs = []) {
   const toDrop = [];
   const bases = [scanPath, ...serviceDirs];
   graph.forEachEdge((id, attrs) => {
     const edge = attrs;
-    if (edge.provenance !== import_types18.Provenance.EXTRACTED) return;
+    if (edge.provenance !== import_types19.Provenance.EXTRACTED) return;
     const evidenceFile = edge.evidence?.file;
     if (!evidenceFile) return;
     if (import_node_path29.default.isAbsolute(evidenceFile)) {
@@ -4363,6 +4550,7 @@ function retireExtractedEdgesByMissingFile(graph, scanPath, serviceDirs = []) {
     if (!found) toDrop.push(id);
   });
   for (const id of toDrop) graph.dropEdge(id);
+  dropOrphanedFileNodes(graph);
   return toDrop.length;
 }
 
@@ -4432,7 +4620,7 @@ async function extractFromDirectory(graph, scanPath, opts = {}) {
 init_cjs_shims();
 var import_node_fs18 = require("fs");
 var import_node_path31 = __toESM(require("path"), 1);
-var import_types19 = require("@neat.is/types");
+var import_types20 = require("@neat.is/types");
 var SCHEMA_VERSION = 4;
 function migrateV1ToV2(payload) {
   const nodes = payload.graph.nodes;
@@ -4454,12 +4642,12 @@ function migrateV2ToV3(payload) {
     for (const edge of edges) {
       const attrs = edge.attributes;
       if (!attrs || attrs.provenance !== "FRONTIER") continue;
-      attrs.provenance = import_types19.Provenance.OBSERVED;
+      attrs.provenance = import_types20.Provenance.OBSERVED;
       const type = typeof attrs.type === "string" ? attrs.type : void 0;
       const source = typeof attrs.source === "string" ? attrs.source : void 0;
       const target = typeof attrs.target === "string" ? attrs.target : void 0;
       if (type && source && target) {
-        const newId = (0, import_types19.observedEdgeId)(source, target, type);
+        const newId = (0, import_types20.observedEdgeId)(source, target, type);
         attrs.id = newId;
         if (edge.key) edge.key = newId;
       }
@@ -4545,11 +4733,11 @@ function startPersistLoop(graph, outPath, intervalMs = 6e4) {
 init_cjs_shims();
 var import_fastify = __toESM(require("fastify"), 1);
 var import_cors = __toESM(require("@fastify/cors"), 1);
-var import_types22 = require("@neat.is/types");
+var import_types23 = require("@neat.is/types");
 
 // src/divergences.ts
 init_cjs_shims();
-var import_types20 = require("@neat.is/types");
+var import_types21 = require("@neat.is/types");
 function bucketKey(source, target, type) {
   return `${type}|${source}|${target}`;
 }
@@ -4557,22 +4745,22 @@ function bucketEdges(graph) {
   const buckets = /* @__PURE__ */ new Map();
   graph.forEachEdge((id, attrs) => {
     const e = attrs;
-    const parsed = (0, import_types20.parseEdgeId)(id);
+    const parsed = (0, import_types21.parseEdgeId)(id);
     const provenance = parsed?.provenance ?? e.provenance;
     const key = bucketKey(e.source, e.target, e.type);
     const cur = buckets.get(key) ?? { source: e.source, target: e.target, type: e.type };
     switch (provenance) {
-      case import_types20.Provenance.EXTRACTED:
+      case import_types21.Provenance.EXTRACTED:
         cur.extracted = e;
         break;
-      case import_types20.Provenance.OBSERVED:
+      case import_types21.Provenance.OBSERVED:
         cur.observed = e;
         break;
-      case import_types20.Provenance.INFERRED:
+      case import_types21.Provenance.INFERRED:
         cur.inferred = e;
         break;
       default:
-        if (e.provenance === import_types20.Provenance.STALE) cur.stale = e;
+        if (e.provenance === import_types21.Provenance.STALE) cur.stale = e;
     }
     buckets.set(key, cur);
   });
@@ -4581,7 +4769,7 @@ function bucketEdges(graph) {
 function nodeIsFrontier(graph, nodeId) {
   if (!graph.hasNode(nodeId)) return false;
   const attrs = graph.getNodeAttributes(nodeId);
-  return attrs.type === import_types20.NodeType.FrontierNode;
+  return attrs.type === import_types21.NodeType.FrontierNode;
 }
 function clampConfidence(n) {
   if (!Number.isFinite(n)) return 0;
@@ -4602,6 +4790,7 @@ function gradedConfidence(edge) {
 }
 function detectMissingDivergences(graph, bucket) {
   const out = [];
+  if (bucket.type === import_types21.EdgeType.CONTAINS) return out;
   if (bucket.extracted && !bucket.observed) {
     if (!nodeIsFrontier(graph, bucket.target)) {
       out.push({
@@ -4642,7 +4831,7 @@ function declaredHostFor(svc) {
 function hasExtractedConfiguredBy(graph, svcId) {
   for (const edgeId of graph.outboundEdges(svcId)) {
     const e = graph.getEdgeAttributes(edgeId);
-    if (e.type === import_types20.EdgeType.CONFIGURED_BY && e.provenance === import_types20.Provenance.EXTRACTED) {
+    if (e.type === import_types21.EdgeType.CONFIGURED_BY && e.provenance === import_types21.Provenance.EXTRACTED) {
       return true;
     }
   }
@@ -4655,10 +4844,10 @@ function detectHostMismatch(graph, svcId, svc) {
   const out = [];
   for (const edgeId of graph.outboundEdges(svcId)) {
     const edge = graph.getEdgeAttributes(edgeId);
-    if (edge.type !== import_types20.EdgeType.CONNECTS_TO) continue;
-    if (edge.provenance !== import_types20.Provenance.OBSERVED) continue;
+    if (edge.type !== import_types21.EdgeType.CONNECTS_TO) continue;
+    if (edge.provenance !== import_types21.Provenance.OBSERVED) continue;
     const target = graph.getNodeAttributes(edge.target);
-    if (target.type !== import_types20.NodeType.DatabaseNode) continue;
+    if (target.type !== import_types21.NodeType.DatabaseNode) continue;
     const observedHost = target.host?.trim();
     if (!observedHost) continue;
     if (observedHost === declaredHost) continue;
@@ -4680,10 +4869,10 @@ function detectCompatDivergences(graph, svcId, svc) {
   const deps = svc.dependencies ?? {};
   for (const edgeId of graph.outboundEdges(svcId)) {
     const edge = graph.getEdgeAttributes(edgeId);
-    if (edge.type !== import_types20.EdgeType.CONNECTS_TO) continue;
-    if (edge.provenance !== import_types20.Provenance.OBSERVED) continue;
+    if (edge.type !== import_types21.EdgeType.CONNECTS_TO) continue;
+    if (edge.provenance !== import_types21.Provenance.OBSERVED) continue;
     const target = graph.getNodeAttributes(edge.target);
-    if (target.type !== import_types20.NodeType.DatabaseNode) continue;
+    if (target.type !== import_types21.NodeType.DatabaseNode) continue;
     for (const pair of compatPairs()) {
       if (pair.engine !== target.engine) continue;
       const declared = deps[pair.driver];
@@ -4744,7 +4933,7 @@ function computeDivergences(graph, opts = {}) {
   }
   graph.forEachNode((nodeId, attrs) => {
     const n = attrs;
-    if (n.type !== import_types20.NodeType.ServiceNode) return;
+    if (n.type !== import_types21.NodeType.ServiceNode) return;
     const svc = n;
     for (const d of detectHostMismatch(graph, nodeId, svc)) all.push(d);
     for (const d of detectCompatDivergences(graph, nodeId, svc)) all.push(d);
@@ -4777,7 +4966,7 @@ function computeDivergences(graph, opts = {}) {
     if (a.source !== b.source) return a.source.localeCompare(b.source);
     return a.target.localeCompare(b.target);
   });
-  return import_types20.DivergenceResultSchema.parse({
+  return import_types21.DivergenceResultSchema.parse({
     divergences: filtered,
     totalAffected: filtered.length,
     computedAt: (/* @__PURE__ */ new Date()).toISOString()
@@ -4918,7 +5107,7 @@ init_cjs_shims();
 var import_node_fs20 = require("fs");
 var import_node_os2 = __toESM(require("os"), 1);
 var import_node_path33 = __toESM(require("path"), 1);
-var import_types21 = require("@neat.is/types");
+var import_types22 = require("@neat.is/types");
 var LOCK_TIMEOUT_MS = 5e3;
 var LOCK_RETRY_MS = 50;
 function neatHome() {
@@ -4997,10 +5186,10 @@ async function readRegistry() {
     throw err;
   }
   const parsed = JSON.parse(raw);
-  return import_types21.RegistryFileSchema.parse(parsed);
+  return import_types22.RegistryFileSchema.parse(parsed);
 }
 async function writeRegistry(reg) {
-  const validated = import_types21.RegistryFileSchema.parse(reg);
+  const validated = import_types22.RegistryFileSchema.parse(reg);
   await writeAtomically(registryPath(), JSON.stringify(validated, null, 2) + "\n");
 }
 var ProjectNameCollisionError = class extends Error {
@@ -5272,11 +5461,11 @@ function registerRoutes(scope, ctx) {
       const candidates = req.query.type.split(",").map((s) => s.trim()).filter((s) => s.length > 0);
       const parsed = [];
       for (const c of candidates) {
-        const r = import_types22.DivergenceTypeSchema.safeParse(c);
+        const r = import_types23.DivergenceTypeSchema.safeParse(c);
         if (!r.success) {
           return reply.code(400).send({
             error: `unknown divergence type "${c}"`,
-            allowed: import_types22.DivergenceTypeSchema.options
+            allowed: import_types23.DivergenceTypeSchema.options
           });
         }
         parsed.push(r.data);
@@ -5489,7 +5678,7 @@ function registerRoutes(scope, ctx) {
     const log = new PolicyViolationsLog(proj.paths.policyViolationsPath);
     let violations = await log.readAll();
     if (req.query.severity) {
-      const sev = import_types22.PolicySeveritySchema.safeParse(req.query.severity);
+      const sev = import_types23.PolicySeveritySchema.safeParse(req.query.severity);
       if (!sev.success) {
         return reply.code(400).send({
           error: "invalid severity",
@@ -5506,7 +5695,7 @@ function registerRoutes(scope, ctx) {
   scope.post("/policies/check", async (req, reply) => {
     const proj = resolveProject(registry, req, reply, ctx.bootstrap);
     if (!proj) return;
-    const parsed = import_types22.PoliciesCheckBodySchema.safeParse(req.body ?? {});
+    const parsed = import_types23.PoliciesCheckBodySchema.safeParse(req.body ?? {});
     if (!parsed.success) {
       return reply.code(400).send({
         error: "invalid /policies/check body",
@@ -5543,14 +5732,18 @@ function registerRoutes(scope, ctx) {
 async function buildApi(opts) {
   const app = (0, import_fastify.default)({ logger: false });
   await app.register(import_cors.default, { origin: true });
+  const env = readAuthEnv();
+  const authToken = opts.authToken ?? env.authToken;
+  const trustProxy = opts.trustProxy ?? env.trustProxy;
+  const publicRead = opts.publicRead ?? env.publicRead;
   mountBearerAuth(app, {
-    token: opts.authToken,
-    trustProxy: opts.trustProxy,
-    publicRead: opts.publicRead
+    token: authToken,
+    trustProxy,
+    publicRead
   });
   app.get("/api/config", async () => ({
-    publicRead: opts.publicRead === true,
-    authProxy: opts.trustProxy === true
+    publicRead: publicRead === true,
+    authProxy: trustProxy === true
   }));
   const startedAt = opts.startedAt ?? Date.now();
   const registry = buildLegacyRegistry(opts);