gitnexus 1.6.7-rc.1 → 1.6.7-rc.3

package/dist/_shared/graph/types.d.ts

@@ -5,7 +5,7 @@
  * Do NOT add Node.js-specific or browser-specific imports here.
  */
 import { SupportedLanguages } from '../languages.js';
-export type NodeLabel = 'Project' | 'Package' | 'Module' | 'Folder' | 'File' | 'Class' | 'Function' | 'Method' | 'Variable' | 'Interface' | 'Enum' | 'Decorator' | 'Import' | 'Type' | 'CodeElement' | 'Community' | 'Process' | 'Struct' | 'Macro' | 'Typedef' | 'Union' | 'Namespace' | 'Trait' | 'Impl' | 'TypeAlias' | 'Const' | 'Static' | 'Property' | 'Record' | 'Delegate' | 'Annotation' | 'Constructor' | 'Template' | 'Section' | 'Route' | 'Tool';
+export type NodeLabel = 'Project' | 'Package' | 'Module' | 'Folder' | 'File' | 'Class' | 'Function' | 'Method' | 'Variable' | 'Interface' | 'Enum' | 'Decorator' | 'Import' | 'Type' | 'CodeElement' | 'Community' | 'Process' | 'Struct' | 'Macro' | 'Typedef' | 'Union' | 'Namespace' | 'Trait' | 'Impl' | 'TypeAlias' | 'Const' | 'Static' | 'Property' | 'Record' | 'Delegate' | 'Annotation' | 'Constructor' | 'Template' | 'Section' | 'Route' | 'Tool' | 'BasicBlock';
 export type NodeProperties = {
     name: string;
     filePath: string;
@@ -45,6 +45,7 @@ export type NodeProperties = {
     responseKeys?: string[];
     errorKeys?: string[];
     middleware?: string[];
+    text?: string;
     [key: string]: unknown;
 };
 export type RelationshipType = 'CONTAINS' | 'CALLS' | 'INHERITS' | 'METHOD_OVERRIDES' | 'METHOD_IMPLEMENTS' | 'IMPORTS' | 'USES' | 'DEFINES' | 'DECORATES' | 'IMPLEMENTS' | 'EXTENDS' | 'HAS_METHOD' | 'HAS_PROPERTY' | 'ACCESSES' | 'MEMBER_OF' | 'STEP_IN_PROCESS' | 'HANDLES_ROUTE' | 'FETCHES' | 'HANDLES_TOOL' | 'ENTRY_POINT_OF' | 'WRAPS' | 'QUERIES'
@@ -63,7 +64,22 @@ export type RelationshipType = 'CONTAINS' | 'CALLS' | 'INHERITS' | 'METHOD_OVERR
  *  `reason` encodes the event name: `vue-emit: <eventName>`.
  *  Complements `BINDS_EVENT_HANDLER`; a Cypher query joining on the
  *  component File node reveals all (emitter, handler) pairs. */
- | 'EMITS_EVENT';
+ | 'EMITS_EVENT'
+/** Control-flow edge between two BasicBlock nodes (intra-procedural CFG). */
+ | 'CFG'
+/** Data-dependence edge: a definition of `variable` reaches a use of it.
+ *  The `variable` name is stored in the relation's existing `reason` column
+ *  (M0/S1 verdict: LadybugDB has no secondary index on relationship
+ *  properties, so a dedicated indexed column would not speed the
+ *  variable-filtered path query). */
+ | 'REACHING_DEF'
+/** A tainted value flows from source toward sink. */
+ | 'TAINTED'
+/** A sanitizer clears taint along a flow. */
+ | 'SANITIZES'
+/** Materialized source→sink taint path. Working name — final name/representation
+ *  is confirmed when M3/M4 emits it; no persisted edge exists before then. */
+ | 'TAINT_PATH';
 export interface GraphNode {
     id: string;
     label: NodeLabel;

package/dist/_shared/graph/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/graph/types.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AAErD,MAAM,MAAM,SAAS,GACjB,SAAS,GACT,SAAS,GACT,QAAQ,GACR,QAAQ,GACR,MAAM,GACN,OAAO,GACP,UAAU,GACV,QAAQ,GACR,UAAU,GACV,WAAW,GACX,MAAM,GACN,WAAW,GACX,QAAQ,GACR,MAAM,GACN,aAAa,GACb,WAAW,GACX,SAAS,GAET,QAAQ,GACR,OAAO,GACP,SAAS,GACT,OAAO,GACP,WAAW,GACX,OAAO,GACP,MAAM,GACN,WAAW,GACX,OAAO,GACP,QAAQ,GACR,UAAU,GACV,QAAQ,GACR,UAAU,GACV,YAAY,GACZ,aAAa,GACb,UAAU,GACV,SAAS,GACT,OAAO,GACP,MAAM,GAGN,YAAY,CAAC;AAEjB,MAAM,MAAM,cAAc,GAAG;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,kBAAkB,GAAG,MAAM,CAAC;IACvC,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAE5B,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,WAAW,GAAG,KAAK,CAAC;IAEjC,WAAW,CAAC,EAAE,iBAAiB,GAAG,iBAAiB,CAAC;IACpD,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAE1B,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IAEvB,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;IAEtB,IAAI,CAAC,EAAE,MAAM,CAAC;IAEd,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;CACxB,CAAC;AAEF,MAAM,MAAM,gBAAgB,GACxB,UAAU,GACV,OAAO,GACP,UAAU,GACV,kBAAkB,GAClB,mBAAmB,GACnB,SAAS,GACT,MAAM,GACN,SAAS,GACT,WAAW,GACX,YAAY,GACZ,SAAS,GACT,YAAY,GACZ,cAAc,GACd,UAAU,GACV,WAAW,GACX,iBAAiB,GACjB,eAAe,GACf,SAAS,GACT,cAAc,GACd,gBAAgB,GAChB,OAAO,GACP,SAAS;AACX;;;;;;qEAMqE;GACnE,qBAAqB;AACvB;;;;;;gEAMgE;GAC9D,aAAa;AAOf,6EAA6E;GAC3E,KAAK;AACP;;;;qCAIqC;GACnC,cAAc;AAChB,qDAAqD;GACnD,SAAS;AACX,6CAA6C;GAC3C,WAAW;AACb;8EAC8E;GAC5E,YAAY,CAAC;AAEjB,MAAM,WAAW,SAAS;IACxB,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,SAAS,CAAC;IACjB,UAAU,EAAE,cAAc,CAAC;CAC5B;AAED,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,gBAAgB,CAAC;IACvB,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;IACd;;;;;;;;;;OAUG;IACH,QAAQ,CAAC,EAAE,SAAS;QAClB,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;QACtB,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;QACxB,QAAQ,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;KACxB,EAAE,CAAC;CACL"}

package/dist/_shared/lbug/schema-constants.d.ts

@@ -7,10 +7,10 @@
  * Full DDL schemas remain in each package's own schema.ts because
  * the CLI uses native LadybugDB and the web uses WASM.
  */
-export declare const NODE_TABLES: readonly ["File", "Folder", "Function", "Class", "Interface", "Method", "CodeElement", "Community", "Process", "Section", "Struct", "Enum", "Macro", "Typedef", "Union", "Namespace", "Trait", "Impl", "TypeAlias", "Const", "Static", "Variable", "Property", "Record", "Delegate", "Annotation", "Constructor", "Template", "Module", "Route", "Tool"];
+export declare const NODE_TABLES: readonly ["File", "Folder", "Function", "Class", "Interface", "Method", "CodeElement", "Community", "Process", "Section", "Struct", "Enum", "Macro", "Typedef", "Union", "Namespace", "Trait", "Impl", "TypeAlias", "Const", "Static", "Variable", "Property", "Record", "Delegate", "Annotation", "Constructor", "Template", "Module", "Route", "Tool", "BasicBlock"];
 export type NodeTableName = (typeof NODE_TABLES)[number];
 export declare const REL_TABLE_NAME = "CodeRelation";
-export declare const REL_TYPES: readonly ["CONTAINS", "DEFINES", "IMPORTS", "CALLS", "EXTENDS", "IMPLEMENTS", "HAS_METHOD", "HAS_PROPERTY", "ACCESSES", "METHOD_OVERRIDES", "OVERRIDES", "METHOD_IMPLEMENTS", "MEMBER_OF", "STEP_IN_PROCESS", "HANDLES_ROUTE", "FETCHES", "HANDLES_TOOL", "ENTRY_POINT_OF", "WRAPS", "QUERIES"];
+export declare const REL_TYPES: readonly ["CONTAINS", "DEFINES", "IMPORTS", "CALLS", "EXTENDS", "IMPLEMENTS", "HAS_METHOD", "HAS_PROPERTY", "ACCESSES", "METHOD_OVERRIDES", "OVERRIDES", "METHOD_IMPLEMENTS", "MEMBER_OF", "STEP_IN_PROCESS", "HANDLES_ROUTE", "FETCHES", "HANDLES_TOOL", "ENTRY_POINT_OF", "WRAPS", "QUERIES", "CFG", "REACHING_DEF", "TAINTED", "SANITIZES", "TAINT_PATH"];
 export type RelType = (typeof REL_TYPES)[number];
 export declare const EMBEDDING_TABLE_NAME = "CodeEmbedding";
 //# sourceMappingURL=schema-constants.d.ts.map

package/dist/_shared/lbug/schema-constants.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"schema-constants.d.ts","sourceRoot":"","sources":["../../src/lbug/schema-constants.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,eAAO,MAAM,WAAW,0VAgCd,CAAC;AAEX,MAAM,MAAM,aAAa,GAAG,CAAC,OAAO,WAAW,CAAC,CAAC,MAAM,CAAC,CAAC;AAEzD,eAAO,MAAM,cAAc,iBAAiB,CAAC;AAE7C,eAAO,MAAM,SAAS,iSAqBZ,CAAC;AAEX,MAAM,MAAM,OAAO,GAAG,CAAC,OAAO,SAAS,CAAC,CAAC,MAAM,CAAC,CAAC;AAEjD,eAAO,MAAM,oBAAoB,kBAAkB,CAAC"}
+{"version":3,"file":"schema-constants.d.ts","sourceRoot":"","sources":["../../src/lbug/schema-constants.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,eAAO,MAAM,WAAW,wWAkCd,CAAC;AAEX,MAAM,MAAM,aAAa,GAAG,CAAC,OAAO,WAAW,CAAC,CAAC,MAAM,CAAC,CAAC;AAEzD,eAAO,MAAM,cAAc,iBAAiB,CAAC;AAE7C,eAAO,MAAM,SAAS,8VA6BZ,CAAC;AAEX,MAAM,MAAM,OAAO,GAAG,CAAC,OAAO,SAAS,CAAC,CAAC,MAAM,CAAC,CAAC;AAEjD,eAAO,MAAM,oBAAoB,kBAAkB,CAAC"}

package/dist/_shared/lbug/schema-constants.js

@@ -39,6 +39,8 @@ export const NODE_TABLES = [
     'Module',
     'Route',
     'Tool',
+    // Taint/PDG substrate (issue #2080) — inert until M1 (#2081) emits blocks.
+    'BasicBlock',
 ];
 export const REL_TABLE_NAME = 'CodeRelation';
 export const REL_TYPES = [
@@ -62,6 +64,14 @@ export const REL_TYPES = [
     'ENTRY_POINT_OF',
     'WRAPS',
     'QUERIES',
+    // Taint/PDG substrate (issue #2080) — reserved edge types, emitted by no
+    // phase yet (CFG → M1, REACHING_DEF → M2, TAINTED/SANITIZES/TAINT_PATH →
+    // M3/M4). REACHING_DEF's variable name rides the relation's `reason` column.
+    'CFG',
+    'REACHING_DEF',
+    'TAINTED',
+    'SANITIZES',
+    'TAINT_PATH',
 ];
 export const EMBEDDING_TABLE_NAME = 'CodeEmbedding';
 //# sourceMappingURL=schema-constants.js.map

package/dist/_shared/lbug/schema-constants.js.map

@@ -1 +1 @@
-{"version":3,"file":"schema-constants.js","sourceRoot":"","sources":["../../src/lbug/schema-constants.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,MAAM,CAAC,MAAM,WAAW,GAAG;IACzB,MAAM;IACN,QAAQ;IACR,UAAU;IACV,OAAO;IACP,WAAW;IACX,QAAQ;IACR,aAAa;IACb,WAAW;IACX,SAAS;IACT,SAAS;IACT,QAAQ;IACR,MAAM;IACN,OAAO;IACP,SAAS;IACT,OAAO;IACP,WAAW;IACX,OAAO;IACP,MAAM;IACN,WAAW;IACX,OAAO;IACP,QAAQ;IACR,UAAU;IACV,UAAU;IACV,QAAQ;IACR,UAAU;IACV,YAAY;IACZ,aAAa;IACb,UAAU;IACV,QAAQ;IACR,OAAO;IACP,MAAM;CACE,CAAC;AAIX,MAAM,CAAC,MAAM,cAAc,GAAG,cAAc,CAAC;AAE7C,MAAM,CAAC,MAAM,SAAS,GAAG;IACvB,UAAU;IACV,SAAS;IACT,SAAS;IACT,OAAO;IACP,SAAS;IACT,YAAY;IACZ,YAAY;IACZ,cAAc;IACd,UAAU;IACV,kBAAkB;IAClB,WAAW,EAAE,mEAAmE;IAChF,mBAAmB;IACnB,WAAW;IACX,iBAAiB;IACjB,eAAe;IACf,SAAS;IACT,cAAc;IACd,gBAAgB;IAChB,OAAO;IACP,SAAS;CACD,CAAC;AAIX,MAAM,CAAC,MAAM,oBAAoB,GAAG,eAAe,CAAC"}
+{"version":3,"file":"schema-constants.js","sourceRoot":"","sources":["../../src/lbug/schema-constants.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,MAAM,CAAC,MAAM,WAAW,GAAG;IACzB,MAAM;IACN,QAAQ;IACR,UAAU;IACV,OAAO;IACP,WAAW;IACX,QAAQ;IACR,aAAa;IACb,WAAW;IACX,SAAS;IACT,SAAS;IACT,QAAQ;IACR,MAAM;IACN,OAAO;IACP,SAAS;IACT,OAAO;IACP,WAAW;IACX,OAAO;IACP,MAAM;IACN,WAAW;IACX,OAAO;IACP,QAAQ;IACR,UAAU;IACV,UAAU;IACV,QAAQ;IACR,UAAU;IACV,YAAY;IACZ,aAAa;IACb,UAAU;IACV,QAAQ;IACR,OAAO;IACP,MAAM;IACN,2EAA2E;IAC3E,YAAY;CACJ,CAAC;AAIX,MAAM,CAAC,MAAM,cAAc,GAAG,cAAc,CAAC;AAE7C,MAAM,CAAC,MAAM,SAAS,GAAG;IACvB,UAAU;IACV,SAAS;IACT,SAAS;IACT,OAAO;IACP,SAAS;IACT,YAAY;IACZ,YAAY;IACZ,cAAc;IACd,UAAU;IACV,kBAAkB;IAClB,WAAW,EAAE,mEAAmE;IAChF,mBAAmB;IACnB,WAAW;IACX,iBAAiB;IACjB,eAAe;IACf,SAAS;IACT,cAAc;IACd,gBAAgB;IAChB,OAAO;IACP,SAAS;IACT,yEAAyE;IACzE,yEAAyE;IACzE,6EAA6E;IAC7E,KAAK;IACL,cAAc;IACd,SAAS;IACT,WAAW;IACX,YAAY;CACJ,CAAC;AAIX,MAAM,CAAC,MAAM,oBAAoB,GAAG,eAAe,CAAC"}

package/dist/cli/analyze.js

@@ -19,7 +19,7 @@ import { getGitRoot, hasGitDir, getDefaultBranch } from '../storage/git.js';
 import { loadAnalyzeConfig, mergeAnalyzeOptions, resolveDefaultBranch, validateBranchName, GitNexusRcError, } 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';
@@ -691,11 +691,13 @@ const analyzeCommandImpl = async (inputPath, cliOptions) => {
         console.log('  Note: --index-only overrides --skills; community skill files will not be written.\n');
     }
     // 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,

package/dist/cli/optional-grammars.d.ts

@@ -4,19 +4,33 @@
  * 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.
  */
+/**
+ * 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 declare function getOptionalGrammarExtensions(): string[];
 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';
 }
 /**
  * Returns the list of optional grammars whose native binding cannot be

package/dist/cli/optional-grammars.js

@@ -4,24 +4,51 @@
  * 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 '../_shared/index.js';
+import { isGrammarRuntimeSkipped } from '../core/tree-sitter/parser-loader.js';
 import { cliWarn } from './cli-message.js';
 const _require = createRequire(import.meta.url);
 const OPTIONAL_GRAMMARS = [
-    { 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() {
+    return [...new Set(OPTIONAL_GRAMMARS.flatMap((g) => g.extensions))];
+}
 /**
  * Returns the list of optional grammars whose native binding cannot be
  * loaded. Actually `require()`s the package — `require.resolve` would
@@ -41,6 +68,13 @@ const OPTIONAL_GRAMMARS = [
 export function detectMissingOptionalGrammars() {
     const missing = [];
     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);
         }
@@ -59,7 +93,7 @@ export function detectMissingOptionalGrammars() {
                 // there for tool-data stdout output).
                 cliWarn(`GitNexus: optional grammar "${g.name}" is installed but failed to load (${msg.slice(0, 200)}). ${g.extensions.join('/')} files will not be parsed.`, { grammar: g.name, extensions: g.extensions, error: msg });
             }
-            missing.push({ name: g.name, extensions: g.extensions });
+            missing.push({ name: g.name, extensions: g.extensions, reason: 'missing' });
         }
     }
     return missing;
@@ -86,6 +120,15 @@ export function warnMissingOptionalGrammars(opts) {
         if (relevantExtensions && !g.extensions.some((e) => relevantExtensions.has(e))) {
             continue;
         }
-        cliWarn(`GitNexus${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,
+        });
     }
 }

package/dist/core/ingestion/languages/dart/query.js

@@ -22,7 +22,15 @@
  *   - Parameter / return / receiver type bindings and arity metadata.
  */
 import Parser from 'tree-sitter';
-import Dart from 'tree-sitter-dart';
+import { SupportedLanguages } from '../../../../_shared/index.js';
+// `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 ───────────────────────────────────────────────────────────────────
 (program) @scope.module
@@ -130,13 +138,13 @@ let _query = null;
 export function getDartParser() {
     if (_parser === null) {
         _parser = new Parser();
-        _parser.setLanguage(Dart);
+        _parser.setLanguage(getLanguageGrammar(SupportedLanguages.Dart));
     }
     return _parser;
 }
 export function getDartScopeQuery() {
     if (_query === null) {
-        _query = new Parser.Query(Dart, DART_SCOPE_QUERY);
+        _query = new Parser.Query(getLanguageGrammar(SupportedLanguages.Dart), DART_SCOPE_QUERY);
     }
     return _query;
 }

package/dist/core/ingestion/languages/kotlin/query.js

@@ -1,5 +1,13 @@
 import Parser from 'tree-sitter';
-import Kotlin from 'tree-sitter-kotlin';
+import { SupportedLanguages } from '../../../../_shared/index.js';
+// `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
 (source_file) @scope.module
@@ -176,13 +184,13 @@ let query = null;
 export function getKotlinParser() {
     if (parser === null) {
         parser = new Parser();
-        parser.setLanguage(Kotlin);
+        parser.setLanguage(getLanguageGrammar(SupportedLanguages.Kotlin));
     }
     return parser;
 }
 export function getKotlinScopeQuery() {
     if (query === null) {
-        query = new Parser.Query(Kotlin, KOTLIN_SCOPE_QUERY);
+        query = new Parser.Query(getLanguageGrammar(SupportedLanguages.Kotlin), KOTLIN_SCOPE_QUERY);
     }
     return query;
 }

package/dist/core/ingestion/languages/swift/query.js

@@ -42,7 +42,15 @@
  * tree-sitter init cost per file.
  */
 import Parser from 'tree-sitter';
-import Swift from 'tree-sitter-swift';
+import { SupportedLanguages } from '../../../../_shared/index.js';
+// `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 ──────────────────────────────────────────────────────────
 (source_file) @scope.module
@@ -182,13 +190,13 @@ let _query = null;
 export function getSwiftParser() {
     if (_parser === null) {
         _parser = new Parser();
-        _parser.setLanguage(Swift);
+        _parser.setLanguage(getLanguageGrammar(SupportedLanguages.Swift));
     }
     return _parser;
 }
 export function getSwiftScopeQuery() {
     if (_query === null) {
-        _query = new Parser.Query(Swift, SWIFT_SCOPE_QUERY);
+        _query = new Parser.Query(getLanguageGrammar(SupportedLanguages.Swift), SWIFT_SCOPE_QUERY);
     }
     return _query;
 }

package/dist/core/ingestion/model/registration-table.js

@@ -116,6 +116,9 @@ const LABEL_BEHAVIOR = {
     Section: 'inert',
     Route: 'inert',
     Tool: 'inert',
+    // Taint/PDG substrate (issue #2080) — a control-flow node, never a
+    // symbol-resolution target. Inert: file index only, no owner scope.
+    BasicBlock: 'inert',
 };
 // ---------------------------------------------------------------------------
 // Derived runtime collections — all keyed off LABEL_BEHAVIOR

package/dist/core/ingestion/pipeline-phases/index.d.ts

@@ -21,3 +21,4 @@ export { processesPhase, type ProcessesOutput } from './processes.js';
 export { runPipeline } from './runner.js';
 export type { PipelinePhase, PipelineContext, PhaseResult } from './types.js';
 export { getPhaseOutput } from './types.js';
+export { PhaseRegistry, type RegisterPhaseOptions } from './registry.js';

package/dist/core/ingestion/pipeline-phases/index.js

@@ -22,3 +22,4 @@ export { processesPhase } from './processes.js';
 // ── Infrastructure ─────────────────────────────────────────────────────────
 export { runPipeline } from './runner.js';
 export { getPhaseOutput } from './types.js';
+export { PhaseRegistry } from './registry.js';

package/dist/core/ingestion/pipeline-phases/parse-impl.js

@@ -20,9 +20,9 @@ import { fileContentHash, computeChunkHash, loadParseCacheChunk, persistParseCac
 import { clearParsedFileStore, persistParsedFileChunk, getDurableParsedFileDir, loadDurableParsedFileIndex, restoreDurableParsedFileShard, } from '../../../storage/parsedfile-store.js';
 import { processRoutesFromExtracted, buildExportedTypeMapFromGraph, } from '../call-processor.js';
 import { createSemanticModel } from '../model/index.js';
-import { getLanguageFromFilename } from '../../../_shared/index.js';
+import { getLanguageFromFilename, } from '../../../_shared/index.js';
 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, resolveAutoPoolSize, WorkerPoolInitializationError, WorkerPoolDisabledError, } from '../workers/worker-pool.js';
 import fs from 'node:fs';
 import path from 'node:path';
@@ -167,7 +167,15 @@ export async function runChunkedParseAndResolve(graph, scannedFiles, allPaths, t
         }
     }
     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)) {
+            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
     // across runs (Finding 4). Without this, filesystem-scan order can

package/dist/core/ingestion/pipeline-phases/registry.d.ts

@@ -0,0 +1,56 @@
+/**
+ * Phase registry seam (issue #2080, taint/PDG substrate M0).
+ *
+ * A small, behaviour-preserving abstraction over phase-list *assembly*. Today
+ * `buildPhaseList` is a hand-maintained array with a single ad-hoc
+ * `if (!skipGraphPhases)` guard; this registry generalises that guard into a
+ * per-phase `enabledWhen` predicate so later milestones can register opt-in
+ * phases (e.g. CFG → M1 #2081) without editing the array each time.
+ *
+ * M0 wires the seam with **no behaviour change**: `build(options)` must return
+ * a phase list identical in membership and order to the legacy array for every
+ * options combination. The registry covers only list assembly — the runner,
+ * topological sort, `PipelinePhase.execute`, and any result-extraction guards
+ * (e.g. the `skipGraphPhases` check in `runPipelineFromRepo`) are untouched.
+ *
+ * Generic over the options type so this module depends only on `PipelinePhase`
+ * (no import of `PipelineOptions`, which lives in `pipeline.ts` and would
+ * otherwise create an import cycle).
+ */
+import type { PipelinePhase } from './types.js';
+/** Options accepted when registering a phase. */
+export interface RegisterPhaseOptions<TOptions> {
+    /**
+     * Predicate deciding whether this phase is included for a given options
+     * object. Absent ⇒ the phase is always enabled. This is the generalised
+     * form of the legacy `if (!skipGraphPhases)` guard.
+     *
+     * `options` is required, not optional: callers normalize an absent options
+     * object once at `build()` (e.g. `buildPhaseList` passes `options ?? {}`), so
+     * individual predicates read `(o) => !o.skipGraphPhases` without a defensive
+     * `?.` on every phase (#2080 review S1).
+     */
+    readonly enabledWhen?: (options: TOptions) => boolean;
+}
+/**
+ * Ordered registry of pipeline phases. Not a global singleton — callers
+ * construct a fresh registry (so registration order is deterministic and there
+ * is no import-order or test-isolation hazard) and `build()` it per run.
+ */
+export declare class PhaseRegistry<TOptions = unknown> {
+    private readonly registrations;
+    /**
+     * Register a phase. This is the `registerPhase(phase, { enabledWhen })` seam
+     * named in issue #2080. Returns `this` for fluent chaining. Registration
+     * order is preserved by `build()`.
+     */
+    register(phase: PipelinePhase, options?: RegisterPhaseOptions<TOptions>): this;
+    /**
+     * Build the ordered phase list for the given options. A phase is included
+     * iff it has no `enabledWhen` predicate or its predicate returns `true`.
+     * Order matches registration order. `options` is required — callers that may
+     * have no options normalize once at the call site (`options ?? {}`) so the
+     * predicates never see `undefined`.
+     */
+    build(options: TOptions): PipelinePhase[];
+}

package/dist/core/ingestion/pipeline-phases/registry.js

@@ -0,0 +1,48 @@
+/**
+ * Phase registry seam (issue #2080, taint/PDG substrate M0).
+ *
+ * A small, behaviour-preserving abstraction over phase-list *assembly*. Today
+ * `buildPhaseList` is a hand-maintained array with a single ad-hoc
+ * `if (!skipGraphPhases)` guard; this registry generalises that guard into a
+ * per-phase `enabledWhen` predicate so later milestones can register opt-in
+ * phases (e.g. CFG → M1 #2081) without editing the array each time.
+ *
+ * M0 wires the seam with **no behaviour change**: `build(options)` must return
+ * a phase list identical in membership and order to the legacy array for every
+ * options combination. The registry covers only list assembly — the runner,
+ * topological sort, `PipelinePhase.execute`, and any result-extraction guards
+ * (e.g. the `skipGraphPhases` check in `runPipelineFromRepo`) are untouched.
+ *
+ * Generic over the options type so this module depends only on `PipelinePhase`
+ * (no import of `PipelineOptions`, which lives in `pipeline.ts` and would
+ * otherwise create an import cycle).
+ */
+/**
+ * Ordered registry of pipeline phases. Not a global singleton — callers
+ * construct a fresh registry (so registration order is deterministic and there
+ * is no import-order or test-isolation hazard) and `build()` it per run.
+ */
+export class PhaseRegistry {
+    registrations = [];
+    /**
+     * Register a phase. This is the `registerPhase(phase, { enabledWhen })` seam
+     * named in issue #2080. Returns `this` for fluent chaining. Registration
+     * order is preserved by `build()`.
+     */
+    register(phase, options) {
+        this.registrations.push({ phase, enabledWhen: options?.enabledWhen });
+        return this;
+    }
+    /**
+     * Build the ordered phase list for the given options. A phase is included
+     * iff it has no `enabledWhen` predicate or its predicate returns `true`.
+     * Order matches registration order. `options` is required — callers that may
+     * have no options normalize once at the call site (`options ?? {}`) so the
+     * predicates never see `undefined`.
+     */
+    build(options) {
+        return this.registrations
+            .filter((r) => r.enabledWhen === undefined || r.enabledWhen(options))
+            .map((r) => r.phase);
+    }
+}

package/dist/core/ingestion/pipeline.d.ts

@@ -16,6 +16,7 @@
  */
 import { type PipelineProgress } from '../../_shared/index.js';
 import { PipelineResult } from '../../types/pipeline.js';
+import { type PipelinePhase } from './pipeline-phases/index.js';
 export interface PipelineOptions {
     /**
      * Skip MRO, community detection, and process extraction for faster test runs.
@@ -104,4 +105,24 @@ export interface PipelineOptions {
      */
     keepLocalValueSymbols?: boolean;
 }
+/**
+ * All pipeline phases with their dependency relationships.
+ *
+ * Phase dependency graph:
+ *
+ *   scan → structure → [markdown, cobol] → parse → [routes, tools, orm]
+ *     → crossFile → scopeResolution → pruneLocalSymbols
+ *     → mro → communities → processes
+ *
+ * To add a new phase: create a file in pipeline-phases/, export the phase
+ * object, and `.register()` it at the appropriate position below. Opt-in
+ * phases pass an `enabledWhen` predicate (issue #2080 phase-registry seam) —
+ * the legacy `if (!skipGraphPhases)` guard is now expressed that way on the
+ * three graph phases, with no change in behaviour.
+ *
+ * Exported for the parity test (`pipeline-phase-registry.test.ts`), which
+ * asserts the produced list is byte-identical to the legacy array for every
+ * options combination.
+ */
+export declare function buildPhaseList(options?: PipelineOptions): PipelinePhase[];
 export declare const runPipelineFromRepo: (repoPath: string, onProgress: (progress: PipelineProgress) => void, options?: PipelineOptions) => Promise<PipelineResult>;

package/dist/core/ingestion/pipeline.js

@@ -15,7 +15,7 @@
  * See ARCHITECTURE.md for the full phase dependency diagram.
  */
 import { createKnowledgeGraph } from '../graph/graph.js';
-import { runPipeline, getPhaseOutput, scanPhase, structurePhase, markdownPhase, cobolPhase, parsePhase, routesPhase, toolsPhase, ormPhase, crossFilePhase, scopeResolutionPhase, pruneLocalSymbolsPhase, mroPhase, communitiesPhase, processesPhase, } from './pipeline-phases/index.js';
+import { runPipeline, getPhaseOutput, scanPhase, structurePhase, markdownPhase, cobolPhase, parsePhase, routesPhase, toolsPhase, ormPhase, crossFilePhase, scopeResolutionPhase, pruneLocalSymbolsPhase, mroPhase, communitiesPhase, processesPhase, PhaseRegistry, } from './pipeline-phases/index.js';
 // ── Phase registry ─────────────────────────────────────────────────────────
 /**
  * All pipeline phases with their dependency relationships.
@@ -27,26 +27,34 @@ import { runPipeline, getPhaseOutput, scanPhase, structurePhase, markdownPhase,
  *     → mro → communities → processes
  *
  * To add a new phase: create a file in pipeline-phases/, export the phase
- * object, and add it to the appropriate position in this array.
+ * object, and `.register()` it at the appropriate position below. Opt-in
+ * phases pass an `enabledWhen` predicate (issue #2080 phase-registry seam) —
+ * the legacy `if (!skipGraphPhases)` guard is now expressed that way on the
+ * three graph phases, with no change in behaviour.
+ *
+ * Exported for the parity test (`pipeline-phase-registry.test.ts`), which
+ * asserts the produced list is byte-identical to the legacy array for every
+ * options combination.
  */
-function buildPhaseList(options) {
-    const phases = [
-        scanPhase,
-        structurePhase,
-        markdownPhase,
-        cobolPhase,
-        parsePhase,
-        routesPhase,
-        toolsPhase,
-        ormPhase,
-        crossFilePhase,
-        scopeResolutionPhase,
-        pruneLocalSymbolsPhase,
-    ];
-    if (!options?.skipGraphPhases) {
-        phases.push(mroPhase, communitiesPhase, processesPhase);
-    }
-    return phases;
+export function buildPhaseList(options) {
+    return (new PhaseRegistry()
+        .register(scanPhase)
+        .register(structurePhase)
+        .register(markdownPhase)
+        .register(cobolPhase)
+        .register(parsePhase)
+        .register(routesPhase)
+        .register(toolsPhase)
+        .register(ormPhase)
+        .register(crossFilePhase)
+        .register(scopeResolutionPhase)
+        .register(pruneLocalSymbolsPhase)
+        .register(mroPhase, { enabledWhen: (o) => !o.skipGraphPhases })
+        .register(communitiesPhase, { enabledWhen: (o) => !o.skipGraphPhases })
+        .register(processesPhase, { enabledWhen: (o) => !o.skipGraphPhases })
+        // Normalize a missing options object once here so phase predicates above
+        // take a required PipelineOptions and need no `?.` guard (#2080 review S1).
+        .build(options ?? {}));
 }
 // ── Pipeline orchestrator ─────────────────────────────────────────────────
 export const runPipelineFromRepo = async (repoPath, onProgress, options) => {