diff --git a/gitnexus/src/cli/analyze.ts b/gitnexus/src/cli/analyze.ts
index 3f196b11d1..a3bf6cd5a6 100644
--- a/gitnexus/src/cli/analyze.ts
+++ b/gitnexus/src/cli/analyze.ts
@@ -37,7 +37,7 @@ import {
 } from './analyze-config.js';
 import { runFullAnalysis } from '../core/run-analyze.js';
 import { getMaxFileSizeBannerMessage } from '../core/ingestion/utils/max-file-size.js';
-import { warnMissingOptionalGrammars } from './optional-grammars.js';
+import { warnMissingOptionalGrammars, getOptionalGrammarExtensions } from './optional-grammars.js';
 import { glob } from 'glob';
 import fs from 'fs/promises';
 import { cliError } from './cli-message.js';
@@ -943,11 +943,13 @@ const analyzeCommandImpl = async (
   }
 
   // If the target repo contains files an optional grammar would parse but
-  // that grammar's native binding is absent, warn before analysis so users
-  // learn why those files end up unparsed instead of silently getting a
-  // degraded index.
+  // that grammar's native binding is absent (or disabled via
+  // GITNEXUS_SKIP_OPTIONAL_GRAMMARS), warn before analysis so users learn why
+  // those files end up unparsed instead of silently getting a degraded index.
+  // The extension set is derived from OPTIONAL_GRAMMARS so it can't drift.
   try {
-    const matches = await glob(['**/*.dart', '**/*.proto'], {
+    const optionalGlobs = getOptionalGrammarExtensions().map((e) => `**/*${e}`);
+    const matches = await glob(optionalGlobs, {
       cwd: repoPath,
       ignore: ['**/node_modules/**', '**/.git/**', '**/dist/**', '**/build/**'],
       dot: false,
diff --git a/gitnexus/src/cli/optional-grammars.ts b/gitnexus/src/cli/optional-grammars.ts
index e12b471e0e..994016a569 100644
--- a/gitnexus/src/cli/optional-grammars.ts
+++ b/gitnexus/src/cli/optional-grammars.ts
@@ -4,18 +4,22 @@
  * tree-sitter-dart, tree-sitter-proto, and tree-sitter-swift are vendored
  * under vendor/ and materialized into node_modules/ at postinstall. Dart
  * and Proto are built from source with node-gyp; Swift ships platform
- * prebuilds activated via node-gyp-build. All three can be skipped via
+ * prebuilds activated via node-gyp-build. tree-sitter-kotlin is a declared
+ * optionalDependency (not vendored). All can be skipped via
  * GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 (postinstall scripts), or can silently
- * soft-fail when the toolchain is missing (Dart/Proto) or no prebuild
- * matches the host platform (Swift).
+ * soft-fail when the toolchain is missing (Dart/Proto), when no prebuild
+ * matches the host platform (Swift), or when the optional install was
+ * skipped or its native build failed (Kotlin).
  *
  * Either path produces the same observable: the .node binding is absent
  * at runtime. This helper detects that condition and surfaces a single
- * stderr line per missing grammar so users learn why .dart/.proto/.swift
+ * stderr line per missing grammar so users learn why .dart/.proto/.swift/.kt
  * support is unavailable instead of silently getting a degraded index.
  */
 
 import { createRequire } from 'module';
+import { SupportedLanguages } from 'gitnexus-shared';
+import { isGrammarRuntimeSkipped } from '../core/tree-sitter/parser-loader.js';
 import { cliWarn } from './cli-message.js';
 
 const _require = createRequire(import.meta.url);
@@ -27,17 +31,55 @@ interface OptionalGrammar {
   pkg: string;
   /** File extensions this grammar parses */
   extensions: string[];
+  /**
+   * SupportedLanguages id, when this grammar backs an ingestion language.
+   * Used to ask `isGrammarRuntimeSkipped` whether the grammar was disabled via
+   * `GITNEXUS_SKIP_OPTIONAL_GRAMMARS` (vs. genuinely missing). Omitted for
+   * `.proto`, which is a gRPC-extractor concern, not a SupportedLanguages.
+   */
+  language?: SupportedLanguages;
 }
 
 const OPTIONAL_GRAMMARS: OptionalGrammar[] = [
-  { name: 'tree-sitter-dart', pkg: 'tree-sitter-dart', extensions: ['.dart'] },
+  {
+    name: 'tree-sitter-dart',
+    pkg: 'tree-sitter-dart',
+    extensions: ['.dart'],
+    language: SupportedLanguages.Dart,
+  },
   { name: 'tree-sitter-proto', pkg: 'tree-sitter-proto', extensions: ['.proto'] },
-  { name: 'tree-sitter-swift', pkg: 'tree-sitter-swift', extensions: ['.swift'] },
+  {
+    name: 'tree-sitter-swift',
+    pkg: 'tree-sitter-swift',
+    extensions: ['.swift'],
+    language: SupportedLanguages.Swift,
+  },
+  {
+    name: 'tree-sitter-kotlin',
+    pkg: 'tree-sitter-kotlin',
+    extensions: ['.kt', '.kts'],
+    language: SupportedLanguages.Kotlin,
+  },
 ];
 
+/**
+ * The file extensions backed by an optional grammar — the single source for
+ * the `analyze` preflight glob (so the glob can't drift from this list).
+ */
+export function getOptionalGrammarExtensions(): string[] {
+  return [...new Set(OPTIONAL_GRAMMARS.flatMap((g) => g.extensions))];
+}
+
 export interface MissingGrammar {
   name: string;
   extensions: string[];
+  /**
+   * `missing` — the native binding could not be loaded (not installed / build
+   * soft-failed / no prebuild). `skipped` — the binding is fine but the user
+   * disabled it via `GITNEXUS_SKIP_OPTIONAL_GRAMMARS`. Drives the warning text
+   * so a deliberate opt-out is not told to reinstall.
+   */
+  reason: 'missing' | 'skipped';
 }
 
 /**
@@ -59,6 +101,13 @@ export interface MissingGrammar {
 export function detectMissingOptionalGrammars(): MissingGrammar[] {
   const missing: MissingGrammar[] = [];
   for (const g of OPTIONAL_GRAMMARS) {
+    // Deliberate runtime opt-out comes first: even an installed binding is
+    // treated as unavailable, with a `skipped` reason so the warning says so
+    // instead of suggesting a reinstall (#2101 review).
+    if (g.language !== undefined && isGrammarRuntimeSkipped(g.language)) {
+      missing.push({ name: g.name, extensions: g.extensions, reason: 'skipped' });
+      continue;
+    }
     try {
       _require(g.pkg);
     } catch (err) {
@@ -80,7 +129,7 @@ export function detectMissingOptionalGrammars(): MissingGrammar[] {
           { grammar: g.name, extensions: g.extensions, error: msg },
         );
       }
-      missing.push({ name: g.name, extensions: g.extensions });
+      missing.push({ name: g.name, extensions: g.extensions, reason: 'missing' });
     }
   }
   return missing;
@@ -110,9 +159,16 @@ export function warnMissingOptionalGrammars(opts?: {
     if (relevantExtensions && !g.extensions.some((e) => relevantExtensions.has(e))) {
       continue;
     }
-    cliWarn(
-      `GitNexus${ctx}: optional grammar "${g.name}" is unavailable — ${g.extensions.join('/')} files will not be parsed. Reinstall without GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 (and ensure python3, make, g++) to enable.`,
-      { grammar: g.name, extensions: g.extensions, context: opts?.context },
-    );
+    const exts = g.extensions.join('/');
+    const message =
+      g.reason === 'skipped'
+        ? `GitNexus${ctx}: optional grammar "${g.name}" is disabled via GITNEXUS_SKIP_OPTIONAL_GRAMMARS — ${exts} files will not be parsed. Unset the variable to re-enable.`
+        : `GitNexus${ctx}: optional grammar "${g.name}" is unavailable — ${exts} files will not be parsed. Reinstall without GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 (and ensure python3, make, g++) to enable.`;
+    cliWarn(message, {
+      grammar: g.name,
+      extensions: g.extensions,
+      reason: g.reason,
+      context: opts?.context,
+    });
   }
 }
diff --git a/gitnexus/src/core/ingestion/languages/dart/query.ts b/gitnexus/src/core/ingestion/languages/dart/query.ts
index 7d66b1c4a5..5314b0c8b1 100644
--- a/gitnexus/src/core/ingestion/languages/dart/query.ts
+++ b/gitnexus/src/core/ingestion/languages/dart/query.ts
@@ -23,7 +23,15 @@
  */
 
 import Parser from 'tree-sitter';
-import Dart from 'tree-sitter-dart';
+import { SupportedLanguages } from 'gitnexus-shared';
+// `tree-sitter-dart` is an optional/vendored grammar that may be absent on a
+// default install. Loaded lazily + guarded via parser-loader rather than
+// statically imported: this module is pulled onto the main thread eagerly by
+// the scope-resolution registry and the language-provider index, so a top-level
+// `import Dart from 'tree-sitter-dart'` would throw ERR_MODULE_NOT_FOUND at
+// module-load and crash `analyze` even for repos with no Dart files (#2091,
+// #2093). The grammar is only ever needed inside the lazy getters below.
+import { getLanguageGrammar } from '../../../tree-sitter/parser-loader.js';
 
 const DART_SCOPE_QUERY = `
 ; ── Scopes ───────────────────────────────────────────────────────────────────
@@ -134,14 +142,19 @@ let _query: Parser.Query | null = null;
 export function getDartParser(): Parser {
   if (_parser === null) {
     _parser = new Parser();
-    _parser.setLanguage(Dart as Parameters<Parser['setLanguage']>[0]);
+    _parser.setLanguage(
+      getLanguageGrammar(SupportedLanguages.Dart) as Parameters<Parser['setLanguage']>[0],
+    );
   }
   return _parser;
 }
 
 export function getDartScopeQuery(): Parser.Query {
   if (_query === null) {
-    _query = new Parser.Query(Dart as Parameters<Parser['setLanguage']>[0], DART_SCOPE_QUERY);
+    _query = new Parser.Query(
+      getLanguageGrammar(SupportedLanguages.Dart) as Parameters<Parser['setLanguage']>[0],
+      DART_SCOPE_QUERY,
+    );
   }
   return _query;
 }
diff --git a/gitnexus/src/core/ingestion/languages/kotlin/query.ts b/gitnexus/src/core/ingestion/languages/kotlin/query.ts
index 31613a38e3..f3a7490866 100644
--- a/gitnexus/src/core/ingestion/languages/kotlin/query.ts
+++ b/gitnexus/src/core/ingestion/languages/kotlin/query.ts
@@ -1,5 +1,13 @@
 import Parser from 'tree-sitter';
-import Kotlin from 'tree-sitter-kotlin';
+import { SupportedLanguages } from 'gitnexus-shared';
+// `tree-sitter-kotlin` is an optionalDependency that may be absent on a default
+// install (or fail its native build). Loaded lazily + guarded via parser-loader
+// rather than statically imported: this module is pulled onto the main thread
+// eagerly by the scope-resolution registry and the language-provider index, so
+// a top-level `import Kotlin from 'tree-sitter-kotlin'` would throw
+// ERR_MODULE_NOT_FOUND at module-load and crash `analyze` even for repos with no
+// Kotlin files (#2091, #2093). The grammar is only ever needed in the getters.
+import { getLanguageGrammar } from '../../../tree-sitter/parser-loader.js';
 
 const KOTLIN_SCOPE_QUERY = `
 ;; Scopes
@@ -179,14 +187,19 @@ let query: Parser.Query | null = null;
 export function getKotlinParser(): Parser {
   if (parser === null) {
     parser = new Parser();
-    parser.setLanguage(Kotlin as Parameters<Parser['setLanguage']>[0]);
+    parser.setLanguage(
+      getLanguageGrammar(SupportedLanguages.Kotlin) as Parameters<Parser['setLanguage']>[0],
+    );
   }
   return parser;
 }
 
 export function getKotlinScopeQuery(): Parser.Query {
   if (query === null) {
-    query = new Parser.Query(Kotlin as Parameters<Parser['setLanguage']>[0], KOTLIN_SCOPE_QUERY);
+    query = new Parser.Query(
+      getLanguageGrammar(SupportedLanguages.Kotlin) as Parameters<Parser['setLanguage']>[0],
+      KOTLIN_SCOPE_QUERY,
+    );
   }
   return query;
 }
diff --git a/gitnexus/src/core/ingestion/languages/swift/query.ts b/gitnexus/src/core/ingestion/languages/swift/query.ts
index cf26994232..78c1efa417 100644
--- a/gitnexus/src/core/ingestion/languages/swift/query.ts
+++ b/gitnexus/src/core/ingestion/languages/swift/query.ts
@@ -43,7 +43,15 @@
  */
 
 import Parser from 'tree-sitter';
-import Swift from 'tree-sitter-swift';
+import { SupportedLanguages } from 'gitnexus-shared';
+// `tree-sitter-swift` is an optional/vendored grammar that may be absent on a
+// default install. It is loaded lazily + guarded via parser-loader rather than
+// statically imported: this module is pulled onto the main thread eagerly by
+// the scope-resolution registry and the language-provider index, so a top-level
+// `import Swift from 'tree-sitter-swift'` would throw ERR_MODULE_NOT_FOUND at
+// module-load and crash `analyze` even for repos with no Swift files (#2091,
+// #2093). The grammar is only ever needed inside the lazy getters below.
+import { getLanguageGrammar } from '../../../tree-sitter/parser-loader.js';
 
 const SWIFT_SCOPE_QUERY = `
 ;; ── Scopes ──────────────────────────────────────────────────────────
@@ -186,14 +194,19 @@ let _query: Parser.Query | null = null;
 export function getSwiftParser(): Parser {
   if (_parser === null) {
     _parser = new Parser();
-    _parser.setLanguage(Swift as Parameters<Parser['setLanguage']>[0]);
+    _parser.setLanguage(
+      getLanguageGrammar(SupportedLanguages.Swift) as Parameters<Parser['setLanguage']>[0],
+    );
   }
   return _parser;
 }
 
 export function getSwiftScopeQuery(): Parser.Query {
   if (_query === null) {
-    _query = new Parser.Query(Swift as Parameters<Parser['setLanguage']>[0], SWIFT_SCOPE_QUERY);
+    _query = new Parser.Query(
+      getLanguageGrammar(SupportedLanguages.Swift) as Parameters<Parser['setLanguage']>[0],
+      SWIFT_SCOPE_QUERY,
+    );
   }
   return _query;
 }
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts b/gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts
index 244f178dd5..ddc8c902e1 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts
@@ -43,9 +43,13 @@ import {
   type ExportedTypeMap,
 } from '../call-processor.js';
 import { createSemanticModel, type MutableSemanticModel } from '../model/index.js';
-import { type PipelineProgress, getLanguageFromFilename } from 'gitnexus-shared';
+import {
+  type PipelineProgress,
+  getLanguageFromFilename,
+  SupportedLanguages,
+} from 'gitnexus-shared';
 import { readFileContents } from '../filesystem-walker.js';
-import { isLanguageAvailable } from '../../tree-sitter/parser-loader.js';
+import { isLanguageAvailable, isGrammarRuntimeSkipped } from '../../tree-sitter/parser-loader.js';
 import {
   createWorkerPool,
   workerPoolDisabledByEnv,
@@ -274,9 +278,18 @@ export async function runChunkedParseAndResolve(
     }
   }
   for (const [lang, count] of skippedByLang) {
-    logger.warn(
-      `Skipping ${count} ${lang} file(s) — ${lang} parser not available (native binding may not have built). Try: npm rebuild tree-sitter-${lang}`,
-    );
+    // Distinguish a deliberate runtime opt-out from a genuinely-missing binding
+    // so we don't tell a user who set GITNEXUS_SKIP_OPTIONAL_GRAMMARS to
+    // `npm rebuild` a grammar that built fine (#2091/#2093 review).
+    if (isGrammarRuntimeSkipped(lang as SupportedLanguages)) {
+      logger.warn(
+        `Skipping ${count} ${lang} file(s) — ${lang} parsing disabled via GITNEXUS_SKIP_OPTIONAL_GRAMMARS.`,
+      );
+    } else {
+      logger.warn(
+        `Skipping ${count} ${lang} file(s) — ${lang} parser not available (native binding may not have built). Try: npm rebuild tree-sitter-${lang}`,
+      );
+    }
   }
 
   // Sort parseableScanned alphabetically for stable chunk membership
diff --git a/gitnexus/src/core/ingestion/scope-resolution/pipeline/phase.ts b/gitnexus/src/core/ingestion/scope-resolution/pipeline/phase.ts
index 3c3f688ec6..d686bdd430 100644
--- a/gitnexus/src/core/ingestion/scope-resolution/pipeline/phase.ts
+++ b/gitnexus/src/core/ingestion/scope-resolution/pipeline/phase.ts
@@ -31,6 +31,7 @@ import type { ParseOutput } from '../../pipeline-phases/parse.js';
 import { SupportedLanguages, getLanguageFromFilename } from 'gitnexus-shared';
 import { readFileContents } from '../../filesystem-walker.js';
 import { runScopeResolution, type ScopeResolutionSubPhase } from './run.js';
+import { isLanguageAvailable } from '../../../tree-sitter/parser-loader.js';
 import { buildGraphNodeLookup } from '../graph-bridge/node-lookup.js';
 import { SCOPE_RESOLVERS } from './registry.js';
 import { isDev, isSemanticModelValidatorEnabled } from '../../utils/env.js';
@@ -170,6 +171,15 @@ export const scopeResolutionPhase: PipelinePhase<ScopeResolutionOutput> = {
     for (const f of scannedFiles) {
       const fileLang = getLanguageFromFilename(f.path);
       if (fileLang === null) continue;
+      // Skip files whose grammar isn't available (optional grammars like
+      // swift/dart/kotlin on an install where the binding is absent or the
+      // user set GITNEXUS_SKIP_OPTIONAL_GRAMMARS). The parse phase already
+      // excluded and warned about these (parse-impl.ts); without this guard the
+      // file would fall through to the main-thread re-extract in run.ts and
+      // throw "Unsupported language" (caught, but noisy, and it needlessly
+      // loads the grammar on the main thread). `isLanguageAvailable` is
+      // memoized, so this stays O(1) per language. (#2091, #2093)
+      if (!isLanguageAvailable(fileLang)) continue;
       let bucket = filesByLang.get(fileLang);
       if (bucket === undefined) {
         bucket = [];
diff --git a/gitnexus/src/core/ingestion/workers/parse-worker.ts b/gitnexus/src/core/ingestion/workers/parse-worker.ts
index b0f7878550..b32d957589 100644
--- a/gitnexus/src/core/ingestion/workers/parse-worker.ts
+++ b/gitnexus/src/core/ingestion/workers/parse-worker.ts
@@ -36,6 +36,19 @@ import type {
 /** Language grammar type accepted by Parser.setLanguage(). */
 type TreeSitterLanguage = Parameters<typeof Parser.prototype.setLanguage>[0];
 
+// ── Worker grammar loading — enforcement boundary (#2091/#2093, #2101) ───────
+// The worker maintains its own grammar table (the guarded `_require`s below +
+// `languageMap`) and intentionally does NOT consult the runtime
+// `GITNEXUS_SKIP_OPTIONAL_GRAMMARS` opt-out. It does not need to: the MAIN
+// THREAD's `parseableScanned` filter (pipeline-phases/parse-impl.ts, gated on
+// `parser-loader.isLanguageAvailable`, which honors the runtime opt-out and a
+// genuinely-absent binding alike) excludes files of an unavailable/opted-out
+// language BEFORE any chunk is dispatched, so the worker never receives them.
+// That main-thread filter is the single enforcement point. Any future change
+// that dispatches files to the worker WITHOUT first passing them through
+// `isLanguageAvailable` must re-introduce the gate here. (The cleaner end-state
+// — routing this table through `parser-loader.getLanguageGrammar` so there is
+// one loader — is the deferred Tier-1 consolidation.)
 // tree-sitter-swift is an optionalDependency — may not be installed
 const _require = createRequire(import.meta.url);
 let Swift: TreeSitterLanguage | null = null;
diff --git a/gitnexus/src/core/tree-sitter/parser-loader.ts b/gitnexus/src/core/tree-sitter/parser-loader.ts
index a51634fbe5..3d378f2f03 100644
--- a/gitnexus/src/core/tree-sitter/parser-loader.ts
+++ b/gitnexus/src/core/tree-sitter/parser-loader.ts
@@ -39,6 +39,15 @@ interface GrammarSource {
   unavailableNote: string;
   optional?: boolean;
   severity?: 'warn' | 'error';
+  /**
+   * When true, this grammar may be disabled at runtime via
+   * `GITNEXUS_SKIP_OPTIONAL_GRAMMARS`. Set ONLY on genuinely-optional grammars
+   * (optionalDependencies / vendored — swift/dart/kotlin). Required dependencies
+   * routed through the optional machinery for ABI safety (e.g. C, which is
+   * `optional: true` + `severity: 'error'`) must NOT set this — opting out of a
+   * required parser is always an install/platform problem, never a user choice.
+   */
+  userSkippable?: boolean;
 }
 
 const ISSUES_URL = 'https://github.com/abhigyanpatwari/GitNexus/issues';
@@ -139,6 +148,7 @@ const SOURCES: Record<string, GrammarSource> = {
   [SupportedLanguages.Swift]: {
     load: () => _require('tree-sitter-swift'),
     optional: true,
+    userSkippable: true,
     unavailableNote:
       'Swift parsing disabled: vendored `tree-sitter-swift` (under ' +
       '`gitnexus/vendor/tree-sitter-swift`) failed to load. ' +
@@ -148,6 +158,7 @@ const SOURCES: Record<string, GrammarSource> = {
   [SupportedLanguages.Dart]: {
     load: () => _require('tree-sitter-dart'),
     optional: true,
+    userSkippable: true,
     unavailableNote:
       'Dart parsing disabled: vendored `tree-sitter-dart` (under ' +
       '`gitnexus/vendor/tree-sitter-dart`) failed to load. ' +
@@ -157,6 +168,7 @@ const SOURCES: Record<string, GrammarSource> = {
   [SupportedLanguages.Kotlin]: {
     load: () => _require('tree-sitter-kotlin'),
     optional: true,
+    userSkippable: true,
     unavailableNote:
       'Kotlin parsing disabled: `tree-sitter-kotlin` is an optionalDependency ' +
       'and is not installed (or its native binding failed to build).',
@@ -189,6 +201,63 @@ type LoadResult =
 const loadCache = new Map<string, LoadResult>();
 const logged = new Set<string>();
 
+/**
+ * Runtime opt-out for genuinely-optional grammars (Swift/Dart/Kotlin).
+ *
+ * `GITNEXUS_SKIP_OPTIONAL_GRAMMARS` has historically been an *install-time*
+ * env only — the postinstall build scripts read it to skip building the
+ * vendored grammars. There was no way to disable an optional grammar at
+ * analyze time, so users on a platform with a broken/partial binding had no
+ * escape hatch short of uninstalling the package (#2091, #2093). This honors
+ * the same env name at runtime: when set, the named optional grammars report
+ * as unavailable and the pipeline skips their files (mirroring a genuinely
+ * absent binding) instead of attempting to load them.
+ *
+ * Accepts `1` / `true` / `all` / `*` (every skippable grammar), or a
+ * comma-separated list of language ids and/or package names
+ * (e.g. `swift,tree-sitter-dart`). Only grammars flagged `userSkippable` (the
+ * genuinely-optional swift/dart/kotlin) can be skipped — required dependencies
+ * routed through the optional machinery for ABI safety (C) carry no
+ * `userSkippable` and are never skippable here.
+ */
+type SkipDirective = 'all' | Set<string> | null;
+
+// Parsed form of GITNEXUS_SKIP_OPTIONAL_GRAMMARS, resolved lazily ONCE per
+// process. The env is set before analyze runs, so re-reading + re-allocating a
+// Set on every call was wasted work (and a latent trap for any future per-file
+// caller). `vi.resetModules()` gives the unit tests a fresh module — and thus a
+// fresh memo — per case, so this stays test-friendly.
+//   'all' → every userSkippable grammar; Set → only the named ids
+//   (and `tree-sitter-<id>` spellings); null → env unset/empty (nothing).
+let _skipDirective: SkipDirective | undefined;
+const skipDirective = (): SkipDirective => {
+  if (_skipDirective !== undefined) return _skipDirective;
+  const raw = (process.env.GITNEXUS_SKIP_OPTIONAL_GRAMMARS ?? '').trim().toLowerCase();
+  if (raw === '') return (_skipDirective = null);
+  if (raw === '1' || raw === 'true' || raw === 'all' || raw === '*')
+    return (_skipDirective = 'all');
+  return (_skipDirective = new Set(
+    raw
+      .split(',')
+      .map((s) => s.trim())
+      .filter(Boolean)
+      .flatMap((s) => [s, s.replace(/^tree-sitter-/, '')]),
+  ));
+};
+
+const isRuntimeSkippedGrammar = (key: string, source: GrammarSource): boolean => {
+  // Only grammars explicitly flagged user-skippable (swift/dart/kotlin) — never
+  // required deps that use the optional machinery for ABI safety (C carries no
+  // `userSkippable`).
+  if (source.userSkippable !== true) return false;
+  const directive = skipDirective();
+  if (directive === null) return false;
+  if (directive === 'all') return true;
+  // `key` is the SupportedLanguages value (e.g. `swift`); the directive Set
+  // already holds both the bare id and the `tree-sitter-<id>` spelling.
+  return directive.has(key) || directive.has(`tree-sitter-${key}`);
+};
+
 const logFailure = (key: string, result: LoadResult): void => {
   if (result.ok === true) return;
   if (logged.has(key)) return;
@@ -227,6 +296,25 @@ const loadGrammar = (key: string): LoadResult => {
     return result;
   }
 
+  // Runtime opt-out: treat a user-skipped optional grammar exactly like an
+  // absent binding (non-fatal unavailable + one warning), without attempting
+  // the native load. See `isRuntimeSkippedGrammar`.
+  if (isRuntimeSkippedGrammar(key, source)) {
+    // Deliberate opt-out: emit an accurate "disabled on purpose" note rather
+    // than `source.unavailableNote` (which blames a missing/unbuilt binding and
+    // would mislead a user who set the env intentionally — #2101 review).
+    const result: LoadResult = {
+      ok: false,
+      error: new Error('runtime opt-out'),
+      note: `${key} parsing disabled via GITNEXUS_SKIP_OPTIONAL_GRAMMARS (unset it to re-enable).`,
+      fatal: false,
+      severity: 'warn',
+    };
+    loadCache.set(key, result);
+    logFailure(key, result);
+    return result;
+  }
+
   let result: LoadResult;
   try {
     result = { ok: true, grammar: source.load() };
@@ -248,6 +336,22 @@ const loadGrammar = (key: string): LoadResult => {
 export const isLanguageAvailable = (language: SupportedLanguages, filePath?: string): boolean =>
   loadGrammar(resolveLanguageKey(language, filePath)).ok;
 
+/**
+ * True when `language`'s grammar is being treated as unavailable specifically
+ * because of the runtime GITNEXUS_SKIP_OPTIONAL_GRAMMARS opt-out — as opposed
+ * to a genuinely-missing/broken native binding. Lets callers surface an
+ * accurate "skipped on purpose" message instead of a spurious "npm rebuild"
+ * recovery hint. Returns false for required grammars and for an absent env.
+ */
+export const isGrammarRuntimeSkipped = (
+  language: SupportedLanguages,
+  filePath?: string,
+): boolean => {
+  const key = resolveLanguageKey(language, filePath);
+  const source = SOURCES[key];
+  return source !== undefined && isRuntimeSkippedGrammar(key, source);
+};
+
 export const getLanguageGrammar = (language: SupportedLanguages, filePath?: string): unknown => {
   const key = resolveLanguageKey(language, filePath);
   const result = loadGrammar(key);
diff --git a/gitnexus/test/integration/optional-grammars/registry-import-closure.test.ts b/gitnexus/test/integration/optional-grammars/registry-import-closure.test.ts
new file mode 100644
index 0000000000..09acea0264
--- /dev/null
+++ b/gitnexus/test/integration/optional-grammars/registry-import-closure.test.ts
@@ -0,0 +1,130 @@
+/**
+ * Optional-grammar static-import-closure regression test (#2091, #2093).
+ *
+ * The scope-resolution registry (`scope-resolution/pipeline/registry.ts`) and
+ * the language-provider index statically import all 16 language providers. Each
+ * per-language `query.ts` used to do a top-level `import X from 'tree-sitter-Y'`.
+ * For the OPTIONAL grammars (swift/dart/kotlin) that import resolved — and on a
+ * default install where the vendored/optional binding is absent, THREW
+ * `ERR_MODULE_NOT_FOUND` — at module-load on the main thread, before any runtime
+ * gate, crashing `gitnexus analyze` regardless of the repo's actual languages.
+ *
+ * The fix routes those three `query.ts` modules through the lazy, guarded
+ * `parser-loader.getLanguageGrammar()` so the grammar binding is only required
+ * at first use (inside the worker, for a file of that language) — never at
+ * module-load.
+ *
+ * This test locks the fix in WITHOUT needing to simulate a missing grammar:
+ * spawn a child Node process, import the built scope-resolution `registry.js`
+ * (the crash-chain root), and assert no OPTIONAL tree-sitter binding
+ * (swift/dart/kotlin) appears in the module cache. Pre-fix the static imports
+ * loaded those bindings at import time (this assertion fails); post-fix they
+ * are lazy (it passes). Required grammars (python/typescript/...) still load
+ * eagerly via their own `query.ts` — that is expected and NOT asserted against.
+ *
+ * Characterization-first: this MUST fail against the pre-fix code (run against
+ * the parent commit to verify the regression signal works).
+ */
+
+import { describe, it, expect } from 'vitest';
+import { spawnSync } from 'node:child_process';
+import path from 'node:path';
+import fs from 'node:fs';
+import { fileURLToPath, pathToFileURL } from 'node:url';
+
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+const REPO_ROOT = path.resolve(__dirname, '..', '..', '..');
+const DIST_REGISTRY = path.join(
+  REPO_ROOT,
+  'dist',
+  'core',
+  'ingestion',
+  'scope-resolution',
+  'pipeline',
+  'registry.js',
+);
+const DIST_REGISTRY_URL = pathToFileURL(DIST_REGISTRY).href;
+
+// Import the registry, then report every newly-loaded CJS-cache key. The cache
+// tracks native/.node bindings loaded by either ESM or CJS importers, which is
+// exactly how a tree-sitter grammar binding surfaces.
+const PROBE = `
+  import { createRequire } from 'node:module';
+  const req = createRequire(import.meta.url);
+  const before = new Set(Object.keys(req.cache));
+  await import(process.env.PROBE_TARGET);
+  const after = new Set(Object.keys(req.cache));
+  process.stdout.write(JSON.stringify([...after].filter((k) => !before.has(k))));
+`;
+
+const OPTIONAL_GRAMMAR_RE = /tree-sitter-(swift|dart|kotlin)[\\/]/;
+
+describe('optional-grammar static-import closure (#2091/#2093)', () => {
+  it('importing the scope-resolution registry loads NO optional grammar binding', () => {
+    if (!fs.existsSync(DIST_REGISTRY)) {
+      throw new Error(
+        `${DIST_REGISTRY} missing — run \`npm run build\` first (or \`npm run test:integration\`, ` +
+          `which builds via pretest:integration).`,
+      );
+    }
+
+    const result = spawnSync(process.execPath, ['--input-type=module', '-e', PROBE], {
+      cwd: REPO_ROOT,
+      // NODE_OPTIONS cleared so a session-pinned --max-old-space-size etc. can't
+      // perturb the child. The skip env is cleared so install state is probed.
+      env: {
+        ...process.env,
+        PROBE_TARGET: DIST_REGISTRY_URL,
+        NODE_OPTIONS: '',
+        GITNEXUS_SKIP_OPTIONAL_GRAMMARS: '',
+      },
+      timeout: 60_000,
+      encoding: 'utf8',
+    });
+
+    // Post-fix, importing the registry must not throw even though the chain
+    // reaches swift/dart/kotlin query.ts. (Pre-fix on a machine missing a
+    // grammar this would be ERR_MODULE_NOT_FOUND; here the grammar is present
+    // so pre-fix it would instead surface as a loaded binding below.)
+    if (result.status !== 0) {
+      // status is null when the child was killed by a signal (e.g. a native
+      // addon SIGSEGV) — surface the signal so that's distinguishable from a
+      // non-zero exit / module-not-found.
+      const exit =
+        result.status !== null ? `status ${result.status}` : `signal ${result.signal ?? 'unknown'}`;
+      throw new Error(
+        `importing the scope-resolution registry failed (${exit}):\n` +
+          `stderr:\n${result.stderr}\nstdout:\n${result.stdout}`,
+      );
+    }
+
+    const newlyLoaded = JSON.parse(result.stdout) as string[];
+
+    // Non-vacuity guard: the registry's static-import closure MUST still reach
+    // the per-language query.ts modules (which is what makes "no optional
+    // binding loaded" meaningful). The REQUIRED grammars (python/typescript/…)
+    // still import their binding eagerly in their own query.ts, so at least one
+    // non-optional tree-sitter binding must appear. If a future refactor severs
+    // the registry→query.ts edge, this fails loudly instead of letting the
+    // optional-binding assertion pass green on a no-longer-exercised path.
+    const requiredLoaded = newlyLoaded.filter(
+      (p) => /tree-sitter-[a-z-]+[\\/]/.test(p) && !OPTIONAL_GRAMMAR_RE.test(p),
+    );
+    expect(
+      requiredLoaded.length,
+      `Expected the registry import closure to load at least one REQUIRED tree-sitter ` +
+        `binding (proving the chain still reaches the per-language query.ts modules). ` +
+        `Newly-loaded (${newlyLoaded.length}):\n${newlyLoaded.join('\n')}`,
+    ).toBeGreaterThan(0);
+
+    // Headline assertion: no OPTIONAL grammar binding (swift/dart/kotlin) is
+    // loaded at registry static-import time — they must load lazily.
+    const optionalLoaded = newlyLoaded.filter((p) => OPTIONAL_GRAMMAR_RE.test(p));
+    expect(
+      optionalLoaded,
+      `Optional tree-sitter grammar binding(s) loaded at registry static-import time. ` +
+        `query.ts must load swift/dart/kotlin lazily via parser-loader, not via a ` +
+        `top-level \`import\`. Offending paths:\n${optionalLoaded.join('\n')}`,
+    ).toEqual([]);
+  });
+});
diff --git a/gitnexus/test/integration/optional-grammars/skip-optional-pipeline.test.ts b/gitnexus/test/integration/optional-grammars/skip-optional-pipeline.test.ts
new file mode 100644
index 0000000000..d60fca427b
--- /dev/null
+++ b/gitnexus/test/integration/optional-grammars/skip-optional-pipeline.test.ts
@@ -0,0 +1,110 @@
+/**
+ * Pipeline-level regression for the optional-grammar exclusion (#2091, #2093).
+ *
+ * Locks the scope-resolution phase guard added alongside the lazy query.ts
+ * load: `scopeResolutionPhase` filters its `filesByLang` partition by
+ * `isLanguageAvailable`, so a file of an unavailable optional grammar never
+ * falls through to the main-thread re-extract in `run.ts` (which would throw
+ * "Unsupported language" — caught, but noisy, and it needlessly loads the
+ * grammar on the main thread).
+ *
+ * Drives the REAL pipeline over a mixed Python+Swift repo with the runtime
+ * `GITNEXUS_SKIP_OPTIONAL_GRAMMARS` opt-out set (so Swift is treated as
+ * unavailable even though its binding is installed). This is the automated
+ * analog of the manual end-to-end verification: Python indexes, Swift is
+ * cleanly skipped, and the "scope extraction failed for …swift" noise never
+ * appears.
+ *
+ * `parser-loader` memoizes availability per process, so we `vi.resetModules()`
+ * BEFORE setting the env and dynamically import the pipeline + logger from the
+ * same fresh registry. That makes the first `isLanguageAvailable` call observe
+ * our env regardless of import order, and keeps the logger capture wired to the
+ * loader's logger instance (a static import would not survive resetModules).
+ */
+
+import { describe, it, expect, beforeAll, afterAll, vi } from 'vitest';
+import fs from 'node:fs';
+import os from 'node:os';
+import path from 'node:path';
+import type { PipelineResult } from '../resolvers/helpers.js';
+
+const ENV = 'GITNEXUS_SKIP_OPTIONAL_GRAMMARS';
+
+describe('optional-grammar pipeline exclusion (#2091/#2093)', () => {
+  let repoDir = '';
+  let result: PipelineResult;
+  let messages: string[] = [];
+  let prevEnv: string | undefined;
+  let getNodesByLabel: (r: PipelineResult, label: string) => string[];
+
+  beforeAll(async () => {
+    prevEnv = process.env[ENV];
+    vi.resetModules();
+    process.env[ENV] = 'swift';
+    const helpers = await import('../resolvers/helpers.js');
+    const loggerMod = await import('../../../src/core/logger.js');
+    getNodesByLabel = helpers.getNodesByLabel;
+
+    repoDir = fs.mkdtempSync(path.join(os.tmpdir(), 'og-skip-pipeline-'));
+    fs.writeFileSync(
+      path.join(repoDir, 'app.py'),
+      'def greet(name):\n    return f"hi {name}"\n\n\nclass Service:\n    def run(self):\n        return greet("world")\n',
+    );
+    fs.writeFileSync(
+      path.join(repoDir, 'Foo.swift'),
+      'struct Foo {\n  func bar() -> Int { return 42 }\n}\n',
+    );
+
+    const cap = loggerMod._captureLogger();
+    try {
+      result = await helpers.runPipelineFromRepo(repoDir, () => {}, { skipGraphPhases: true });
+      messages = cap
+        .records()
+        .map((r) => (typeof r.msg === 'string' ? r.msg : ''))
+        .filter(Boolean);
+    } finally {
+      cap.restore();
+    }
+  }, 60_000);
+
+  afterAll(() => {
+    if (prevEnv === undefined) delete process.env[ENV];
+    else process.env[ENV] = prevEnv;
+    if (repoDir) fs.rmSync(repoDir, { recursive: true, force: true });
+  });
+
+  it('completes without crashing when an optional grammar is opted out', () => {
+    expect(result).toBeDefined();
+  });
+
+  it('skips the Swift file at the parse phase (non-vacuity: Swift was present)', () => {
+    expect(messages.some((m) => /Skipping 1 swift file\(s\)/.test(m))).toBe(true);
+  });
+
+  it('routes the opt-out message, not the missing-binding "npm rebuild" hint', () => {
+    // The "Skipping N swift file(s)" prefix is shared by BOTH the opt-out and
+    // the missing-binding branches — so assert the opt-out branch specifically:
+    // a message naming the env var, and NO "npm rebuild" hint anywhere. This is
+    // what proves the isGrammarRuntimeSkipped routing in parse-impl.ts fired.
+    expect(messages.some((m) => /GITNEXUS_SKIP_OPTIONAL_GRAMMARS/.test(m))).toBe(true);
+    expect(
+      messages.every((m) => !/npm rebuild/i.test(m)),
+      messages.join('\n'),
+    ).toBe(true);
+  });
+
+  it('never falls through to the main-thread re-extract (no "scope extraction failed")', () => {
+    // This is the precise signal the scope-resolution phase guard eliminates.
+    // Without the `if (!isLanguageAvailable(fileLang)) continue;` in phase.ts
+    // the Swift file would reach run.ts's extractParsedFile and log this.
+    const offending = messages.filter((m) => /scope extraction failed/i.test(m));
+    expect(offending, offending.join('\n')).toEqual([]);
+  });
+
+  it('indexes the available Python language and excludes Swift symbols', () => {
+    // Python indexed (proves the pipeline actually ran end-to-end).
+    expect(getNodesByLabel(result, 'Class')).toContain('Service');
+    // Swift's struct must not be in the graph — it was excluded, not parsed.
+    expect(getNodesByLabel(result, 'Struct')).not.toContain('Foo');
+  });
+});
diff --git a/gitnexus/test/unit/parser-loader-skip-optional.test.ts b/gitnexus/test/unit/parser-loader-skip-optional.test.ts
new file mode 100644
index 0000000000..ae8cff396f
--- /dev/null
+++ b/gitnexus/test/unit/parser-loader-skip-optional.test.ts
@@ -0,0 +1,141 @@
+import { describe, it, expect, afterEach, vi } from 'vitest';
+import { SupportedLanguages } from '../../src/config/supported-languages.js';
+
+/**
+ * Runtime opt-out for optional grammars (#2091, #2093).
+ *
+ * `GITNEXUS_SKIP_OPTIONAL_GRAMMARS` used to be an install-time-only env (the
+ * postinstall build scripts read it). `parser-loader` now also honors it at
+ * analyze time: when set, genuinely-optional grammars (swift/dart/kotlin)
+ * report unavailable so the ingestion pipeline skips their files, mirroring a
+ * genuinely-absent binding. Grammars that are required `dependencies` routed
+ * through the optional machinery for ABI safety (C — `severity: 'error'`) are
+ * NEVER skippable this way.
+ *
+ * `parser-loader` memoizes load results at module scope, so each case loads a
+ * fresh copy via `vi.resetModules()` after setting the env. These assertions
+ * are install-state-robust: they only assert the SKIP direction (skip → false)
+ * and that required grammars are unaffected (true) — never that an optional
+ * grammar is positively available, which depends on the install/platform.
+ */
+
+const ENV = 'GITNEXUS_SKIP_OPTIONAL_GRAMMARS';
+
+async function freshLoader(skipValue: string | undefined) {
+  vi.resetModules();
+  if (skipValue === undefined) delete process.env[ENV];
+  else process.env[ENV] = skipValue;
+  return import('../../src/core/tree-sitter/parser-loader.js');
+}
+
+afterEach(() => {
+  delete process.env[ENV];
+  vi.resetModules();
+});
+
+describe('parser-loader GITNEXUS_SKIP_OPTIONAL_GRAMMARS runtime gate', () => {
+  it('skip=1 reports every optional grammar as unavailable', async () => {
+    const { isLanguageAvailable } = await freshLoader('1');
+    expect(isLanguageAvailable(SupportedLanguages.Swift)).toBe(false);
+    expect(isLanguageAvailable(SupportedLanguages.Dart)).toBe(false);
+    expect(isLanguageAvailable(SupportedLanguages.Kotlin)).toBe(false);
+  });
+
+  it('skip=all/true/* also skip every optional grammar', async () => {
+    for (const v of ['all', 'true', '*']) {
+      const { isLanguageAvailable } = await freshLoader(v);
+      expect(isLanguageAvailable(SupportedLanguages.Swift), `value=${v}`).toBe(false);
+      expect(isLanguageAvailable(SupportedLanguages.Dart), `value=${v}`).toBe(false);
+      expect(isLanguageAvailable(SupportedLanguages.Kotlin), `value=${v}`).toBe(false);
+    }
+  });
+
+  it('does NOT skip required grammars — skip=all is a no-op for C / Python', async () => {
+    // Compare availability WITH skip=all against the baseline (no skip). The
+    // runtime opt-out must never change a required grammar's availability:
+    // C is `optional: true` + `severity: 'error'` (a required dep routed
+    // through the optional machinery for ABI safety, #1242), and Python is a
+    // plain required dep. Asserting EQUALITY (not positive truth) keeps this
+    // install-state-robust — C's native binding is intentionally fallible, so
+    // a positive assertion could flake on an ABI-mismatched matrix.
+    const base = await freshLoader(undefined);
+    const cBase = base.isLanguageAvailable(SupportedLanguages.C);
+    const pyBase = base.isLanguageAvailable(SupportedLanguages.Python);
+    const skipped = await freshLoader('all');
+    expect(skipped.isLanguageAvailable(SupportedLanguages.C)).toBe(cBase);
+    expect(skipped.isLanguageAvailable(SupportedLanguages.Python)).toBe(pyBase);
+  });
+
+  it('a comma list skips ONLY the named grammars — un-named ones unaffected', async () => {
+    // Baseline (no skip) so the isolation check is install-state-robust.
+    const base = await freshLoader(undefined);
+    const dartBase = base.isLanguageAvailable(SupportedLanguages.Dart);
+    const kotlinBase = base.isLanguageAvailable(SupportedLanguages.Kotlin);
+    const { isLanguageAvailable } = await freshLoader('swift');
+    expect(isLanguageAvailable(SupportedLanguages.Swift)).toBe(false);
+    // A prefix/union bug would skip these too — assert they match baseline.
+    expect(isLanguageAvailable(SupportedLanguages.Dart)).toBe(dartBase);
+    expect(isLanguageAvailable(SupportedLanguages.Kotlin)).toBe(kotlinBase);
+  });
+
+  it('accepts the tree-sitter-<lang> package spelling — others unaffected', async () => {
+    const base = await freshLoader(undefined);
+    const swiftBase = base.isLanguageAvailable(SupportedLanguages.Swift);
+    const kotlinBase = base.isLanguageAvailable(SupportedLanguages.Kotlin);
+    const { isLanguageAvailable } = await freshLoader('tree-sitter-dart');
+    expect(isLanguageAvailable(SupportedLanguages.Dart)).toBe(false);
+    expect(isLanguageAvailable(SupportedLanguages.Swift)).toBe(swiftBase);
+    expect(isLanguageAvailable(SupportedLanguages.Kotlin)).toBe(kotlinBase);
+  });
+
+  it('accepts a multi-entry list', async () => {
+    const { isLanguageAvailable } = await freshLoader('kotlin, dart');
+    expect(isLanguageAvailable(SupportedLanguages.Kotlin)).toBe(false);
+    expect(isLanguageAvailable(SupportedLanguages.Dart)).toBe(false);
+  });
+
+  it('getLanguageGrammar throws a clean "Unsupported language" for a skipped optional grammar', async () => {
+    const { getLanguageGrammar } = await freshLoader('all');
+    expect(() => getLanguageGrammar(SupportedLanguages.Swift)).toThrow(/Unsupported language/);
+  });
+
+  it('an empty / unset env does not skip (required grammars load)', async () => {
+    const { isLanguageAvailable } = await freshLoader(undefined);
+    expect(isLanguageAvailable(SupportedLanguages.Python)).toBe(true);
+  });
+
+  it('isGrammarRuntimeSkipped reflects the opt-out, never for required grammars', async () => {
+    const swiftOnly = await freshLoader('swift');
+    expect(swiftOnly.isGrammarRuntimeSkipped(SupportedLanguages.Swift)).toBe(true);
+    expect(swiftOnly.isGrammarRuntimeSkipped(SupportedLanguages.Dart)).toBe(false);
+    const all = await freshLoader('all');
+    expect(all.isGrammarRuntimeSkipped(SupportedLanguages.Swift)).toBe(true);
+    // C is not `userSkippable` (required dep via the optional machinery) — even
+    // `all` must not mark it runtime-skipped.
+    expect(all.isGrammarRuntimeSkipped(SupportedLanguages.C)).toBe(false);
+  });
+
+  it('logs an accurate runtime-skip note, not a missing-binding message', async () => {
+    // Import the logger AND parser-loader from the SAME fresh module registry so
+    // the capture intercepts the loader's logger instance.
+    vi.resetModules();
+    process.env[ENV] = 'swift';
+    const { _captureLogger } = await import('../../src/core/logger.js');
+    const { isLanguageAvailable } = await import('../../src/core/tree-sitter/parser-loader.js');
+    const cap = _captureLogger();
+    try {
+      isLanguageAvailable(SupportedLanguages.Swift); // triggers the one-time skip log
+      const msgs = cap
+        .records()
+        .map((r) => (typeof r.msg === 'string' ? r.msg : ''))
+        .filter(Boolean);
+      const skipMsg = msgs.find((m) => m.includes('GITNEXUS_SKIP_OPTIONAL_GRAMMARS'));
+      expect(skipMsg, `captured:\n${msgs.join('\n')}`).toBeTruthy();
+      // The opt-out note must NOT borrow the install/platform "missing binding"
+      // language — that would tell a deliberate opt-out to reinstall/rebuild.
+      expect(skipMsg).not.toMatch(/no prebuilt|failed to load|npm rebuild/i);
+    } finally {
+      cap.restore();
+    }
+  });
+});