@nanonets/graft 0.13.0 → 0.16.0

package/dist/graph/bindings.js

@@ -45,6 +45,8 @@ export function defName(node, lang) {
     }
     if (lang === "r")
         return rDefName(node);
+    if (lang === "swift")
+        return swiftDefName(node);
     if (lang === "php") {
         const phpDefTypes = new Set([
             "class_declaration",
@@ -86,6 +88,37 @@ export function defName(node, lang) {
     }
     return null;
 }
+/** The scope segment a Swift definition pushes, mirroring extract.ts's
+ * `describeSwift` (duplicated, not imported, per this file's
+ * no-value-import-of-extract rule): types and extensions push the type's name
+ * (an extension is named after the type it extends), functions their own name,
+ * and an `init` the enclosing type's name — extract.ts names initializers after
+ * their type, so the two scope stacks stay in lockstep inside an init body.
+ * Typealias and top-level properties DO mint nodes in extract.ts but are
+ * deliberately absent here: neither has a body a binding could be set in (a
+ * property initializer's closure is the one vanishing exception, mis-keying
+ * only bindings set inside itself). */
+function swiftDefName(node) {
+    if (node.type === "class_declaration") {
+        if (node.children.some((c) => c.type === "extension")) {
+            const ut = node.namedChildren.find((c) => c.type === "user_type");
+            const ids = ut?.namedChildren.filter((c) => c.type === "type_identifier") ?? [];
+            return ids.at(-1)?.text ?? null;
+        }
+        return node.namedChildren.find((c) => c.type === "type_identifier")?.text ?? null;
+    }
+    if (node.type === "protocol_declaration") {
+        return node.namedChildren.find((c) => c.type === "type_identifier")?.text ?? null;
+    }
+    if (node.type === "function_declaration" || node.type === "protocol_function_declaration") {
+        return node.namedChildren.find((c) => c.type === "simple_identifier")?.text ?? null;
+    }
+    if (node.type === "init_declaration") {
+        const owner = node.parent?.parent; // class_body / protocol_body → the declaration
+        return owner ? swiftDefName(owner) : null;
+    }
+    return null;
+}
 const R_ASSIGN_OPS = new Set(["<-", "<<-", "="]);
 const R_RIGHT_ASSIGN_OPS = new Set(["->", "->>"]);
 /**
@@ -147,11 +180,12 @@ function goReceiverTypeOf(node) {
 }
 /** Resolves a call site's receiver text (from `calleeName`) to a bound type
  * name, given the enclosing walk state. `self`/`cls`/`this`/the Go receiver
- * var resolve directly to the enclosing class; R6's `super` (Phase 3) resolves
- * to the PARENT class instead (`ctx.rSuperClass`, not `ctx.enclosingClass` —
- * a `super$method()` call must climb past the current class's own same-named
- * override, not find it); anything else is a bindings-map lookup, normalizing
- * `this.` to `self.` since both are stored the same way. */
+ * var resolve directly to the enclosing class; `super` — R6's `super$` and
+ * Swift's `super.` alike — resolves to the PARENT class instead
+ * (`ctx.rSuperClass`, not `ctx.enclosingClass` — a super call must climb past
+ * the current class's own same-named override, not find it); anything else is
+ * a bindings-map lookup, normalizing `this.` to `self.` since both are stored
+ * the same way. */
 export function resolveRecvType(receiver, ctx) {
     if (!receiver)
         return undefined;
@@ -170,6 +204,10 @@ export function resolveRecvType(receiver, ctx) {
         return receiver;
     return ((ctx.lang === "go" && receiver === ctx.goReceiverVar ? ctx.enclosingClass : undefined) ??
         ctx.bindings.lookup(ctx.scope, receiver) ??
+        // Swift type-member call `Animal.staticThing()`: an uppercase receiver with no
+        // local binding is the type itself (Swift naming: types are UpperCamelCase,
+        // values lowerCamelCase — and a shadowing binding was already tried above).
+        (ctx.lang === "swift" && /^[A-Z]/.test(receiver) ? receiver : undefined) ??
         undefined);
 }
 function isClassNode(node, lang) {
@@ -180,6 +218,11 @@ function isClassNode(node, lang) {
     if (lang === "typescript" || lang === "tsx") {
         return node.type === "class_declaration" || node.type === "abstract_class_declaration";
     }
+    // Swift: class_declaration covers class/struct/enum/actor/extension — all can
+    // hold members whose `self.field` bindings live at the type's scope.
+    if (lang === "swift") {
+        return node.type === "class_declaration" || node.type === "protocol_declaration";
+    }
     return false;
 }
 /** Java declarations that push a scope segment — mirrors extract.ts's JAVA_KINDS. */
@@ -244,6 +287,8 @@ function visit(node, lang, scope, classScope, bindings, aliases) {
         void 0;
     else if (lang === "java")
         handleJava(node, scope, classScope, bindings);
+    else if (lang === "swift")
+        handleSwift(node, scope, classScope, bindings);
     else if (lang === "php")
         handlePhp(node, scope, bindings);
     else
@@ -285,6 +330,73 @@ function callTypeName(node, aliases) {
         return null;
     return aliases.get(fn.text) ?? fn.text;
 }
+/** Swift variable->type bindings from the confident, syntax-local clues:
+ * a typed parameter (`func feed(animal: Animal)`, `init(keeper k: Keeper)` —
+ * the LAST simple_identifier before the `:` is the local name, the first may be
+ * an external argument label), a typed property (`var d: Doctor`), and an
+ * initializer-call assignment (`let vet = Vet()` — an initializer call is an
+ * ordinary call whose callee is the type's own UpperCamelCase name; Swift's
+ * naming convention makes the case split reliable, the same way Go's `NewX`
+ * convention is trusted in handleGo). A property directly inside a type body is
+ * a field: bound at the type's scope, both bare (`repo.save()`) and
+ * `self.`-prefixed (`self.repo.save()`), like Java's fields. */
+function handleSwift(node, scope, classScope, bindings) {
+    const scopePath = scope.join(".");
+    if (node.type === "parameter") {
+        const ids = node.namedChildren.filter((c) => c.type === "simple_identifier");
+        const name = ids.at(-1)?.text;
+        const type = swiftTypeName(node.namedChildren.find((c) => c.type === "user_type" || c.type === "optional_type"));
+        if (name && type)
+            bindings.set(scopePath, name, type);
+        return;
+    }
+    if (node.type !== "property_declaration")
+        return;
+    const name = node.namedChildren
+        .find((c) => c.type === "pattern")
+        ?.namedChildren.find((c) => c.type === "simple_identifier")?.text;
+    if (!name)
+        return;
+    const annotated = node.namedChildren
+        .find((c) => c.type === "type_annotation")
+        ?.namedChildren.find((c) => c.type === "user_type" || c.type === "optional_type");
+    const type = swiftTypeName(annotated) ??
+        swiftCtorTypeName(node.namedChildren.find((c) => c.type === "call_expression"));
+    if (!type)
+        return;
+    const isField = node.parent?.type === "class_body" || node.parent?.type === "protocol_body";
+    const target = isField ? (classScope ?? scopePath) : scopePath;
+    bindings.set(target, name, type);
+    if (isField)
+        bindings.set(target, `self.${name}`, type);
+}
+/** A Swift type node's bare name: a `user_type`'s LAST type_identifier (so a
+ * module-qualified `Foundation.Date` binds as `Date`, generic arguments live in
+ * nested nodes and never leak in), unwrapping one level of optional (`Animal?`).
+ * Collections, tuples, and function types bind nothing — no single confident
+ * receiver type to name. */
+function swiftTypeName(node) {
+    if (!node)
+        return null;
+    if (node.type === "optional_type") {
+        return swiftTypeName(node.namedChildren.find((c) => c.type === "user_type"));
+    }
+    if (node.type !== "user_type")
+        return null;
+    const ids = node.namedChildren.filter((c) => c.type === "type_identifier");
+    return ids.at(-1)?.text ?? null;
+}
+/** The type constructed by an initializer call (`Vet()` → `Vet`), or null when
+ * the callee isn't a bare UpperCamelCase name — a lowercase callee is an
+ * ordinary function whose return type a single-file pass cannot know. */
+function swiftCtorTypeName(call) {
+    if (call?.type !== "call_expression")
+        return null;
+    const fn = call.namedChildren[0];
+    if (fn?.type !== "simple_identifier")
+        return null;
+    return /^[A-Z]/.test(fn.text) ? fn.text : null;
+}
 /** PHP variable->type bindings from the two confident, syntax-local clues:
  * a type-hinted parameter (`function f(Foo $x)`) and a `new` assignment
  * (`$x = new Foo()`). Keyed by the `$var` text (with the `$`) so a

package/dist/graph/bindings.js.map

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package/dist/graph/build.d.ts

@@ -22,6 +22,10 @@ export interface GraphBuildOptions {
     summarizer?: CruxSummarizer;
     /** Max files summarized in parallel during the Tier-2 pass. Default is set in enrich. */
     concurrency?: number;
+    /** Repo-relative directory prefixes to limit the build to (`--only-dir`). When
+     * set, only files under these prefixes are indexed; the list is recorded in the
+     * fingerprint so the freshness probe enumerates the same set. */
+    onlyDirs?: string[];
     onProgress?: (info: {
         phase: "parse" | "enrich";
         index: number;

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

@@ -1 +1 @@
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package/dist/graph/build.js

@@ -23,11 +23,11 @@ import { containerLangOf, extractContainer, warmContainerGrammars } from "./cont
 import { contentHash } from "../util/id.js";
 import { relPosix } from "../util/paths.js";
 import { readSourceFile } from "../util/source.js";
-import { readFollowSubmodules, readIncludeDirs } from "../util/state.js";
+import { readFollowNestedRepos, readFollowSubmodules, readIncludeDirs } from "../util/state.js";
 import { emptyExtractCache, readExtractCache, writeExtractCache, } from "./extract-cache.js";
 import { writeFingerprint } from "./fingerprint.js";
 import { seedGraph } from "./seed.js";
-import { listSourceStats } from "./source-files.js";
+import { filterByOnlyDirs, listSourceStats } from "./source-files.js";
 import { resolveEdges } from "./resolve.js";
 import { enrichGraph } from "./enrich.js";
 import { readGraph, writeGraph, wiringPath } from "./write.js";
@@ -95,9 +95,12 @@ export async function buildGraph(dir, opts = {}) {
     // Enumerate once: source extraction, scope discovery, and Go module
     // resolution must agree on the same Git-ignore-aware working-tree view —
     // including the repo's persisted directory and submodule choices.
-    const repoFiles = walkDir(root, readIncludeDirs(root), {
+    const walked = walkDir(root, readIncludeDirs(root), {
         followSubmodules: readFollowSubmodules(root),
+        followNestedRepos: readFollowNestedRepos(root),
     });
+    const onlyDirs = opts.onlyDirs && opts.onlyDirs.length > 0 ? new Set(opts.onlyDirs) : undefined;
+    const repoFiles = filterByOnlyDirs(walked, root, onlyDirs);
     const files = listSourceStats(root, outDir, repoFiles);
     const discoveredScopes = discoverScopes(root, repoFiles);
     const nodes = [];
@@ -274,7 +277,7 @@ export async function buildGraph(dir, opts = {}) {
     // these source bytes." Nothing about the projections below — which is why it is
     // safe to write here, and why `graphOnly` builds (the query path, which stops
     // right after this line) are still recorded as fresh.
-    writeFingerprint(outDir, entries);
+    writeFingerprint(outDir, entries, opts.onlyDirs);
     // Tier-2 passive surface: project the nodes into per-file markdown cards, and
     // refresh the INDEX roster. Pure projection — no LLM, no network.
     //

package/dist/graph/build.js.map

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package/dist/graph/cards.d.ts

@@ -37,9 +37,10 @@ export interface CoverRef {
  *
  * A surgical frontmatter patch: the generated body and every other key are
  * preserved verbatim; only `covers` is added/replaced. Concept nodes are the
- * top-level `.md` files (cards live in subdirs; INDEX.md is skipped). On a $0
- * structure-only build there are no concept nodes, so this is a no-op. Returns
- * the number of nodes enriched.
+ * top-level `.md` files that carry a `slug` (cards live in subdirs, or at the
+ * top level without a slug when they mirror a root source; INDEX.md is skipped).
+ * On a $0 structure-only build there are no concept nodes, so this is a no-op.
+ * Returns the number of nodes enriched.
  */
 export declare function writeCovers(graph: GraphV1, outDir: string): number;
 //# sourceMappingURL=cards.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"cards.d.ts","sourceRoot":"","sources":["../../src/graph/cards.ts"],"names":[],"mappings":"AAoBA,OAAO,KAAK,EAAE,OAAO,EAAU,MAAM,YAAY,CAAC;AAMlD,MAAM,WAAW,YAAY;IAC3B,yEAAyE;IACzE,IAAI,EAAE,MAAM,CAAC;IACb,gEAAgE;IAChE,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,SAAS;IACxB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,YAAY,EAAE,CAAC;CACvB;AA4GD;;;GAGG;AACH,wBAAgB,UAAU,CAAC,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,SAAS,CAiCpE;AAED;;;GAGG;AACH,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,YAAY,EAAE,GAAG,IAAI,CAyCtE;AAED,iFAAiF;AACjF,MAAM,WAAW,QAAQ;IACvB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,MAAM,CAAC;IACb,2EAA2E;IAC3E,EAAE,EAAE,MAAM,CAAC;CACZ;AAED;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,CAoClE"}
+{"version":3,"file":"cards.d.ts","sourceRoot":"","sources":["../../src/graph/cards.ts"],"names":[],"mappings":"AAoBA,OAAO,KAAK,EAAE,OAAO,EAAU,MAAM,YAAY,CAAC;AASlD,MAAM,WAAW,YAAY;IAC3B,yEAAyE;IACzE,IAAI,EAAE,MAAM,CAAC;IACb,gEAAgE;IAChE,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,SAAS;IACxB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,YAAY,EAAE,CAAC;CACvB;AA6HD;;;GAGG;AACH,wBAAgB,UAAU,CAAC,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,SAAS,CAiCpE;AAED;;;GAGG;AACH,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,YAAY,EAAE,GAAG,IAAI,CAyCtE;AAED,iFAAiF;AACjF,MAAM,WAAW,QAAQ;IACvB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,MAAM,CAAC;IACb,2EAA2E;IAC3E,EAAE,EAAE,MAAM,CAAC;CACZ;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,CAuClE"}

package/dist/graph/cards.js

@@ -21,10 +21,32 @@ import matter from "gray-matter";
 import { CACHE_DIR, readNodes } from "../context/node-file.js";
 import { GRAPH_DIR } from "./write.js";
 const INDEX_FILE = "INDEX.md";
-/** The card path for a source path: mirror the tree, swap the extension for .md. */
+/** Where a root-level file card goes when `graft/<stem>.md` is already a concept
+ * node (same stem as a slug — Laravel `server.php` vs a "Server" concept). */
+const ROOT_CARD_DIR = "_root";
+/** True when `path` is an existing concept node (frontmatter carries `slug`). */
+function isConceptNodeFile(path) {
+    if (!existsSync(path))
+        return false;
+    try {
+        const fm = matter(readFileSync(path, "utf8")).data;
+        return fm.slug != null && String(fm.slug).length > 0;
+    }
+    catch {
+        return false;
+    }
+}
+/** The card path for a source path: mirror the tree, swap the extension for .md.
+ * Root-level sources share `graft/` with concept nodes. If that filename is
+ * already a concept, park the file card under `_root/` instead of clobbering it. */
 function cardPathFor(outDir, sourcePath) {
     const md = sourcePath.replace(/\.[^./]+$/, "") + ".md";
-    return join(outDir, md);
+    const primary = join(outDir, md);
+    if (sourcePath.includes("/"))
+        return primary;
+    if (isConceptNodeFile(primary))
+        return join(outDir, ROOT_CARD_DIR, md);
+    return primary;
 }
 /** Starting line of an "L43-L55" span, for stable ordering (0 if unparseable). */
 function spanStart(span) {
@@ -87,7 +109,8 @@ function listExistingCards(outDir) {
         }
     };
     for (const e of readdirSync(outDir, { withFileTypes: true })) {
-        // Concept nodes and INDEX.md are top-level files — skip. Cards are in subdirs.
+        // Concept nodes and INDEX.md are top-level files — skip. Cards live in
+        // subdirs (`src/…`, and `_root/` when a root card would collide with a concept).
         if (e.isDirectory() && e.name !== CACHE_DIR && e.name !== GRAPH_DIR) {
             walk(join(outDir, e.name));
         }
@@ -202,9 +225,10 @@ export function writeIndex(outDir, files) {
  *
  * A surgical frontmatter patch: the generated body and every other key are
  * preserved verbatim; only `covers` is added/replaced. Concept nodes are the
- * top-level `.md` files (cards live in subdirs; INDEX.md is skipped). On a $0
- * structure-only build there are no concept nodes, so this is a no-op. Returns
- * the number of nodes enriched.
+ * top-level `.md` files that carry a `slug` (cards live in subdirs, or at the
+ * top level without a slug when they mirror a root source; INDEX.md is skipped).
+ * On a $0 structure-only build there are no concept nodes, so this is a no-op.
+ * Returns the number of nodes enriched.
  */
 export function writeCovers(graph, outDir) {
     if (!existsSync(outDir))
@@ -226,6 +250,10 @@ export function writeCovers(graph, outDir) {
             continue;
         const full = join(outDir, entry);
         const parsed = matter(readFileSync(full, "utf8"));
+        // Root-level file cards have no concept slug; stamping `covers: []` onto
+        // them made readNodes treat them as concept nodes (#261).
+        if (parsed.data.slug == null || String(parsed.data.slug).length === 0)
+            continue;
         const sources = Array.isArray(parsed.data.sources)
             ? parsed.data.sources
             : [];

package/dist/graph/cards.js.map

@@ -1 +1 @@
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package/dist/graph/check.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/graph/check.ts"],"names":[],"mappings":"AA4BA,MAAM,WAAW,gBAAgB;IAC/B,EAAE,EAAE,OAAO,CAAC;IACZ,uEAAuE;IACvE,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,2EAA2E;IAC3E,OAAO,EAAE,MAAM,CAAC;IAChB;qEACiE;IACjE,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB;;sFAEkF;IAClF,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,iBAAiB;IAChC,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAMD,wBAAsB,UAAU,CAC9B,GAAG,EAAE,MAAM,EACX,IAAI,GAAE,iBAAsB,GAC3B,OAAO,CAAC,gBAAgB,CAAC,CA0E3B;AAED,8DAA8D;AAC9D,wBAAgB,sBAAsB,CAAC,CAAC,EAAE,gBAAgB,GAAG,MAAM,CAkClE"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/graph/check.ts"],"names":[],"mappings":"AA8BA,MAAM,WAAW,gBAAgB;IAC/B,EAAE,EAAE,OAAO,CAAC;IACZ,uEAAuE;IACvE,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,2EAA2E;IAC3E,OAAO,EAAE,MAAM,CAAC;IAChB;qEACiE;IACjE,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB;;sFAEkF;IAClF,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,iBAAiB;IAChC,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAMD,wBAAsB,UAAU,CAC9B,GAAG,EAAE,MAAM,EACX,IAAI,GAAE,iBAAsB,GAC3B,OAAO,CAAC,gBAAgB,CAAC,CAuG3B;AAED,8DAA8D;AAC9D,wBAAgB,sBAAsB,CAAC,CAAC,EAAE,gBAAgB,GAAG,MAAM,CAkClE"}

package/dist/graph/check.js

@@ -22,8 +22,10 @@ import { relPosix } from "../util/paths.js";
 import { contextDirFor } from "../context/node-file.js";
 import { extractFile, languageOf } from "./extract.js";
 import { extractGeneric, genericLangOf, warmGenericGrammars } from "./generic.js";
+import { containerLangOf, extractContainer, warmContainerGrammars } from "./container.js";
 import { listSourceFiles } from "./build.js";
 import { readGraph, wiringPath } from "./write.js";
+import { readFingerprint } from "./fingerprint.js";
 import { readSourceFile } from "../util/source.js";
 // async: the breadth tier's WASM grammars load asynchronously and must be warmed
 // before the (synchronous) re-extraction below, exactly as buildGraph does — else
@@ -49,12 +51,27 @@ export async function checkGraph(dir, opts = {}) {
         return result;
     }
     // Freshly extract Tier-1 nodes from the code on disk (same file set as build).
-    const sourceFiles = listSourceFiles(root, outDir);
+    // A `--only-dir` build records its whitelist in the fingerprint; read it back
+    // so `check` diffs the same limited set instead of flagging every excluded
+    // file as "added".
+    const fpOnlyDirs = readFingerprint(outDir)?.onlyDirs;
+    const onlyDirs = fpOnlyDirs && fpOnlyDirs.length > 0 ? new Set(fpOnlyDirs) : undefined;
+    const sourceFiles = listSourceFiles(root, outDir, undefined, onlyDirs);
     await warmGenericGrammars(new Set(sourceFiles.map((f) => genericLangOf(f)?.name).filter((n) => !!n)));
+    // Container-tier grammars need the same warmup as the generic ones, for the same
+    // reason: extraction below is synchronous. Missing this is what made `graft
+    // check` report every `.vue` node as `removed` right after a clean build (#236)
+    // — the tier extracted fine, and then the check had no branch that could see it.
+    await warmContainerGrammars(new Set(sourceFiles.map((f) => containerLangOf(f)?.name).filter((n) => !!n)));
     const current = new Map(); // id → body_hash
     for (const file of sourceFiles) {
+        // The same three-way branch `buildGraph` uses, in the same order. The two must
+        // stay in step: a tier the build extracts and the check cannot see reports as
+        // `removed` forever, and the `graft build` the check tells you to run can never
+        // repair it.
         const lang = languageOf(file);
-        const generic = lang ? null : genericLangOf(file);
+        const container = lang ? null : containerLangOf(file);
+        const generic = lang || container ? null : genericLangOf(file);
         let source;
         try {
             source = readSourceFile(file);
@@ -64,11 +81,24 @@ export async function checkGraph(dir, opts = {}) {
         }
         if (source === null)
             continue; // unsupported encoding (e.g. UTF-16BE)
+        const rel = relPosix(root, file);
         try {
-            const { nodes } = lang
-                ? extractFile(relPosix(root, file), source, lang)
-                : extractGeneric(relPosix(root, file), source, generic.name);
-            for (const n of nodes)
+            const extracted = lang
+                ? extractFile(rel, source, lang)
+                : container
+                    ? extractContainer(rel, source, container)
+                    : generic
+                        ? extractGeneric(rel, source, generic.name)
+                        : null;
+            // No tier claims this file. Spelled out rather than asserted away: the
+            // `generic!` that used to stand in this position threw a TypeError on a
+            // container-tier file, the catch below swallowed it as a parse failure, and
+            // a missing branch became a silent permanent `removed` (#236). Returning
+            // null here means the next tier graft gains fails loudly in the type
+            // checker instead.
+            if (extracted === null)
+                continue;
+            for (const n of extracted.nodes)
                 current.set(n.id, n.body_hash);
         }
         catch {