gitnexus 1.6.9-rc.43 → 1.6.9-rc.45

package/README.md

@@ -40,14 +40,14 @@ To configure MCP for your editor, run `npx gitnexus setup` once — or set it up
 
 | Editor                   | MCP | Skills | Hooks (auto-augment)                                                                       | Support      |
 | ------------------------ | --- | ------ | ------------------------------------------------------------------------------------------ | ------------ |
-| **Claude Code**          | Yes | Yes    | Yes (PreToolUse)                                                                           | **Full**     |
+| **Claude Code**          | Yes | Yes    | Yes (PreToolUse + PostToolUse)                                                             | **Full**     |
 | **Cursor**               | Yes | Yes    | Yes (postToolUse, [manual install](../gitnexus-cursor-integration/README.md#hook-install)) | **Full**     |
 | **Antigravity** (Google) | Yes | Yes    | Yes (AfterTool, [Gemini CLI hooks schema](https://geminicli.com/docs/hooks/reference/))    | **Full**     |
 | **Codex**                | Yes | Yes    | —                                                                                          | MCP + Skills |
-| **Windsurf**             | Yes | —      | —                                                                                          | MCP          |
 | **OpenCode**             | Yes | Yes    | —                                                                                          | MCP + Skills |
+| **Windsurf**             | Yes | —      | —                                                                                          | MCP          |
 
-> **Claude Code** gets the deepest integration: MCP tools + agent skills + PreToolUse hooks that automatically enrich grep/glob/bash calls with knowledge graph context.
+> **Claude Code** gets the deepest integration: MCP tools + agent skills + PreToolUse hooks that automatically enrich grep/glob/bash calls with knowledge graph context + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.
 
 ### Community Integrations
 
@@ -122,31 +122,44 @@ The result is a **LadybugDB graph database** stored locally in `.gitnexus/` with
 
 ## MCP Tools
 
-Your AI agent gets these tools automatically:
-
-| Tool             | What It Does                                                     | `repo` Param |
-| ---------------- | ---------------------------------------------------------------- | ------------ |
-| `list_repos`     | Discover all indexed repositories (paginated — `limit`/`offset`) | —            |
-| `query`          | Process-grouped hybrid search (BM25 + semantic + RRF)            | Optional     |
-| `context`        | 360-degree symbol view — categorized refs, process participation | Optional     |
-| `impact`         | Blast radius analysis with depth grouping and confidence         | Optional     |
-| `detect_changes` | Git-diff impact — maps changed lines to affected processes       | Optional     |
-| `rename`         | Multi-file coordinated rename with graph + text search           | Optional     |
-| `cypher`         | Raw Cypher graph queries                                         | Optional     |
-
-> With one indexed repo, the `repo` param is optional. With multiple, specify which: `query({search_query: "auth", repo: "my-app"})`.
+Your AI agent gets **17 tools** (15 per-repo + 2 group) automatically:
+
+| Tool             | What It Does                                                           |
+| ---------------- | ----------------------------------------------------------------------- |
+| `list_repos`     | Discover all indexed repositories (paginated — `limit`/`offset`)        |
+| `query`          | Process-grouped hybrid search (BM25 + semantic + RRF)                   |
+| `context`        | 360-degree symbol view — categorized refs, process participation        |
+| `impact`         | Blast radius analysis with depth grouping and confidence                |
+| `trace`          | Shortest directed path between two symbols (call + class-member edges)  |
+| `detect_changes` | Git-diff impact — maps changed lines to affected processes              |
+| `check`          | Read-only structural checks against the indexed graph                   |
+| `rename`         | Multi-file coordinated rename with graph + text search                  |
+| `cypher`         | Raw Cypher graph queries                                                |
+| `route_map`      | API route map — which components fetch which endpoints, and handlers    |
+| `tool_map`       | MCP/RPC tool definitions — where they're defined and handled            |
+| `shape_check`    | Validate API response shapes against consumers' property accesses       |
+| `api_impact`     | Pre-change impact report for an API route handler                       |
+| `explain`        | Explain persisted taint findings (source→sink flows, `--pdg` indexes)   |
+| `pdg_query`      | Query control/data dependence at statement level (`--pdg` indexes)      |
+| `group_list`     | List configured repository groups                                       |
+| `group_sync`     | Rebuild a group's Contract Registry and cross-repo links                |
+
+> With one indexed repo, the `repo` param is optional. With multiple, specify which: `query({search_query: "auth", repo: "my-app"})`. Per-repo tools also take an optional `branch` for multi-branch indexes. `explain` and `pdg_query` need an index built with `gitnexus analyze --pdg`.
 
 ## MCP Resources
 
 | Resource                                | Purpose                                              |
 | --------------------------------------- | ---------------------------------------------------- |
 | `gitnexus://repos`                      | List all indexed repositories (read first)           |
+| `gitnexus://setup`                      | Setup and usage guidance for agents                  |
 | `gitnexus://repo/{name}/context`        | Codebase stats, staleness check, and available tools |
 | `gitnexus://repo/{name}/clusters`       | All functional clusters with cohesion scores         |
 | `gitnexus://repo/{name}/cluster/{name}` | Cluster members and details                          |
 | `gitnexus://repo/{name}/processes`      | All execution flows                                  |
 | `gitnexus://repo/{name}/process/{name}` | Full process trace with steps                        |
 | `gitnexus://repo/{name}/schema`         | Graph schema for Cypher queries                      |
+| `gitnexus://group/{name}/contracts`     | A group's extracted contracts and cross-links        |
+| `gitnexus://group/{name}/status`        | Staleness of repos in a group                        |
 
 ## MCP Prompts
 
@@ -164,7 +177,11 @@ gitnexus analyze [path]          # Index a repository (or update stale index)
 gitnexus analyze --repair-fts    # Fast path: rebuild/verify only FTS indexes on existing index data
 gitnexus analyze --force         # Full rebuild: re-parse + graph rebuild + FTS rebuild
 gitnexus analyze --embeddings    # Enable embedding generation (slower, better search)
+gitnexus analyze --skills        # Generate repo-specific skill files from detected communities
 gitnexus analyze --skip-agents-md  # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
+gitnexus analyze --skip-skills   # Skip installing .claude/skills/gitnexus/ skill files
+gitnexus analyze --skip-git      # Index folders that are not Git repositories
+gitnexus analyze --workers <n>   # Parse worker pool size (>=1; default: cores-1, capped at 16)
 gitnexus analyze --verbose       # Log skipped files when parsers are unavailable
 gitnexus analyze --max-file-size 1024  # Skip files larger than N KB (default: 512, cap: 32768)
 gitnexus analyze --worker-timeout 60  # Increase worker idle timeout for slow parses
@@ -177,13 +194,16 @@ gitnexus status                  # Show index status for current repo
 gitnexus clean                   # Delete index for current repo
 gitnexus clean --all --force     # Delete all indexes
 gitnexus wiki [path]             # Generate LLM-powered docs from knowledge graph
-gitnexus wiki --model <model>    # Wiki with custom LLM model (default: gpt-4o-mini)
+gitnexus wiki --model <model>    # Wiki with custom LLM model (default: minimax/minimax-m2.5)
+gitnexus doctor                  # Show runtime platform capabilities and embedding configuration
 
 # Direct graph queries — the same tools the MCP server exposes, no MCP daemon needed
 gitnexus query "<concept>"                                    # Process-grouped hybrid search
 gitnexus context <symbol> [--uid <uid> | --file <path>]       # 360° symbol view; flags disambiguate a shared name
 gitnexus impact <symbol> [--uid <uid> | --file <path> | --kind <kind>]  # Blast radius; flags disambiguate a shared name
+gitnexus trace <from> <to>       # Shortest directed path between two symbols
 gitnexus detect-changes          # Map the working-tree diff to affected symbols and execution flows
+gitnexus check                   # Read-only structural checks against the indexed graph
 gitnexus cypher "<query>"        # Run a raw Cypher query against the knowledge graph
 
 # Repository groups (multi-repo / monorepo service tracking)
@@ -195,6 +215,7 @@ gitnexus group sync <name>                                     # Extract contrac
 gitnexus group contracts <name>  # Inspect extracted contracts and cross-links
 gitnexus group query <name> <q>  # Search execution flows across all repos in a group
 gitnexus group status <name>     # Check staleness of repos in a group
+gitnexus group impact <name> --target <symbol> --repo <groupPath>  # Cross-repo blast radius
 ```
 
 > **`gitnexus uninstall`** reverses `gitnexus setup` — it removes the GitNexus MCP entries, hooks, and skill directories it added to each detected editor. Skill directories are identified **by bundled gitnexus skill name** (e.g. `gitnexus-cli/`), so if you customized files inside an installed skill directory, back them up first. It is a dry-run preview by default and prints the exact paths it would remove; pass `--force` to apply. Per-repo indexes (`gitnexus clean --all`) and the global npm package (`npm uninstall -g gitnexus`) are left for you to remove.
@@ -219,7 +240,7 @@ GitNexus supports indexing multiple repositories. Each `gitnexus analyze` regist
 
 ## Supported Languages
 
-TypeScript, JavaScript, Python, Java, C, C++, C#, Go, Rust, PHP, Kotlin, Swift, Ruby
+TypeScript, JavaScript, Python, Java, C, C++, C#, Go, Rust, PHP, Kotlin, Swift, Ruby, Dart
 
 ### Language Feature Matrix
 
@@ -238,6 +259,7 @@ TypeScript, JavaScript, Python, Java, C, C++, C#, Go, Rust, PHP, Kotlin, Swift,
 | Swift      | —       | —              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
 | C          | —       | —              | ✓       | —        | ✓                | ✓                     | —      | ✓          | ✓            |
 | C++        | —       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
+| Dart       | ✓       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
 
 **Imports** — cross-file import resolution · **Named Bindings** — `import { X as Y }` / re-export tracking · **Exports** — public/exported symbol detection · **Heritage** — class inheritance, interfaces, mixins · **Type Annotations** — explicit type extraction for receiver resolution · **Constructor Inference** — infer receiver type from constructor calls (`self`/`this` resolution included for all languages) · **Config** — language toolchain config parsing (tsconfig, go.mod, etc.) · **Frameworks** — AST-based framework pattern detection · **Entry Points** — entry point scoring heuristics
 
@@ -249,12 +271,14 @@ GitNexus ships with skill files that teach AI agents how to use the tools effect
 - **Debugging** — Trace bugs through call chains
 - **Impact Analysis** — Analyze blast radius before changes
 - **Refactoring** — Plan safe refactors using dependency mapping
+- **Guide** — GitNexus tool/resource/schema reference for the agent
+- **CLI** — Run analyze/status/clean/wiki commands on request
 
-Installed automatically by both `gitnexus analyze` (per-repo) and `gitnexus setup` (global).
+Installed automatically by both `gitnexus analyze` (per-repo) and `gitnexus setup` (global). Run `gitnexus analyze --skills` to additionally generate repo-specific skills for each detected functional area under `.claude/skills/generated/`.
 
 ## Requirements
 
-- Node.js >= 18
+- Node.js >= 22
 - Git repository (uses git for commit tracking)
 
 ## Release candidates
@@ -340,7 +364,7 @@ gitnexus serve
 
 ### Installation fails with native module errors
 
-Some optional language grammars (Dart, Kotlin, Swift) require native compilation. If they fail, GitNexus still works — those languages will be skipped.
+Some optional language grammars (Dart, Proto, Swift, Kotlin) require native compilation. If they fail, GitNexus still works — those languages will be skipped. To skip them intentionally (no C++ toolchain needed), set `GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1` before installing.
 
 If `npm install -g gitnexus` fails on native modules:
 

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

@@ -32,6 +32,9 @@ export type NodeProperties = {
     level?: number;
     returnType?: string;
     declaredType?: string;
+    /** Verbatim declared-type source text with generics preserved
+     *  (e.g. `List<Shape>` where `declaredType` is the stripped `List`). */
+    rawDeclaredType?: string;
     visibility?: string;
     isStatic?: boolean;
     isReadonly?: boolean;
@@ -52,6 +55,19 @@ export type NodeProperties = {
     [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'
+/** Dependency-injection edge: a consumer class receives every implementer
+ *  of interface `T` via a container-injected collection-typed field
+ *  (`List<T>`, `Set<T>`, `Collection<T>`, or `Map<K,T>`). Precondition: the
+ *  field carries an injection annotation recognized by a per-language
+ *  matcher registered in `di-extractors/` (Java/Spring today: `@Autowired`
+ *  or `@Inject`; `@Resource` is excluded — by-name-first semantics).
+ *  Source = the consumer Class node (the one owning the field).
+ *  Target = an implementing Class node.
+ *  Framework specifics live in the `reason` payload (e.g.
+ *  `Spring DI: @Autowired List<T>`), not in this type contract.
+ *  Lets Cypher queries trace which beans the container injects into a given
+ *  consumer, complementing the structural `IMPLEMENTS` heritage edges. */
+ | 'INJECTS'
 /** Vue component event system: a handler function in a parent component is
  *  bound to an event emitted by a child component (`@event="handlerFn"`).
  *  Source = handler Function/Method node in the parent.

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

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

@@ -10,7 +10,7 @@
 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", "CFG", "REACHING_DEF", "TAINTED", "SANITIZES", "TAINT_PATH", "CDG", "POST_DOMINATE"];
+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", "INJECTS", "CFG", "REACHING_DEF", "TAINTED", "SANITIZES", "TAINT_PATH", "CDG", "POST_DOMINATE"];
 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 @@
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+{"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,iYAoCZ,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

@@ -64,6 +64,7 @@ export const REL_TYPES = [
     'ENTRY_POINT_OF',
     'WRAPS',
     'QUERIES',
+    'INJECTS',
     // 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.

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

@@ -1 +1 @@
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package/dist/cli/i18n/en.d.ts

@@ -162,7 +162,7 @@ export declare const en: {
     readonly 'help.option.analyze.embeddingBatchSize': "Number of nodes per embedding batch";
     readonly 'help.option.analyze.embeddingSubBatchSize': "Number of chunks per embedding model call";
     readonly 'help.option.analyze.embeddingDevice': "Embedding device: auto, cpu, dml, cuda, or wasm";
-    readonly 'help.option.index.force': "Register even if meta.json is missing (stats will be empty)";
+    readonly 'help.option.index.force': "Register even if index metadata is missing (stats will be empty)";
     readonly 'help.option.index.allowNonGit': "Allow registering folders that are not Git repositories";
     readonly 'help.option.port': "Port number";
     readonly 'help.option.serve.host': "Bind address (default: 127.0.0.1, use 0.0.0.0 for remote access)";

package/dist/cli/i18n/en.js

@@ -162,7 +162,7 @@ export const en = {
     'help.option.analyze.embeddingBatchSize': 'Number of nodes per embedding batch',
     'help.option.analyze.embeddingSubBatchSize': 'Number of chunks per embedding model call',
     'help.option.analyze.embeddingDevice': 'Embedding device: auto, cpu, dml, cuda, or wasm',
-    'help.option.index.force': 'Register even if meta.json is missing (stats will be empty)',
+    'help.option.index.force': 'Register even if index metadata is missing (stats will be empty)',
     'help.option.index.allowNonGit': 'Allow registering folders that are not Git repositories',
     'help.option.port': 'Port number',
     'help.option.serve.host': 'Bind address (default: 127.0.0.1, use 0.0.0.0 for remote access)',

package/dist/cli/i18n/resources.d.ts

@@ -163,7 +163,7 @@ export declare const cliResources: {
         readonly 'help.option.analyze.embeddingBatchSize': "Number of nodes per embedding batch";
         readonly 'help.option.analyze.embeddingSubBatchSize': "Number of chunks per embedding model call";
         readonly 'help.option.analyze.embeddingDevice': "Embedding device: auto, cpu, dml, cuda, or wasm";
-        readonly 'help.option.index.force': "Register even if meta.json is missing (stats will be empty)";
+        readonly 'help.option.index.force': "Register even if index metadata is missing (stats will be empty)";
         readonly 'help.option.index.allowNonGit': "Allow registering folders that are not Git repositories";
         readonly 'help.option.port': "Port number";
         readonly 'help.option.serve.host': "Bind address (default: 127.0.0.1, use 0.0.0.0 for remote access)";

package/dist/cli/i18n/zh-CN.js

@@ -162,7 +162,7 @@ export const zhCN = {
     'help.option.analyze.embeddingBatchSize': '每个嵌入批次的节点数',
     'help.option.analyze.embeddingSubBatchSize': '每次嵌入模型调用的分块数',
     'help.option.analyze.embeddingDevice': '嵌入设备：auto、cpu、dml、cuda 或 wasm',
-    'help.option.index.force': '即使缺少 meta.json 也注册（统计为空）',
+    'help.option.index.force': '即使缺少索引元数据也注册（统计为空）',
     'help.option.index.allowNonGit': '允许注册非 Git 仓库文件夹',
     'help.option.port': '端口号',
     'help.option.serve.host': '绑定地址（默认：127.0.0.1；远程访问可用 0.0.0.0）',

package/dist/cli/index-repo.d.ts

@@ -1,10 +1,14 @@
 /**
  * Index Command
  *
- * Registers an existing .gitnexus/ folder into the global registry so the
+ * Registers an existing GitNexus index into the global registry so the
  * MCP server can discover the repo without running a full `gitnexus analyze`.
  *
- * Useful when a pre-built .gitnexus/ directory is already present (e.g. after
+ * The index can be either:
+ * - A per-worktree gitnexus.json file under .gitnexus/ (new format, worktree-compatible)
+ * - A legacy .gitnexus/meta.json file (auto-migrated on analyze)
+ *
+ * Useful when a pre-built index is already present (e.g. after
  * cloning a repo that ships its index, restoring from backup, or using a
  * shared team index).
  */

package/dist/cli/index-repo.js

@@ -1,16 +1,20 @@
 /**
  * Index Command
  *
- * Registers an existing .gitnexus/ folder into the global registry so the
+ * Registers an existing GitNexus index into the global registry so the
  * MCP server can discover the repo without running a full `gitnexus analyze`.
  *
- * Useful when a pre-built .gitnexus/ directory is already present (e.g. after
+ * The index can be either:
+ * - A per-worktree gitnexus.json file under .gitnexus/ (new format, worktree-compatible)
+ * - A legacy .gitnexus/meta.json file (auto-migrated on analyze)
+ *
+ * Useful when a pre-built index is already present (e.g. after
  * cloning a repo that ships its index, restoring from backup, or using a
  * shared team index).
  */
 import path from 'path';
 import fs from 'fs/promises';
-import { getStoragePaths, loadMeta, ensureGitNexusIgnored, registerRepo, } from '../storage/repo-manager.js';
+import { getStoragePaths, INDEX_METADATA_FILE, loadMeta, ensureGitNexusIgnored, registerRepo, } from '../storage/repo-manager.js';
 import { getGitRoot, getRemoteUrl, isGitRepo } from '../storage/git.js';
 export const indexCommand = async (inputPathParts, options) => {
     console.log('\n  GitNexus Index\n');
@@ -50,22 +54,35 @@ export const indexCommand = async (inputPathParts, options) => {
         return;
     }
     const { storagePath, lbugPath } = getStoragePaths(repoPath);
-    // ── Verify .gitnexus/ exists ──────────────────────────────────────
+    // ── Verify index exists (metadata file, legacy metadata, or restorable DB) ─
+    let hasMetadataIndex = false;
+    let hasLegacyIndex = false;
+    let hasLbugIndex = false;
+    try {
+        await fs.access(path.join(storagePath, INDEX_METADATA_FILE));
+        hasMetadataIndex = true;
+    }
+    catch { }
     try {
-        await fs.access(storagePath);
+        await fs.access(path.join(storagePath, 'meta.json'));
+        hasLegacyIndex = true;
     }
-    catch {
-        console.log(`  No .gitnexus/ folder found at: ${storagePath}`);
+    catch { }
+    try {
+        await fs.access(lbugPath);
+        hasLbugIndex = true;
+    }
+    catch { }
+    if (!hasMetadataIndex && !hasLegacyIndex && !hasLbugIndex) {
+        console.log(`  No GitNexus index found.`);
+        console.log(`  Expected gitnexus.json, .gitnexus/meta.json, or LadybugDB at: ${storagePath}`);
         console.log('  Run `gitnexus analyze` to build the index first.\n');
         process.exitCode = 1;
         return;
     }
     // ── Verify lbug database exists ───────────────────────────────────
-    try {
-        await fs.access(lbugPath);
-    }
-    catch {
-        console.log(`  .gitnexus/ folder exists but contains no LadybugDB index.`);
+    if (!hasLbugIndex) {
+        console.log(`  Index exists but contains no LadybugDB database.`);
         console.log('  Run `gitnexus analyze` to build the index.\n');
         process.exitCode = 1;
         return;
@@ -74,7 +91,7 @@ export const indexCommand = async (inputPathParts, options) => {
     let meta = await loadMeta(storagePath);
     if (!meta) {
         if (!options?.force) {
-            console.log(`  .gitnexus/ exists but meta.json is missing.`);
+            console.log(`  gitnexus.json or .gitnexus/meta.json is missing.`);
             console.log('  Use --force to register anyway (stats will be empty),');
             console.log('  or run `gitnexus analyze` to rebuild properly.\n');
             process.exitCode = 1;

package/dist/cli/index.js

@@ -123,7 +123,7 @@ program
 program
     .command('index [path...]')
     .description('Register an existing .gitnexus/ folder into the global registry (no re-analysis needed)')
-    .option('-f, --force', 'Register even if meta.json is missing (stats will be empty)')
+    .option('-f, --force', 'Register even if index metadata is missing (stats will be empty)')
     .option('--allow-non-git', 'Allow registering folders that are not Git repositories')
     .action(createLazyAction(() => import('./index-repo.js'), 'indexCommand'));
 program

package/dist/cli/remove.d.ts

@@ -1,9 +1,12 @@
 /**
  * Remove Command (#664)
  *
- * Delete the `.gitnexus/` index for a registered repo and unregister it
- * from the global registry (~/.gitnexus/registry.json). The target is
- * identified by alias / basename-derived name / remote-inferred name /
+ * Delete the `.gitnexus/` index directory for a registered repo (including
+ * both metadata filenames — gitnexus.json and its legacy meta.json mirror —
+ * which live inside it) and unregister it from the global registry
+ * (~/.gitnexus/registry.json).
+ *
+ * The target is identified by alias / basename-derived name / remote-inferred name /
  * absolute path — no `--repo` flag, just a positional argument so the
  * destructive-command ergonomics match `clean` (which is also
  * destructive but scoped to `process.cwd()`).

package/dist/cli/remove.js

@@ -1,9 +1,12 @@
 /**
  * Remove Command (#664)
  *
- * Delete the `.gitnexus/` index for a registered repo and unregister it
- * from the global registry (~/.gitnexus/registry.json). The target is
- * identified by alias / basename-derived name / remote-inferred name /
+ * Delete the `.gitnexus/` index directory for a registered repo (including
+ * both metadata filenames — gitnexus.json and its legacy meta.json mirror —
+ * which live inside it) and unregister it from the global registry
+ * (~/.gitnexus/registry.json).
+ *
+ * The target is identified by alias / basename-derived name / remote-inferred name /
  * absolute path — no `--repo` flag, just a positional argument so the
  * destructive-command ergonomics match `clean` (which is also
  * destructive but scoped to `process.cwd()`).

package/dist/core/group/bridge-db.d.ts

@@ -110,7 +110,6 @@ export declare function queryBridge<T>(handle: BridgeHandle, cypher: string, par
  * is a lease release, so the file may stay open under other readers.
  */
 export declare function closeBridgeDb(handle: BridgeHandle): Promise<void>;
-export declare function retryRename(src: string, dst: string, attempts?: number): Promise<void>;
 export declare function writeBridgeMeta(groupDir: string, meta: BridgeMeta): Promise<void>;
 export declare function readBridgeMeta(groupDir: string): Promise<BridgeMeta>;
 export interface WriteBridgeInput {

package/dist/core/group/bridge-db.js

@@ -6,6 +6,7 @@ import { BRIDGE_SCHEMA_QUERIES, BRIDGE_SCHEMA_VERSION } from './bridge-schema.js
 import { closeLbugConnection, openLbugConnection, } from '../lbug/lbug-config.js';
 import { dedupeContracts, dedupeCrossLinks } from './normalization.js';
 import { createLogger } from '../logger.js';
+import { retryRename } from '../../storage/fs-atomic.js';
 const bridgeLogger = createLogger('bridge-db', {
     debugEnvVar: 'GITNEXUS_DEBUG_BRIDGE',
 });
@@ -512,24 +513,6 @@ export async function closeBridgeDb(handle) {
 // The read-only CHECKPOINT skip above remains the load-bearing fix on
 // Linux/macOS.
 /* ------------------------------------------------------------------ */
-/*  retryRename — handles transient EBUSY/EPERM/EACCES on Windows    */
-/* ------------------------------------------------------------------ */
-const RETRY_CODES = new Set(['EBUSY', 'EPERM', 'EACCES']);
-export async function retryRename(src, dst, attempts = 3) {
-    for (let i = 1; i <= attempts; i++) {
-        try {
-            await fsp.rename(src, dst);
-            return;
-        }
-        catch (err) {
-            const code = err.code;
-            if (!code || !RETRY_CODES.has(code) || i === attempts)
-                throw err;
-            await new Promise((r) => setTimeout(r, 100 * Math.pow(2, i - 1)));
-        }
-    }
-}
-/* ------------------------------------------------------------------ */
 /*  writeBridgeMeta / readBridgeMeta                                  */
 /* ------------------------------------------------------------------ */
 export async function writeBridgeMeta(groupDir, meta) {

package/dist/core/group/service.js

@@ -5,6 +5,7 @@
 import fsp from 'node:fs/promises';
 import path from 'node:path';
 import { checkStaleness } from '../git-staleness.js';
+import { loadMeta } from '../../storage/repo-manager.js';
 import { GroupNotFoundError, loadGroupConfig } from './config-parser.js';
 import { fileMatchesServicePrefix, normalizeServicePrefix, repoInSubgroup, } from './group-path-utils.js';
 import { getDefaultGitnexusDir, getGroupDir, listGroups, readContractRegistry } from './storage.js';
@@ -370,9 +371,7 @@ export class GroupService {
         for (const [repoPath, registryName] of Object.entries(config.repos)) {
             try {
                 const repoObj = await this.port.resolveRepo(registryName);
-                const metaPath = path.join(repoObj.storagePath, 'meta.json');
-                const metaRaw = await fsp.readFile(metaPath, 'utf-8').catch(() => '{}');
-                const meta = JSON.parse(metaRaw);
+                const meta = (await loadMeta(repoObj.storagePath)) ?? {};
                 const staleness = meta.lastCommit
                     ? checkStaleness(repoObj.repoPath, meta.lastCommit)
                     : { isStale: true, commitsBehind: -1 };

package/dist/core/group/storage.js

@@ -3,7 +3,7 @@ import * as fsp from 'node:fs/promises';
 import * as path from 'node:path';
 import * as os from 'node:os';
 import { randomBytes } from 'node:crypto';
-import { retryRename } from './bridge-db.js';
+import { retryRename } from '../../storage/fs-atomic.js';
 /**
  * Build an unpredictable suffix for atomic-write tmp files. Replaces the
  * previous `Date.now()` pattern which CodeQL flagged as

package/dist/core/incremental/subgraph-extract.js

@@ -63,7 +63,20 @@ const isGraphWide = (label) => label === 'Community' || label === 'Process';
 // re-included from the FULL fresh graph (which the emit phase recomputes every
 // run) or an unchanged function's summary would be lost. Cheap: one self-loop
 // edge per return-flowing function.
-const isGraphWideRelType = (type) => type === 'TAINT_PATH' || type === 'CALL_SUMMARY';
+//
+// `INJECTS` (DI collection injection, #2200) is the same class as TAINT_PATH
+// (the #2084 M4 U6 pattern above): its validity is a whole-program property —
+// a change to a THIRD file (the interface itself, or a new/removed
+// implementer) creates or invalidates edges between two files that were never
+// touched, so the endpoint-writability rule would strand a stale
+// consumer→implementer edge (or miss a new one). Always re-extracted from the
+// fresh graph; the orchestrator unconditionally delete-alls the old rows
+// first (`deleteAllInjects`). Crash-recovery: delete-then-COPY is not atomic
+// by design — a crash between them loses INJECTS edges until the next
+// analyze, and the `incrementalInProgress` dirty flag (saved before any
+// delete) forces a full rebuild on the next run. Temporary absence is
+// possible; duplicates are not.
+const isGraphWideRelType = (type) => type === 'TAINT_PATH' || type === 'CALL_SUMMARY' || type === 'INJECTS';
 /**
  * Build a Map<nodeId, filePath> for every File-bound node in the graph.
  * Graph-wide nodes (Community/Process) have no filePath and are filtered.

package/dist/core/ingestion/di-extractors/index.d.ts

@@ -0,0 +1,47 @@
+/**
+ * Per-language DI field-matcher registry — the lookup the generic `di`
+ * pipeline phase uses to decide whether a `Property` node is a
+ * dependency-injection fan-out candidate.
+ *
+ * Mirrors `scope-resolution/pipeline/registry.ts` (`SCOPE_RESOLVERS`): a
+ * single-valued `ReadonlyMap<SupportedLanguages, DiFieldMatcher>` consumed by
+ * a framework-neutral phase, so no language or framework names leak into
+ * shared pipeline code. Adding a framework is two lines: implement a
+ * `DiFieldMatcher` in `di-extractors/<framework>.ts` and register it here.
+ *
+ * Scope honesty: matchers are per-language *field-injection* matchers.
+ * Constructor injection (the dominant modern Spring idiom) lives on
+ * Method/parameter nodes and would require widening the phase's routing —
+ * deliberately out of scope (see the plan's Deferred work). The registry is
+ * single-valued per language, matching the `SCOPE_RESOLVERS` shape; widen the
+ * value type to arrays only when a second same-language framework actually
+ * lands (a one-line type change then).
+ */
+import { SupportedLanguages } from '../../../_shared/index.js';
+import type { GraphNode } from '../../../_shared/index.js';
+/** A successful DI field match, produced by a per-language matcher. */
+export interface DiFieldMatch {
+    /** The element type name `T` — the injected bean interface. */
+    elementTypeName: string;
+    /** Human-readable edge reason. Framework specifics (names, idioms,
+     *  collection wrapper, gating annotation) live in this payload so the
+     *  shared `di` phase stays framework-neutral. */
+    reason: string;
+}
+/**
+ * A per-language field-injection matcher: given a `Property` node, return the
+ * parsed DI match or `null` when the field is not container-injected. The
+ * matcher receives the whole node (not pre-plucked fields) so the shared
+ * phase stays ignorant of which properties matter.
+ */
+export type DiFieldMatcher = (node: GraphNode) => DiFieldMatch | null;
+/**
+ * Type guard narrowing an arbitrary graph `language` string to
+ * `SupportedLanguages`, so `DI_MATCHERS.get()` needs no cast.
+ */
+export declare function isSupportedLanguage(value: string): value is SupportedLanguages;
+/** Map of `SupportedLanguages` → `DiFieldMatcher`. The `di` phase routes each
+ *  `Property` node here by `node.properties.language`; no entry ⇒ the node is
+ *  skipped. This is the single source of truth for which languages (and,
+ *  transitively, frameworks) produce INJECTS edges. */
+export declare const DI_MATCHERS: ReadonlyMap<SupportedLanguages, DiFieldMatcher>;

package/dist/core/ingestion/di-extractors/index.js

@@ -0,0 +1,35 @@
+/**
+ * Per-language DI field-matcher registry — the lookup the generic `di`
+ * pipeline phase uses to decide whether a `Property` node is a
+ * dependency-injection fan-out candidate.
+ *
+ * Mirrors `scope-resolution/pipeline/registry.ts` (`SCOPE_RESOLVERS`): a
+ * single-valued `ReadonlyMap<SupportedLanguages, DiFieldMatcher>` consumed by
+ * a framework-neutral phase, so no language or framework names leak into
+ * shared pipeline code. Adding a framework is two lines: implement a
+ * `DiFieldMatcher` in `di-extractors/<framework>.ts` and register it here.
+ *
+ * Scope honesty: matchers are per-language *field-injection* matchers.
+ * Constructor injection (the dominant modern Spring idiom) lives on
+ * Method/parameter nodes and would require widening the phase's routing —
+ * deliberately out of scope (see the plan's Deferred work). The registry is
+ * single-valued per language, matching the `SCOPE_RESOLVERS` shape; widen the
+ * value type to arrays only when a second same-language framework actually
+ * lands (a one-line type change then).
+ */
+import { SupportedLanguages } from '../../../_shared/index.js';
+import { springDiFieldMatcher } from './spring.js';
+/** All `SupportedLanguages` string values, for narrowing raw graph strings. */
+const SUPPORTED_LANGUAGE_VALUES = new Set(Object.values(SupportedLanguages));
+/**
+ * Type guard narrowing an arbitrary graph `language` string to
+ * `SupportedLanguages`, so `DI_MATCHERS.get()` needs no cast.
+ */
+export function isSupportedLanguage(value) {
+    return SUPPORTED_LANGUAGE_VALUES.has(value);
+}
+/** Map of `SupportedLanguages` → `DiFieldMatcher`. The `di` phase routes each
+ *  `Property` node here by `node.properties.language`; no entry ⇒ the node is
+ *  skipped. This is the single source of truth for which languages (and,
+ *  transitively, frameworks) produce INJECTS edges. */
+export const DI_MATCHERS = new Map([[SupportedLanguages.Java, springDiFieldMatcher]]);