@nanonets/graft 0.12.1 → 0.15.0

package/dist/graph/queries/dart.scm

@@ -0,0 +1,42 @@
+; Dart — breadth-tier tags.scm
+;
+; The Dart grammar does not wrap a function's signature and body in one
+; definition node: `function_signature` / `method_signature` sit as siblings
+; of `function_body` under `program` / `class_body`. Graft's generic extractor
+; expands a captured signature to include a following `function_body` sibling
+; so calls inside the body are attributed to the function (see defScope).
+;
+; Without this query the node-kind walker fallback runs, which:
+;   - skips `function_signature` (type does not match the walker suffixes)
+;   - mints `class_body` as a class (type starts with "class") named after the
+;     first identifier in the body (`int`, `bool`, …)
+;   - mints function-body locals (`initialized_variable_definition`) as symbols
+;
+; Call sites are `identifier` + adjacent `selector`/`argument_part`, not a
+; `call_expression` node. Only that shape is tagged — assignment selectors and
+; bare identifier reads are left alone.
+
+; Top-level functions (direct children of program, not methods)
+(program
+  (function_signature
+    name: (identifier) @name) @definition.function)
+
+; Methods
+(method_signature
+  (function_signature
+    name: (identifier) @name)) @definition.method
+
+(class_definition
+  name: (identifier) @name) @definition.class
+
+; Top-level / static `const`/`final` (`const int kThreshold = 3`)
+(static_final_declaration
+  .
+  (identifier) @name) @definition.constant
+
+; identifier(args) — `isReady(count)`, `Counter.ready → isReady(value)`
+(
+  (identifier) @name
+  .
+  (selector
+    (argument_part))) @reference.call

package/dist/graph/queries/lua.scm

@@ -0,0 +1,36 @@
+(function_declaration
+  name: [
+    (identifier) @name
+    (dot_index_expression
+      field: (identifier) @name)
+  ]) @definition.function
+
+(function_declaration
+  name: (method_index_expression
+    method: (identifier) @name)) @definition.method
+
+(assignment_statement
+  (variable_list
+    .
+    name: [
+      (identifier) @name
+      (dot_index_expression
+        field: (identifier) @name)
+    ])
+  (expression_list
+    .
+    value: (function_definition))) @definition.function
+
+(table_constructor
+  (field
+    name: (identifier) @name
+    value: (function_definition))) @definition.function
+
+(function_call
+  name: [
+    (identifier) @name
+    (dot_index_expression
+      field: (identifier) @name)
+    (method_index_expression
+      method: (identifier) @name)
+  ]) @reference.call

package/dist/graph/queries/nix.scm

@@ -0,0 +1,32 @@
+; Nix tags — standard tree-sitter tags convention (@definition.<kind> + @name + @reference.call).
+; Based on upstream tree-sitter-nix queries, extended for graft's breadth tier.
+;
+; Note: `binding` inside `let_expression` cannot have its children matched in
+; tree-sitter queries (parse error), so let-bound variables are NOT captured as
+; @definition. They are still searchable via the file node's residual body.
+
+; Function definitions: `name = args: body` or `name = body` (where body is a function)
+(binding
+  (attrpath (identifier) @name)
+  (function_expression) @definition.function)
+
+; Inherit statements: `inherit (source) name1 name2`
+(inherit
+  (inherited_attrs (identifier) @name @definition.constant))
+
+; Function calls: `function arg` or `function arg1 arg2` (nested apply_expression)
+; Matches e.g. `import ./path` when `import` is applied to arguments.
+(apply_expression
+  function: (apply_expression
+    function: (variable_expression
+      name: (identifier) @name))) @reference.call
+
+; Method/attribute calls: `builtins.map`, `pkgs.python3.withPackages`, etc.
+(apply_expression
+  function: (select_expression
+    attrpath: (attrpath attr: (identifier) @name))) @reference.call
+
+; Direct function application: `f arg`
+(apply_expression
+  function: (variable_expression
+    name: (identifier) @name)) @reference.call

package/dist/graph/refresh.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"refresh.d.ts","sourceRoot":"","sources":["../../src/graph/refresh.ts"],"names":[],"mappings":"AAuCA,OAAO,EAAoD,KAAK,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAWhG,MAAM,WAAW,aAAa;IAC5B,4DAA4D;IAC5D,SAAS,EAAE,OAAO,CAAC;IACnB,6DAA6D;IAC7D,KAAK,CAAC,EAAE,KAAK,CAAC;IACd,oFAAoF;IACpF,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,cAAc;IAC7B,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,iDAAiD;IACjD,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAcD;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,IAAI,CAWzD;AAuCD;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,GAAE,cAAmB,GAAG,OAAO,CAAC,aAAa,CAAC,CA6EtG;AAED;;;;;GAKG;AACH,wBAAsB,mBAAmB,CACvC,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAAE,EAClB,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,aAAa,CAAC,CAsBxB;AAED;wEACwE;AACxE,wBAAgB,WAAW,CAAC,CAAC,EAAE,aAAa,GAAG,MAAM,GAAG,IAAI,CAQ3D"}

package/dist/graph/refresh.js

@@ -37,7 +37,7 @@ import { contextDirFor } from "../context/node-file.js";
 import { acquireLockIn, releaseLockIn } from "../util/state.js";
 import { CACHE_DIR } from "../context/node-file.js";
 import { buildGraph } from "./build.js";
-import { driftCount, isClean, probeDrift } from "./fingerprint.js";
+import { driftCount, isClean, probeDrift, readFingerprint } from "./fingerprint.js";
 import { invalidateGraphCaches } from "./load.js";
 import { seedGraph } from "./seed.js";
 import { wiringPath } from "./write.js";
@@ -189,7 +189,11 @@ export async function ensureFreshGraph(root, opts = {}) {
             // else. The markdown projections under `graft/` stay the `Stop` hook's job —
             // a query has no business rewriting the repo's `.gitignore` or churning every
             // card's mtime, and skipping them is most of what keeps this cheap.
-            await buildGraph(dir, { contextDir: opts.contextDir, graphOnly: true });
+            // A `--only-dir` build recorded its whitelist in the fingerprint; re-apply it
+            // here so an auto-rebuild keeps the same limited file set instead of silently
+            // widening to the whole tree.
+            const onlyDirs = readFingerprint(outDir)?.onlyDirs;
+            await buildGraph(dir, { contextDir: opts.contextDir, graphOnly: true, onlyDirs });
             invalidateGraphCaches(outDir);
             return { refreshed: true, drift: drift ?? undefined, note: seedNote };
         }

package/dist/graph/refresh.js.map

@@ -1 +1 @@
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package/dist/graph/resolve.d.ts

@@ -1,5 +1,5 @@
 import type { EdgeV1, NodeV1 } from "./types.js";
-import type { RawEdge } from "./extract.js";
+import { type RawEdge } from "./extract.js";
 /** A Go module discovered in the repo: its `module` path from `go.mod` and the repo
  * directory that `go.mod` lives in (posix, `.` for the repo root). A monorepo may hold
  * several — e.g. `backend/go.mod`, `tools/go.mod`. */

package/dist/graph/resolve.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"resolve.d.ts","sourceRoot":"","sources":["../../src/graph/resolve.ts"],"names":[],"mappings":"AAgBA,OAAO,KAAK,EAAE,MAAM,EAAQ,MAAM,EAAY,MAAM,YAAY,CAAC;AACjE,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAM5C;;sDAEsD;AACtD,MAAM,WAAW,QAAQ;IACvB,MAAM,EAAE,MAAM,CAAC;IACf,GAAG,EAAE,MAAM,CAAC;CACb;AAED,MAAM,WAAW,cAAc;IAC7B;;6FAEyF;IACzF,SAAS,CAAC,EAAE,QAAQ,EAAE,CAAC;CACxB;AAED,wBAAgB,YAAY,CAC1B,KAAK,EAAE,MAAM,EAAE,EACf,QAAQ,EAAE,OAAO,EAAE,EACnB,IAAI,GAAE,cAAmB,GACxB,MAAM,EAAE,CAoKV"}
+{"version":3,"file":"resolve.d.ts","sourceRoot":"","sources":["../../src/graph/resolve.ts"],"names":[],"mappings":"AAgBA,OAAO,KAAK,EAAE,MAAM,EAAQ,MAAM,EAAY,MAAM,YAAY,CAAC;AACjE,OAAO,EAAc,KAAK,OAAO,EAAE,MAAM,cAAc,CAAC;AAoExD;;sDAEsD;AACtD,MAAM,WAAW,QAAQ;IACvB,MAAM,EAAE,MAAM,CAAC;IACf,GAAG,EAAE,MAAM,CAAC;CACb;AAED,MAAM,WAAW,cAAc;IAC7B;;6FAEyF;IACzF,SAAS,CAAC,EAAE,QAAQ,EAAE,CAAC;CACxB;AAED,wBAAgB,YAAY,CAC1B,KAAK,EAAE,MAAM,EAAE,EACf,QAAQ,EAAE,OAAO,EAAE,EACnB,IAAI,GAAE,cAAmB,GACxB,MAAM,EAAE,CAwOV"}

package/dist/graph/resolve.js

@@ -14,9 +14,73 @@
  */
 import { posix } from "node:path";
 import { toPosixPath } from "../util/paths.js";
+import { languageOf } from "./extract.js";
+import { genericLangOf } from "./generic.js";
 const IMPORT_EXTS = [".ts", ".tsx", ".mts", ".cts", ".js", ".jsx", ".mjs", ".cjs", ".py"];
 /** C/C++ source + header extensions, for resolving `#include` targets. */
 const C_EXT = /\.(c|h|cc|cpp|cxx|hpp|hh|hxx|inl|ipp|c\+\+|h\+\+)$/i;
+/** Python source + stub extensions, for the constructor-call fallback below. */
+const PY_EXT = /\.pyi?$/i;
+/** What a bare Python call falls back to when no function of that name exists:
+ * construction. Only `class` — Python enums, dataclasses and NamedTuples are all
+ * classes, so no other kind is reachable this way. */
+const PY_CTOR_KINDS = ["class"];
+/** Swift is Python's case with more nominal kinds: `Animal(legs: 4)` is an ordinary
+ * call node with no `new` to mark construction, and struct/enum initializers are as
+ * routine as class ones (a struct gets a memberwise init for free). Same fallback
+ * shape — types are tried only once functions (and methods, see extract.ts's
+ * implicit-self widening) have found nothing. */
+const SWIFT_EXT = /\.swift$/i;
+const SWIFT_CTOR_KINDS = ["class", "struct", "enum"];
+/**
+ * Languages whose symbols can genuinely reach each other. A call edge may not
+ * cross a family boundary.
+ *
+ * This exists because name resolution is repo-wide and used to be language-blind.
+ * A Go file calling the builtin `make(...)` has nothing in the repo to resolve
+ * against, so the unique-global fallback below matched a TypeScript helper named
+ * `make` in a frontend test file — and then every `make(map[...])` in the backend
+ * became an edge into that file. One symbol collected 1040 in-edges across 476
+ * files, and any pull request touching that test dragged the entire Go backend
+ * into its blast radius. Uniqueness is what made it fire: the rarer the collision,
+ * the more confident the old code was that it had found the right target.
+ *
+ * Only real interop is grouped here. TS/TSX/JS import each other freely; Kotlin,
+ * Scala and Clojure compile against Java on one classpath; C and C++ share
+ * headers. Everything else stands alone.
+ */
+const FAMILIES = [
+    ["typescript", "tsx"],
+    ["java", "kotlin", "scala", "clojure"],
+    ["c", "cpp"],
+];
+const FAMILY_OF = new Map();
+for (const group of FAMILIES)
+    for (const lang of group)
+        FAMILY_OF.set(lang, group[0]);
+/**
+ * The language family a path belongs to, or null when no tier claims the file.
+ * A language of its own is its own family, so the common case needs no entry above.
+ */
+function familyOf(path) {
+    const lang = languageOf(path) ?? genericLangOf(path)?.name ?? null;
+    if (!lang)
+        return null;
+    return FAMILY_OF.get(lang) ?? lang;
+}
+/**
+ * Could a reference in `file` reach a definition in `candidatePath`?
+ *
+ * An unknown family never filters: absence of data is not evidence of a mismatch,
+ * and refusing edges for every extension graft cannot name would lose real ones.
+ */
+function reachable(file, candidatePath) {
+    const from = familyOf(file);
+    if (from === null)
+        return true;
+    const to = familyOf(candidatePath);
+    return to === null || from === to;
+}
 export function resolveEdges(nodes, rawEdges, opts = {}) {
     const byId = new Map(nodes.map((n) => [n.id, n]));
     const globalName = new Map();
@@ -82,8 +146,10 @@ export function resolveEdges(nodes, rawEdges, opts = {}) {
         if (!fileMap)
             perFileName.set(n.path, (fileMap = new Map()));
         push(fileMap, n.name, n);
-        if (n.kind === "method" && n.owner) {
-            push(ownerMethod, `${n.owner}.${n.name}`, n);
+        if (n.kind === "method") {
+            const owner = n.owner ?? ownerFromMethodId(n.id);
+            if (owner)
+                push(ownerMethod, `${owner}.${n.name}`, n);
         }
     }
     // classParents: class/interface name → its declared base-class names, from raw
@@ -101,6 +167,18 @@ export function resolveEdges(nodes, rawEdges, opts = {}) {
             continue;
         push(classParents, ownName, e.name);
     }
+    // classTraits: class name → trait names from raw `implements` edges in PHP files.
+    // PHP models `use SomeTrait;` as implements; trait methods live on the trait owner,
+    // not the using class, so resolveTypedMember walks these after the class lookup fails.
+    const classTraits = new Map();
+    for (const e of rawEdges) {
+        if (e.relation !== "implements" || !e.name || !e.file.endsWith(".php"))
+            continue;
+        const ownName = byId.get(e.source)?.name;
+        if (!ownName)
+            continue;
+        push(classTraits, ownName, e.name);
+    }
     const out = [];
     const seen = new Set();
     const add = (source, target, relation, confidence) => {
@@ -141,13 +219,40 @@ export function resolveEdges(nodes, rawEdges, opts = {}) {
                 // A named import gives both halves needed for sound resolution: the module
                 // it came from and the exported name. Resolve inside that file only, so a
                 // same-named symbol elsewhere in the repo cannot become a false edge.
-                const targetFile = resolveImport(e.specifier, e.file, byId);
+                const targetFile = e.file.endsWith(".php")
+                    ? resolvePhpUse(e.specifier, phpFilesBySuffix)
+                    : resolveImport(e.specifier, e.file, byId);
                 if (!byId.has(targetFile))
                     continue; // external or unresolved module
                 const candidates = perFileName.get(targetFile)?.get(e.name) ?? [];
                 if (candidates.length === 1)
                     add(e.source, candidates[0].id, "references", "extracted");
             }
+            else if (e.file.endsWith(".php") && byId.get(e.source)?.origin === "ast") {
+                // PHP attribute without a `use` import (same-file or globally unique class).
+                const refKinds = ["class", "interface", "trait", "enum"];
+                const hit = resolveName(e.name, e.file, refKinds, perFileName, globalName);
+                if (hit && hit.id !== e.source)
+                    add(e.source, hit.id, "references", hit.confidence);
+            }
+            else if (e.file.endsWith(".java") && byId.get(e.source)?.origin === "ast") {
+                // Java annotation without a specifier (same-file or globally unique
+                // `@interface`). Annotation types are `interface` kind — a class of the
+                // same name is not a match, so `@Entity` cannot collapse onto an in-repo
+                // `class Entity` (#103). Kind alone still cannot tell `@interface Service`
+                // from `interface Service`, so only accept a candidate whose header
+                // contains the literal `@interface` (`includes`, not `startsWith`: a
+                // meta-annotated type is `@Documented @Retention(...) public @interface
+                // JsonAdapter`). Unresolved targets keep the bare name, matching
+                // heritage, rather than dropping the way PHP attributes do.
+                const refKinds = ["interface"];
+                const hit = resolveName(e.name, e.file, refKinds, perFileName, globalName);
+                const anno = hit ? byId.get(hit.id) : undefined;
+                if (hit && hit.id !== e.source && anno?.signature?.includes("@interface"))
+                    add(e.source, hit.id, "references", hit.confidence);
+                else
+                    add(e.source, e.name, "references", "inferred");
+            }
             else if (byId.get(e.source)?.origin === "generic") {
                 // Breadth tier: a bare-name structural reference (extends / implements /
                 // object-creation / module alias) the grammar marked but cannot type. Resolve
@@ -164,17 +269,34 @@ export function resolveEdges(nodes, rawEdges, opts = {}) {
             if (e.viaMember) {
                 if (!e.recvType)
                     continue;
-                const hit = resolveTypedMember(e.recvType, e.name, e.file, ownerMethod, classParents, e.argCount);
+                const hit = resolveTypedMember(e.recvType, e.name, e.file, ownerMethod, classParents, classTraits, e.argCount);
                 if (hit === "ambiguous")
                     continue; // drop — never guess past an ambiguous owner
-                if (hit)
+                if (hit) {
                     add(e.source, hit.id, "calls", hit.confidence);
+                    continue;
+                }
                 // No owner-qualified match means the call is unresolved. A unique bare
                 // method name is not evidence that this receiver has that method — a
                 // name-fallback here was measured to HALVE call-edge precision (73%→37%
                 // vs a compiler-grade oracle) for a 3x count inflation, i.e. noise. See #35.
-                continue;
+                //
+                // One carve-out, which is NOT that fallback: a Swift `implicitSelf` edge
+                // carries two readings of one bare call — member (tried above, in
+                // Swift's own inner-scope-first order) and free function. Zero members
+                // on the whole owner chain means the call was a free-function call after
+                // all, so it falls through to bare-name resolution; an ambiguous member
+                // set has already dropped it above, and a resolved member never reaches
+                // here — a name defined as both member and free function yields the
+                // member edge alone, exactly as Swift dispatches it.
+                if (!e.implicitSelf)
+                    continue;
             }
+            // Every language's bare-name call is a free function, except R (Phase 4):
+            // an untyped `obj$method()` there sets e.kinds to also allow a "method"
+            // match — see extract.ts's calleeName R branch for why (R6 methods are
+            // never kind "function", so without this every such call would be
+            // unconditionally unresolvable rather than just occasionally ambiguous).
             // Three cases, because "a bare call" means something different per tier:
             //
             //  - generic (breadth tier): tags.scm captures ALL calls as bare names, since it
@@ -185,13 +307,29 @@ export function resolveEdges(nodes, rawEdges, opts = {}) {
             //    extract.ts, so the only bare call reaching here is `new Foo()`, whose target
             //    is a TYPE. Against the function index every constructor edge would drop.
             //  - everything else: functions, exactly as before.
+            //
+            // R (depth tier, Phase 4) sets `e.kinds` itself for an untyped `obj$method()`
+            // (see above), and that explicit choice wins over the per-tier default.
             const srcOrigin = byId.get(e.source)?.origin;
-            const callKinds = srcOrigin === "generic"
-                ? ["function", "method"]
-                : e.file.endsWith(".java")
-                    ? ["class", "struct", "enum", "interface"]
-                    : ["function"];
-            const hit = resolveName(e.name, e.file, callKinds, perFileName, globalName);
+            const callKinds = e.kinds ??
+                (srcOrigin === "generic"
+                    ? ["function", "method"]
+                    : e.file.endsWith(".java")
+                        ? ["class", "struct", "enum", "interface"]
+                        : ["function"]);
+            let hit = resolveName(e.name, e.file, callKinds, perFileName, globalName);
+            // Python is the Java case without the `new` to mark it: `Widget()` is an
+            // ordinary call node, so a constructor edge dies against the function-only
+            // index. Java can widen to types outright; Python has free functions, so
+            // widening would trade real function edges for type ones. Hence a fallback,
+            // not a swap — types are tried only once functions have found nothing, and
+            // resolveName's same-file-then-unique-global rule still drops the ambiguous.
+            if (!hit && PY_EXT.test(e.file)) {
+                hit = resolveName(e.name, e.file, PY_CTOR_KINDS, perFileName, globalName);
+            }
+            if (!hit && SWIFT_EXT.test(e.file)) {
+                hit = resolveName(e.name, e.file, SWIFT_CTOR_KINDS, perFileName, globalName);
+            }
             if (hit)
                 add(e.source, hit.id, "calls", hit.confidence); // drop unresolved calls (too noisy)
         }
@@ -205,15 +343,30 @@ function push(map, key, val) {
     else
         map.set(key, [val]);
 }
+/** Derive a method's owner from its dotted id when extract did not stamp `owner`
+ * (PHP trait/interface methods today). `app.php#Loggable.log` → `Loggable`. */
+function ownerFromMethodId(id) {
+    const post = id.includes("#") ? id.split("#")[1] : id;
+    const segs = post.split(".");
+    return segs.length >= 2 ? segs[segs.length - 2] : undefined;
+}
 /**
  * Resolve a bare symbol name: same-file match first (certain → `extracted`),
  * else a unique cross-file match (→ `inferred`), else null (ambiguous/unknown).
  */
 function resolveName(name, file, kinds, perFileName, globalName) {
     const local = (perFileName.get(file)?.get(name) ?? []).filter((n) => kinds.includes(n.kind));
-    if (local.length)
+    // Same-file requires a UNIQUE match, exactly as the cross-file branch below does.
+    // Returning `local[0]` meant a file holding two same-named types (`Alpha.Builder` and
+    // `Beta.Builder`, `Alpha.Inner` and `Beta.Inner`) silently resolved to whichever came
+    // first in document order — and labelled it `extracted`, i.e. certain. That is the
+    // guess this module's header says it does not make.
+    if (local.length === 1)
         return { id: local[0].id, confidence: "extracted" };
-    const global = (globalName.get(name) ?? []).filter((n) => kinds.includes(n.kind));
+    // Cross-file: also require a language that could actually reach this one.
+    // Without it a unique name match ANYWHERE in the repo wins, which is how a Go
+    // builtin ended up resolving into a TypeScript test — see FAMILIES above.
+    const global = (globalName.get(name) ?? []).filter((n) => kinds.includes(n.kind) && reachable(file, n.path));
     if (global.length === 1)
         return { id: global[0].id, confidence: "inferred" };
     return null;
@@ -255,24 +408,36 @@ function narrowByArity(candidates, argCount) {
     });
     return fits.length > 0 ? fits : candidates;
 }
-function resolveTypedMember(recvType, name, file, ownerMethod, classParents, argCount) {
+function resolveTypedMember(recvType, name, file, ownerMethod, classParents, classTraits, argCount) {
     const MAX_DEPTH = 3;
     const visited = new Set([recvType]);
     let frontier = [recvType];
     for (let depth = 0; depth <= MAX_DEPTH && frontier.length; depth++) {
         for (const type of frontier) {
-            const all = ownerMethod.get(`${type}.${name}`);
-            if (!all || all.length === 0)
-                continue; // try next ancestor
-            const candidates = narrowByArity(all, argCount);
-            if (candidates.length === 1) {
-                const c = candidates[0];
-                return { id: c.id, confidence: c.path === file ? "extracted" : "inferred" };
+            const all = ownerMethod.get(`${type}.${name}`)?.filter((c) => reachable(file, c.path));
+            if (all && all.length > 0) {
+                const candidates = narrowByArity(all, argCount);
+                if (candidates.length === 1) {
+                    const c = candidates[0];
+                    return { id: c.id, confidence: c.path === file ? "extracted" : "inferred" };
+                }
+                // Swift: several candidates surviving arity narrowing are a genuine
+                // overload set distinguished only by parameter TYPES (`save(Int)` vs
+                // `save(String)`), which this pass cannot read — the same-file tiebreak
+                // below would pick whichever overload appears first in the file and
+                // stamp it `extracted`, a confidently wrong edge. Drop instead.
+                if (SWIFT_EXT.test(file))
+                    return "ambiguous";
+                const sameFile = candidates.find((c) => c.path === file);
+                if (sameFile)
+                    return { id: sameFile.id, confidence: "extracted" };
+                return "ambiguous"; // several, none same-file — drop and stop
             }
-            const sameFile = candidates.find((c) => c.path === file);
-            if (sameFile)
-                return { id: sameFile.id, confidence: "extracted" };
-            return "ambiguous"; // several, none same-file — drop and stop
+            const traitHit = resolveTraitMember(type, name, file, ownerMethod, classTraits, argCount);
+            if (traitHit === "ambiguous")
+                return "ambiguous";
+            if (traitHit)
+                return traitHit;
         }
         const next = [];
         for (const type of frontier) {
@@ -287,6 +452,26 @@ function resolveTypedMember(recvType, name, file, ownerMethod, classParents, arg
     }
     return null; // chain exhausted, no candidate anywhere
 }
+/** Resolve a member call against methods declared on PHP traits used by `type`. */
+function resolveTraitMember(type, name, file, ownerMethod, classTraits, argCount) {
+    const traits = classTraits.get(type);
+    if (!traits?.length)
+        return null;
+    const matches = [];
+    for (const trait of traits) {
+        const all = ownerMethod.get(`${trait}.${name}`)?.filter((c) => reachable(file, c.path));
+        if (!all?.length)
+            continue;
+        matches.push(...narrowByArity(all, argCount));
+    }
+    if (matches.length === 0)
+        return null;
+    if (matches.length === 1) {
+        const c = matches[0];
+        return { id: c.id, confidence: c.path === file ? "extracted" : "inferred" };
+    }
+    return "ambiguous";
+}
 /**
  * Resolve a module specifier to a file node id when it points inside the repo;
  * otherwise return the raw specifier (external package or unresolved path).

package/dist/graph/resolve.js.map

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package/dist/graph/scopes.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scopes.d.ts","sourceRoot":"","sources":["../../src/graph/scopes.ts"],"names":[],"mappings":"AA4BA,OAAO,KAAK,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAsGnD;4CAC4C;AAC5C,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,EACZ,SAAS,GAAE,MAAM,EAEf,GACD,OAAO,EAAE,CAqIX;AAED;;+DAE+D;AAC/D,wBAAgB,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAMhE;AAED;;+DAE+D;AAC/D,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAEjD;AAED;;;sCAGsC;AACtC,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,CAG1D;AAED;;;;2BAI2B;AAC3B,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,OAAO,CAErE;AAED;;;;;;;;;GASG;AACH,wBAAgB,mBAAmB,CAAC,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAKxE;AAED;4CAC4C;AAC5C,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAYhE;AAED;;2EAE2E;AAC3E,wBAAgB,aAAa,CAAC,KAAK,EAAE,OAAO,GAAG,OAAO,EAAE,CAEvD"}
+{"version":3,"file":"scopes.d.ts","sourceRoot":"","sources":["../../src/graph/scopes.ts"],"names":[],"mappings":"AA4BA,OAAO,KAAK,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAsGnD;4CAC4C;AAC5C,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,EACZ,SAAS,GAAE,MAAM,EAGf,GACD,OAAO,EAAE,CAqIX;AAED;;+DAE+D;AAC/D,wBAAgB,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAMhE;AAED;;+DAE+D;AAC/D,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAEjD;AAED;;;sCAGsC;AACtC,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,CAG1D;AAED;;;;2BAI2B;AAC3B,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,OAAO,CAErE;AAED;;;;;;;;;GASG;AACH,wBAAgB,mBAAmB,CAAC,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAKxE;AAED;4CAC4C;AAC5C,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAYhE;AAED;;2EAE2E;AAC3E,wBAAgB,aAAa,CAAC,KAAK,EAAE,OAAO,GAAG,OAAO,EAAE,CAEvD"}

package/dist/graph/scopes.js

@@ -25,7 +25,7 @@ import { existsSync, readdirSync, readFileSync } from "node:fs";
 import { join, resolve } from "node:path";
 import { shouldSkipDir, walkDir } from "../ingest/fs.js";
 import { relPosix } from "../util/paths.js";
-import { readFollowSubmodules, readIncludeDirs } from "../util/state.js";
+import { readFollowNestedRepos, readFollowSubmodules, readIncludeDirs } from "../util/state.js";
 /** Project-marker files, checked in this order (also the order `markers` is built in). */
 const MARKERS = ["package.json", "go.mod", "pyproject.toml", "setup.py", "Cargo.toml", "composer.json", "pom.xml", "build.gradle", "build.gradle.kts"];
 const CANONICAL_ROOT = [{ prefix: "", label: "", markers: [] }];
@@ -135,6 +135,7 @@ function resolveGlob(dirs, pattern) {
  * choices) and find project-marker dirs. */
 export function discoverScopes(root, repoFiles = walkDir(root, readIncludeDirs(resolve(root)), {
     followSubmodules: readFollowSubmodules(resolve(root)),
+    followNestedRepos: readFollowNestedRepos(resolve(root)),
 })) {
     const absRoot = resolve(root);
     const dirs = collectDirs(absRoot, repoFiles);