@nanonets/graft 0.13.0 → 0.16.0

package/dist/graph/invariants.d.ts

@@ -8,8 +8,9 @@
  *   - edge relations and confidences are in the allowed sets
  *   - every edge source is a real node
  *   - every edge target is a real node, EXCEPT the relations that deliberately keep
- *     an unresolved external string (an import specifier, or a bare heritage name for
- *     an out-of-repo supertype) — those are a feature of "drop rather than guess",
+ *     an unresolved external string (an import specifier, a bare heritage name for
+ *     an out-of-repo supertype, or a Java annotation type with no in-repo
+ *     `@interface`) — those are a feature of "drop rather than guess",
  *     not a dangling edge.
  *
  * Self-loop `calls` are NOT a violation: direct recursion is a real edge a function

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

@@ -1 +1 @@
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+{"version":3,"file":"invariants.d.ts","sourceRoot":"","sources":["../../src/graph/invariants.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,YAAY,CAAC;AAoB1C,MAAM,WAAW,eAAe;IAC9B,kFAAkF;IAClF,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,0FAA0F;IAC1F,aAAa,EAAE,MAAM,CAAC;CACvB;AAED,oFAAoF;AACpF,wBAAgB,oBAAoB,CAAC,KAAK,EAAE,OAAO,GAAG,eAAe,CA0BpE"}

package/dist/graph/invariants.js

@@ -9,9 +9,12 @@ const CONFIDENCE = new Set([
     "lsp_resolved", "lsp_dispatch", "extracted", "inferred",
 ]);
 // Relations whose target may be a deliberately-unresolved external string rather
-// than an in-repo node id: an import's module specifier, or a heritage clause naming
-// a supertype defined outside the repo (or a generic type parameter).
-const TARGET_MAY_BE_EXTERNAL = new Set(["imports", "extends", "implements"]);
+// than an in-repo node id: an import's module specifier, a heritage clause naming
+// a supertype defined outside the repo (or a generic type parameter), or a Java
+// annotation whose type is not declared in-repo. The set is language-agnostic —
+// no other producer currently leaves an unresolved `references` target, so a
+// future bug elsewhere would be masked here.
+const TARGET_MAY_BE_EXTERNAL = new Set(["imports", "extends", "implements", "references"]);
 /** Check a graph's structural invariants. `problems` is empty for a valid graph. */
 export function checkGraphInvariants(graph) {
     const problems = [];

package/dist/graph/invariants.js.map

@@ -1 +1 @@
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+{"version":3,"file":"invariants.js","sourceRoot":"","sources":["../../src/graph/invariants.ts"],"names":[],"mappings":"AAyBA,MAAM,KAAK,GAAG,IAAI,GAAG,CAAS;IAC5B,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW;IAClD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,UAAU;CAC3D,CAAC,CAAC;AACH,MAAM,SAAS,GAAG,IAAI,GAAG,CAAS;IAChC,UAAU,EAAE,OAAO,EAAE,SAAS,EAAE,YAAY,EAAE,YAAY,EAAE,SAAS;CACtE,CAAC,CAAC;AACH,MAAM,UAAU,GAAG,IAAI,GAAG,CAAS;IACjC,cAAc,EAAE,cAAc,EAAE,WAAW,EAAE,UAAU;CACxD,CAAC,CAAC;AACH,iFAAiF;AACjF,kFAAkF;AAClF,gFAAgF;AAChF,gFAAgF;AAChF,6EAA6E;AAC7E,6CAA6C;AAC7C,MAAM,sBAAsB,GAAG,IAAI,GAAG,CAAS,CAAC,SAAS,EAAE,SAAS,EAAE,YAAY,EAAE,YAAY,CAAC,CAAC,CAAC;AASnG,oFAAoF;AACpF,MAAM,UAAU,oBAAoB,CAAC,KAAc;IACjD,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IAClD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAE/B,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,KAAK,EAAE,CAAC;QAC5B,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QAChE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;QACf,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE;YAAE,QAAQ,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QAC5E,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACvE,MAAM,CAAC,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC;QAC/C,IAAI,CAAC,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;aAClD,IAAI,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;IAC1F,CAAC;IAED,IAAI,aAAa,GAAG,CAAC,CAAC;IACtB,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,KAAK,EAAE,CAAC;QAC5B,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,QAAQ,MAAM,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;QAC3F,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,UAAU,MAAM,CAAC,CAAC,MAAM,MAAM,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;QAChH,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;QACtE,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,sBAAsB,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC;YAC/D,QAAQ,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,QAAQ,YAAY,CAAC,CAAC,MAAM,MAAM,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;QAC5E,IAAI,CAAC,CAAC,QAAQ,KAAK,OAAO,IAAI,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,MAAM;YAAE,aAAa,EAAE,CAAC;IACvE,CAAC;IAED,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAC;AACrC,CAAC"}

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;AAY5C;;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,CAyMV"}
+{"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

@@ -14,6 +14,8 @@
  */
 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\+\+)$/i;
@@ -23,6 +25,62 @@ const PY_EXT = /\.pyi?$/i;
  * 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();
@@ -177,6 +235,24 @@ export function resolveEdges(nodes, rawEdges, opts = {}) {
                 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
@@ -196,13 +272,25 @@ export function resolveEdges(nodes, rawEdges, opts = {}) {
                 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"
@@ -239,6 +327,9 @@ export function resolveEdges(nodes, rawEdges, opts = {}) {
             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)
         }
@@ -272,7 +363,10 @@ function resolveName(name, file, kinds, perFileName, globalName) {
     // 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;
@@ -320,13 +414,20 @@ function resolveTypedMember(recvType, name, file, ownerMethod, classParents, cla
     let frontier = [recvType];
     for (let depth = 0; depth <= MAX_DEPTH && frontier.length; depth++) {
         for (const type of frontier) {
-            const all = ownerMethod.get(`${type}.${name}`);
+            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" };
@@ -358,7 +459,7 @@ function resolveTraitMember(type, name, file, ownerMethod, classTraits, argCount
         return null;
     const matches = [];
     for (const trait of traits) {
-        const all = ownerMethod.get(`${trait}.${name}`);
+        const all = ownerMethod.get(`${trait}.${name}`)?.filter((c) => reachable(file, c.path));
         if (!all?.length)
             continue;
         matches.push(...narrowByArity(all, argCount));

package/dist/graph/resolve.js.map

@@ -1 +1 @@
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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);

package/dist/graph/scopes.js.map

@@ -1 +1 @@
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package/dist/graph/source-files.d.ts

@@ -15,7 +15,12 @@ export declare function unsupportedExtensions(exts: string[]): string[];
  * none of which ever see a CLI flag) behaves identically to the build that
  * saved those choices.
  */
-export declare function listSourceFiles(root: string, outDir: string, repoFiles?: string[]): string[];
+/** Keep only files whose repo-relative path is at or under one of `onlyDirs`.
+ * No-op when `onlyDirs` is empty/absent. The whitelist is carried in the graph
+ * itself (the fingerprint records it at build time), never in the source repo,
+ * so a build and the query-path freshness probe read the identical set. */
+export declare function filterByOnlyDirs(files: string[], root: string, onlyDirs?: ReadonlySet<string>): string[];
+export declare function listSourceFiles(root: string, outDir: string, repoFiles?: string[], onlyDirs?: ReadonlySet<string>): string[];
 export interface SourceStat {
     /** Absolute path. */
     abs: string;
@@ -31,5 +36,5 @@ export interface SourceStat {
  * both the freshness probe and the extraction cache. Files that vanish between
  * the walk and the stat are dropped (same fail-soft posture as `walkDir`).
  */
-export declare function listSourceStats(root: string, outDir: string, repoFiles?: string[]): SourceStat[];
+export declare function listSourceStats(root: string, outDir: string, repoFiles?: string[], onlyDirs?: ReadonlySet<string>): SourceStat[];
 //# sourceMappingURL=source-files.d.ts.map

package/dist/graph/source-files.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"source-files.d.ts","sourceRoot":"","sources":["../../src/graph/source-files.ts"],"names":[],"mappings":"AAiBA;mFACmF;AACnF,wBAAgB,mBAAmB,IAAI,MAAM,EAAE,CAE9C;AAQD;;;;GAIG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,CAG9D;AAED;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAC7B,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,SAAS,GAAE,MAAM,EAEf,GACD,MAAM,EAAE,CASV;AAED,MAAM,WAAW,UAAU;IACzB,qBAAqB;IACrB,GAAG,EAAE,MAAM,CAAC;IACZ;;oEAEgE;IAChE,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM,EAAE,GAAG,UAAU,EAAE,CAYhG"}
+{"version":3,"file":"source-files.d.ts","sourceRoot":"","sources":["../../src/graph/source-files.ts"],"names":[],"mappings":"AAiBA;mFACmF;AACnF,wBAAgB,mBAAmB,IAAI,MAAM,EAAE,CAE9C;AAQD;;;;GAIG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,CAG9D;AAED;;;;;;;GAOG;AACH;;;2EAG2E;AAC3E,wBAAgB,gBAAgB,CAC9B,KAAK,EAAE,MAAM,EAAE,EACf,IAAI,EAAE,MAAM,EACZ,QAAQ,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,GAC7B,MAAM,EAAE,CAMV;AAED,wBAAgB,eAAe,CAC7B,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,SAAS,GAAE,MAAM,EAGf,EACF,QAAQ,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,GAC7B,MAAM,EAAE,CAaV;AAED,MAAM,WAAW,UAAU;IACzB,qBAAqB;IACrB,GAAG,EAAE,MAAM,CAAC;IACZ;;oEAEgE;IAChE,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAC7B,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,SAAS,CAAC,EAAE,MAAM,EAAE,EACpB,QAAQ,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,GAC7B,UAAU,EAAE,CAYd"}

package/dist/graph/source-files.js

@@ -10,7 +10,7 @@ import { statSync } from "node:fs";
 import { resolve } from "node:path";
 import { 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";
 import { languageOf, depthExtensions } from "./extract.js";
 import { genericLangOf, genericExtensions } from "./generic.js";
 import { containerLangOf, containerExtensions } from "./container.js";
@@ -41,23 +41,36 @@ export function unsupportedExtensions(exts) {
  * none of which ever see a CLI flag) behaves identically to the build that
  * saved those choices.
  */
+/** Keep only files whose repo-relative path is at or under one of `onlyDirs`.
+ * No-op when `onlyDirs` is empty/absent. The whitelist is carried in the graph
+ * itself (the fingerprint records it at build time), never in the source repo,
+ * so a build and the query-path freshness probe read the identical set. */
+export function filterByOnlyDirs(files, root, onlyDirs) {
+    if (!onlyDirs || onlyDirs.size === 0)
+        return files;
+    return files.filter((abs) => {
+        const rel = relPosix(root, abs);
+        return [...onlyDirs].some((d) => rel === d || rel.startsWith(`${d}/`));
+    });
+}
 export function listSourceFiles(root, outDir, repoFiles = walkDir(root, readIncludeDirs(resolve(root)), {
     followSubmodules: readFollowSubmodules(resolve(root)),
-})) {
+    followNestedRepos: readFollowNestedRepos(resolve(root)),
+}), onlyDirs) {
     // A file is a source file if a depth-tier grammar (languageOf), a breadth-tier
     // grammar (genericLangOf) or a container (containerLangOf) claims its extension.
     // All three must agree here or `build` and `check` would enumerate different sets.
-    return repoFiles.filter((f) => !f.startsWith(outDir) &&
-        (languageOf(f) !== null || genericLangOf(f) !== null || containerLangOf(f) !== null));
+    return filterByOnlyDirs(repoFiles.filter((f) => !f.startsWith(outDir) &&
+        (languageOf(f) !== null || genericLangOf(f) !== null || containerLangOf(f) !== null)), root, onlyDirs);
 }
 /**
  * {@link listSourceFiles} plus each file's `(size, mtimeMs)` — the currency of
  * both the freshness probe and the extraction cache. Files that vanish between
  * the walk and the stat are dropped (same fail-soft posture as `walkDir`).
  */
-export function listSourceStats(root, outDir, repoFiles) {
+export function listSourceStats(root, outDir, repoFiles, onlyDirs) {
     const out = [];
-    for (const abs of listSourceFiles(root, outDir, repoFiles)) {
+    for (const abs of listSourceFiles(root, outDir, repoFiles, onlyDirs)) {
         let s;
         try {
             s = statSync(abs);

package/dist/graph/source-files.js.map

@@ -1 +1 @@
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+{"version":3,"file":"source-files.js","sourceRoot":"","sources":["../../src/graph/source-files.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AACH,OAAO,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AACnC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAC;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,qBAAqB,EAAE,oBAAoB,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AAChG,OAAO,EAAE,UAAU,EAAE,eAAe,EAAE,MAAM,cAAc,CAAC;AAC3D,OAAO,EAAE,aAAa,EAAE,iBAAiB,EAAE,MAAM,cAAc,CAAC;AAChE,OAAO,EAAE,eAAe,EAAE,mBAAmB,EAAE,MAAM,gBAAgB,CAAC;AAEtE;mFACmF;AACnF,MAAM,UAAU,mBAAmB;IACjC,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,eAAe,EAAE,EAAE,GAAG,iBAAiB,EAAE,EAAE,GAAG,mBAAmB,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;AACvG,CAAC;AAED,6EAA6E;AAC7E,SAAS,OAAO,CAAC,CAAS;IACxB,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IACjC,OAAO,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;AACzC,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,qBAAqB,CAAC,IAAc;IAClD,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,mBAAmB,EAAE,CAAC,CAAC;IACjD,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AACxD,CAAC;AAED;;;;;;;GAOG;AACH;;;2EAG2E;AAC3E,MAAM,UAAU,gBAAgB,CAC9B,KAAe,EACf,IAAY,EACZ,QAA8B;IAE9B,IAAI,CAAC,QAAQ,IAAI,QAAQ,CAAC,IAAI,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC;IACnD,OAAO,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,EAAE;QAC1B,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;QAChC,OAAO,CAAC,GAAG,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,eAAe,CAC7B,IAAY,EACZ,MAAc,EACd,YAAsB,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,EAAE;IAClE,gBAAgB,EAAE,oBAAoB,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IACrD,iBAAiB,EAAE,qBAAqB,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;CACxD,CAAC,EACF,QAA8B;IAE9B,+EAA+E;IAC/E,iFAAiF;IACjF,mFAAmF;IACnF,OAAO,gBAAgB,CACrB,SAAS,CAAC,MAAM,CACd,CAAC,CAAC,EAAE,EAAE,CACJ,CAAC,CAAC,CAAC,UAAU,CAAC,MAAM,CAAC;QACrB,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,IAAI,IAAI,aAAa,CAAC,CAAC,CAAC,KAAK,IAAI,IAAI,eAAe,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CACvF,EACD,IAAI,EACJ,QAAQ,CACT,CAAC;AACJ,CAAC;AAaD;;;;GAIG;AACH,MAAM,UAAU,eAAe,CAC7B,IAAY,EACZ,MAAc,EACd,SAAoB,EACpB,QAA8B;IAE9B,MAAM,GAAG,GAAiB,EAAE,CAAC;IAC7B,KAAK,MAAM,GAAG,IAAI,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,SAAS,EAAE,QAAQ,CAAC,EAAE,CAAC;QACrE,IAAI,CAAoC,CAAC;QACzC,IAAI,CAAC;YACH,CAAC,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC;QACpB,CAAC;QAAC,MAAM,CAAC;YACP,SAAS;QACX,CAAC;QACD,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,EAAE,QAAQ,CAAC,IAAI,EAAE,GAAG,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;IAChF,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC"}

package/dist/graph/workspace-cli.d.ts

@@ -15,6 +15,8 @@ export interface WorkspaceBuildOptions {
     includeDirs?: string[];
     /** An explicit CLI submodule choice to persist into every child repo. */
     followSubmodules?: boolean;
+    /** An explicit CLI nested-clone choice to persist into every child repo. */
+    followNestedRepos?: boolean;
 }
 /** Build every git child into its own committable `graft/`, then replace the
  * parent's `graft/` with `workspace.json`. Prints the one-time split warning

package/dist/graph/workspace-cli.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"workspace-cli.d.ts","sourceRoot":"","sources":["../../src/graph/workspace-cli.ts"],"names":[],"mappings":"AAUA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAEvD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAa/C,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,OAAO,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB;qEACiE;IACjE,WAAW,EAAE,YAAY,CAAC;IAC1B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB;;;gEAG4D;IAC5D,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,yEAAyE;IACzE,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,4EAA4E;IAC5E,iBAAiB,CAAC,EAAE,OAAO,CAAC;CAC7B;AAED;;kDAEkD;AAClD,wBAAsB,iBAAiB,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,qBAAqB,GAAG,OAAO,CAAC,IAAI,CAAC,CAsChG;AAED,wBAAgB,eAAe,CAC7B,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,GAAG,SAAS,EAC5B,KAAK,EAAE,MAAM,EACb,IAAI,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAC;IAAC,IAAI,CAAC,EAAE,OAAO,CAAC;IAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,OAAO,CAAA;CAAE,GACtF,IAAI,CAIN;AAED,wBAAgB,gBAAgB,CAC9B,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,GAAG,SAAS,EAC5B,OAAO,EAAE,MAAM,EACf,IAAI,EAAE;IAAE,UAAU,CAAC,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,IAAI,CAAC,EAAE,OAAO,CAAA;CAAE,GAC9D,IAAI,CAYN;AAED,wBAAgB,eAAe,CAC7B,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,GAAG,SAAS,EAC5B,IAAI,EAAE;IAAE,OAAO,CAAC,EAAE,MAAM,CAAA;CAAE,GACzB,IAAI,CAEN;AAED,wBAAsB,iBAAiB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAItF;AAED,wBAAgB,mBAAmB,CACjC,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,GAAG,SAAS,EAC5B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE;IAAE,SAAS,CAAC,EAAE,SAAS,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,EAAE,CAAC,EAAE,MAAM,CAAA;CAAE,GAC3D,IAAI,CAON"}