gitnexus 1.6.9 → 1.6.10-rc.1

package/README.md

@@ -2,7 +2,7 @@
 
 **Graph-powered code intelligence for AI agents.** Index any codebase into a knowledge graph, then query it via MCP or CLI.
 
-Works with **Cursor**, **Claude Code**, **Antigravity** (Google), **Codex**, **Windsurf**, **Cline**, **OpenCode**, and any MCP-compatible tool.
+Works with **Cursor**, **Claude Code**, **Antigravity** (Google), **Codex**, **Windsurf**, **Cline**, **OpenCode**, **CodeBuddy** (Tencent), **Qoder** (Alibaba), and any MCP-compatible tool.
 
 [![npm version](https://img.shields.io/npm/v/gitnexus.svg)](https://www.npmjs.com/package/gitnexus)
 [![License: PolyForm Noncommercial](https://img.shields.io/badge/License-PolyForm%20Noncommercial-blue.svg)](https://polyformproject.org/licenses/noncommercial/1.0.0/)
@@ -45,6 +45,8 @@ To configure MCP for your editor, run `npx gitnexus setup` once — or set it up
 | **Antigravity** (Google) | Yes | Yes    | Yes (AfterTool, [Gemini CLI hooks schema](https://geminicli.com/docs/hooks/reference/))    | **Full**     |
 | **Codex**                | Yes | Yes    | —                                                                                          | MCP + Skills |
 | **OpenCode**             | Yes | Yes    | —                                                                                          | MCP + Skills |
+| **CodeBuddy** (Tencent)  | Yes | Yes    | —                                                                                          | MCP + Skills |
+| **Qoder** (Alibaba)      | 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 + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.
@@ -105,6 +107,36 @@ Add to `~/.config/opencode/config.json`:
 }
 ```
 
+### CodeBuddy
+
+CodeBuddy reads only the **first existing file** in its config priority chain: `~/.codebuddy/.mcp.json` (recommended) → `~/.codebuddy/mcp.json` (deprecated) → `~/.codebuddy.json` (legacy). Edit the first non-empty file that exists — creating a higher-priority file would hide the servers in the ones below it. If none exist, create `~/.codebuddy/.mcp.json`:
+
+```json
+{
+  "mcpServers": {
+    "gitnexus": {
+      "command": "npx",
+      "args": ["-y", "gitnexus@latest", "mcp"]
+    }
+  }
+}
+```
+
+### Qoder
+
+Add to `~/.qoder.json`:
+
+```json
+{
+  "mcpServers": {
+    "gitnexus": {
+      "command": "npx",
+      "args": ["-y", "gitnexus@latest", "mcp"]
+    }
+  }
+}
+```
+
 ## How It Works
 
 GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:
@@ -125,24 +157,24 @@ The result is a **LadybugDB graph database** stored locally in `.gitnexus/` with
 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                |
+| ---------------- | ---------------------------------------------------------------------- |
+| `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 indexes pinned with `gitnexus analyze --branch`; omitting it queries the workspace index, which follows your checked-out working tree. `explain` and `pdg_query` need an index built with `gitnexus analyze --pdg`.
 
@@ -383,13 +415,13 @@ GitNexus uses optional DuckDB extensions for BM25 and vector search. The `gitnex
 
 Configure the behavior with these environment variables:
 
-| Variable                                     | Values                       | Default             | Effect                                                                                                                                                                                                                                                                                   |
-| -------------------------------------------- | ---------------------------- | ------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `GITNEXUS_LBUG_EXTENSION_INSTALL`            | `auto`, `load-only`, `never` | `auto`              | `auto` runs one bounded INSTALL if LOAD fails. `load-only` only uses already-installed extensions (recommended for offline / firewalled environments). `never` skips optional extensions entirely.                                                                                       |
-| `GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS` | positive integer             | `15000`             | Wall-clock budget for the out-of-process `INSTALL` child before it is killed.                                                                                                                                                                                                            |
-| `GITNEXUS_FTS_STEMMER`                       | supported LadybugDB stemmer  | `porter`            | Stemmer used when rebuilding BM25/FTS indexes. Use `none` for CJK-heavy repositories, or a language stemmer such as `german`, `french`, or `spanish` when that better matches repository comments and identifiers. Re-run `gitnexus analyze --repair-fts` after changing it.              |
+| Variable                                     | Values                       | Default             | Effect                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| -------------------------------------------- | ---------------------------- | ------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `GITNEXUS_LBUG_EXTENSION_INSTALL`            | `auto`, `load-only`, `never` | `auto`              | `auto` runs one bounded INSTALL if LOAD fails. `load-only` only uses already-installed extensions (recommended for offline / firewalled environments). `never` skips optional extensions entirely.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| `GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS` | positive integer             | `15000`             | Wall-clock budget for the out-of-process `INSTALL` child before it is killed.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
+| `GITNEXUS_FTS_STEMMER`                       | supported LadybugDB stemmer  | `porter`            | Stemmer used when rebuilding BM25/FTS indexes. Use `none` for CJK-heavy repositories, or a language stemmer such as `german`, `french`, or `spanish` when that better matches repository comments and identifiers. Re-run `gitnexus analyze --repair-fts` after changing it.                                                                                                                                                                                                                                                                                                                                                                                                                            |
 | `GITNEXUS_FTS_CJK_SEGMENTATION`              | `none`, `bigram`             | `none`              | `bigram` inserts overlapping character-bigram boundaries into Chinese/Japanese Han-ideograph spans in `content`/`description` before FTS indexing, so LadybugDB's space-only tokenizer can see sub-phrase word boundaries. Scoped to CJK Unified Ideographs only — Japanese Hiragana/Katakana and Korean Hangul are not currently segmented. Unlike `GITNEXUS_FTS_STEMMER`, this rewrites stored text — enabling it on an already-indexed repo requires a full `gitnexus analyze --force`; neither `--repair-fts` nor a plain incremental `analyze` applies it to previously-indexed files. Set the same value wherever `analyze` and search-serving processes (CLI query, MCP server, web server) run. |
-| `GITNEXUS_WAL_CHECKPOINT_THRESHOLD`          | integer `>= -1`              | `67108864` (64 MiB) | LadybugDB WAL auto-checkpoint threshold during analyze (bytes). Auto-checkpoint remains enabled; `-1` keeps Ladybug's stock ~16 MiB. Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments. |
+| `GITNEXUS_WAL_CHECKPOINT_THRESHOLD`          | integer `>= -1`              | `67108864` (64 MiB) | LadybugDB WAL auto-checkpoint threshold during analyze (bytes). Auto-checkpoint remains enabled; `-1` keeps Ladybug's stock ~16 MiB. Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments.                                                                                                                                                                                                                                                                                                                                                                                                                |
 
 ```bash
 # Offline/airgapped: never reach the network for extensions
@@ -464,9 +496,9 @@ Three env vars expose the pool's resilience layers (respawn budget, cumulative-t
 
 After scope resolution, analyze prunes inert block-local value symbols (a function-local `const`/`let`/`var` that ends up with only its structural `File→DEFINES` edge) to keep the graph focused on cross-symbol relationships. Module/file-scope symbols, class members, and any local with a real edge are always kept.
 
-| Variable                             | Default | Effect                                                                                                  |
-| ------------------------------------ | ------- | ------------------------------------------------------------------------------------------------------- |
-| `GITNEXUS_KEEP_LOCAL_VALUE_SYMBOLS`  | unset   | Set to `1`/`true` to keep inert block-local value symbols instead of pruning them.                      |
+| Variable                            | Default | Effect                                                                             |
+| ----------------------------------- | ------- | ---------------------------------------------------------------------------------- |
+| `GITNEXUS_KEEP_LOCAL_VALUE_SYMBOLS` | unset   | Set to `1`/`true` to keep inert block-local value symbols instead of pruning them. |
 
 Programmatic callers can pass `keepLocalValueSymbols: true` in `PipelineOptions` instead of setting the env var.
 

package/dist/cli/ai-context.d.ts

@@ -2,7 +2,7 @@
  * AI Context Generator
  *
  * Creates AGENTS.md and CLAUDE.md with full inline GitNexus context.
- * AGENTS.md is the standard read by Cursor, Windsurf, OpenCode, Codex, Cline, etc.
+ * AGENTS.md is the standard read by Cursor, Windsurf, OpenCode, Codex, Cline, CodeBuddy, Qoder, etc.
  * CLAUDE.md is for Claude Code which only reads that file.
  */
 import { type GeneratedSkillInfo } from './skill-gen.js';

package/dist/cli/ai-context.js

@@ -2,7 +2,7 @@
  * AI Context Generator
  *
  * Creates AGENTS.md and CLAUDE.md with full inline GitNexus context.
- * AGENTS.md is the standard read by Cursor, Windsurf, OpenCode, Codex, Cline, etc.
+ * AGENTS.md is the standard read by Cursor, Windsurf, OpenCode, Codex, Cline, CodeBuddy, Qoder, etc.
  * CLAUDE.md is for Claude Code which only reads that file.
  */
 import fs from 'fs/promises';

package/dist/cli/editor-targets.d.ts

@@ -15,7 +15,7 @@
  * implementations remain behaviourally symmetrical on top of this shared
  * structure.
  */
-export type EditorId = 'cursor' | 'claude' | 'antigravity' | 'opencode' | 'codex';
+export type EditorId = 'cursor' | 'claude' | 'antigravity' | 'opencode' | 'codebuddy' | 'qoder' | 'codex';
 /** An editor whose MCP config is a JSONC document (server keyed by name). */
 export interface McpJsoncTarget {
     id: EditorId;
@@ -29,6 +29,14 @@ export interface McpJsoncTarget {
      * without either side needing a cast.
      */
     keyPath: string[];
+    /**
+     * Older config locations the editor still reads when `file` is absent
+     * (CodeBuddy reads only the FIRST existing file in its priority chain).
+     * Setup writes into the first existing candidate of [file, ...legacyFiles]
+     * so it never shadows a user's servers living in a deprecated file;
+     * uninstall sweeps all of them.
+     */
+    legacyFiles?: string[];
 }
 /** Codex stores MCP config as a TOML table, not JSONC. */
 export interface CodexMcpTarget {
@@ -58,7 +66,7 @@ export interface HookTarget {
     scriptDir: string;
 }
 export interface EditorTargets {
-    /** JSONC-format MCP entries: Cursor, Claude Code, Antigravity, OpenCode. */
+    /** JSONC-format MCP entries: Cursor, Claude Code, Antigravity, OpenCode, CodeBuddy, Qoder. */
     mcpJsonc: McpJsoncTarget[];
     /** Codex MCP (TOML). */
     codex: CodexMcpTarget;
@@ -80,6 +88,13 @@ export declare function mcpTarget(id: EditorId, home?: string): McpJsoncTarget;
 export declare function skillTarget(id: EditorId, home?: string): SkillTarget;
 /** Look up a single hook target by editor id (throws if unknown). */
 export declare function hookTarget(id: EditorId, home?: string): HookTarget;
+/**
+ * True when err is a Node fs error with code ENOENT (file/dir absent).
+ * Shared by setup and uninstall: both must swallow ONLY absence when reading
+ * editor configs — any other read/stat failure (EACCES, EIO) is surfaced so an
+ * unreadable config is never treated as empty and rewritten gitnexus-only.
+ */
+export declare function isEnoent(err: unknown): boolean;
 /**
  * Detect indentation style from file content so JSONC edits preserve the file's
  * existing formatting. Shared by setup (writes) and uninstall (removes).

package/dist/cli/editor-targets.js

@@ -50,6 +50,26 @@ export function getEditorTargets(home = os.homedir()) {
             // OpenCode nests servers under `mcp`, not `mcpServers`.
             keyPath: ['mcp', 'gitnexus'],
         },
+        {
+            id: 'codebuddy',
+            label: 'CodeBuddy',
+            // Recommended user-scope path per https://www.codebuddy.ai/docs/cli/mcp;
+            // CodeBuddy reads only the first existing file in this priority chain.
+            file: path.join(home, '.codebuddy', '.mcp.json'),
+            legacyFiles: [
+                path.join(home, '.codebuddy', 'mcp.json'), // deprecated
+                path.join(home, '.codebuddy.json'), // legacy
+            ],
+            keyPath: ['mcpServers', 'gitnexus'],
+        },
+        {
+            id: 'qoder',
+            label: 'Qoder',
+            // Qoder's documented user-scope MCP config (https://docs.qoder.com/cli/using-cli);
+            // the IDE manages MCP via its Settings UI with no documented file path.
+            file: path.join(home, '.qoder.json'),
+            keyPath: ['mcpServers', 'gitnexus'],
+        },
     ];
     const codex = {
         id: 'codex',
@@ -66,6 +86,10 @@ export function getEditorTargets(home = os.homedir()) {
         },
         { id: 'cursor', label: 'Cursor', dir: path.join(home, '.cursor', 'skills') },
         { id: 'opencode', label: 'OpenCode', dir: path.join(home, '.config', 'opencode', 'skills') },
+        { id: 'codebuddy', label: 'CodeBuddy', dir: path.join(home, '.codebuddy', 'skills') },
+        // Qoder skills live at ~/.qoder/skills/{name}/SKILL.md
+        // (https://docs.qoder.com/extensions/skills).
+        { id: 'qoder', label: 'Qoder', dir: path.join(home, '.qoder', 'skills') },
         // Codex reads skills from ~/.agents/skills (not ~/.codex).
         { id: 'codex', label: 'Codex', dir: path.join(home, '.agents', 'skills') },
     ];
@@ -110,6 +134,15 @@ export function hookTarget(id, home) {
         throw new Error(`No hook target for editor "${id}"`);
     return t;
 }
+/**
+ * True when err is a Node fs error with code ENOENT (file/dir absent).
+ * Shared by setup and uninstall: both must swallow ONLY absence when reading
+ * editor configs — any other read/stat failure (EACCES, EIO) is surfaced so an
+ * unreadable config is never treated as empty and rewritten gitnexus-only.
+ */
+export function isEnoent(err) {
+    return err?.code === 'ENOENT';
+}
 /**
  * Detect indentation style from file content so JSONC edits preserve the file's
  * existing formatting. Shared by setup (writes) and uninstall (removes).

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

@@ -108,7 +108,7 @@ export declare const en: {
     readonly 'help.command.help.description': "display help for command";
     readonly 'help.option.help': "display help for command";
     readonly 'help.option.version': "output the version number";
-    readonly 'help.command.setup.description': "One-time setup: configure MCP for Cursor, Claude Code, OpenCode, Codex";
+    readonly 'help.command.setup.description': "One-time setup: configure MCP for Cursor, Claude Code, Antigravity, OpenCode, CodeBuddy, Qoder, Codex";
     readonly 'help.command.uninstall.description': "Reverse `setup`: remove GitNexus MCP entries, skills, and hooks from all detected editors";
     readonly 'help.command.analyze.description': "Index a repository (full analysis)";
     readonly 'help.command.index.description': "Register an existing .gitnexus/ folder into the global registry (no re-analysis needed)";

package/dist/cli/i18n/en.js

@@ -108,7 +108,7 @@ export const en = {
     'help.command.help.description': 'display help for command',
     'help.option.help': 'display help for command',
     'help.option.version': 'output the version number',
-    'help.command.setup.description': 'One-time setup: configure MCP for Cursor, Claude Code, OpenCode, Codex',
+    'help.command.setup.description': 'One-time setup: configure MCP for Cursor, Claude Code, Antigravity, OpenCode, CodeBuddy, Qoder, Codex',
     'help.command.uninstall.description': 'Reverse `setup`: remove GitNexus MCP entries, skills, and hooks from all detected editors',
     'help.command.analyze.description': 'Index a repository (full analysis)',
     'help.command.index.description': 'Register an existing .gitnexus/ folder into the global registry (no re-analysis needed)',

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

@@ -109,7 +109,7 @@ export declare const cliResources: {
         readonly 'help.command.help.description': "display help for command";
         readonly 'help.option.help': "display help for command";
         readonly 'help.option.version': "output the version number";
-        readonly 'help.command.setup.description': "One-time setup: configure MCP for Cursor, Claude Code, OpenCode, Codex";
+        readonly 'help.command.setup.description': "One-time setup: configure MCP for Cursor, Claude Code, Antigravity, OpenCode, CodeBuddy, Qoder, Codex";
         readonly 'help.command.uninstall.description': "Reverse `setup`: remove GitNexus MCP entries, skills, and hooks from all detected editors";
         readonly 'help.command.analyze.description': "Index a repository (full analysis)";
         readonly 'help.command.index.description': "Register an existing .gitnexus/ folder into the global registry (no re-analysis needed)";

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

@@ -108,7 +108,7 @@ export const zhCN = {
     'help.command.help.description': '显示命令帮助',
     'help.option.help': '显示命令帮助',
     'help.option.version': '输出版本号',
-    'help.command.setup.description': '一次性设置：为 Cursor、Claude Code、OpenCode、Codex 配置 MCP',
+    'help.command.setup.description': '一次性设置：为 Cursor、Claude Code、Antigravity、OpenCode、CodeBuddy、Qoder、Codex 配置 MCP',
     'help.command.uninstall.description': '撤销 `setup`：从所有检测到的编辑器中移除 GitNexus 的 MCP 配置、技能和钩子',
     'help.command.analyze.description': '索引仓库（完整分析）',
     'help.command.index.description': '将现有 .gitnexus/ 文件夹注册到全局注册表（无需重新分析）',

package/dist/cli/index.js

@@ -17,7 +17,7 @@ function collectCodingAgents(value, previous) {
 program.name('gitnexus').description('GitNexus local CLI and MCP server').version(pkg.version);
 program
     .command('setup')
-    .description('One-time setup: configure MCP for Cursor, Claude Code, Antigravity, OpenCode, Codex')
+    .description('One-time setup: configure MCP for Cursor, Claude Code, Antigravity, OpenCode, CodeBuddy, Qoder, Codex')
     .option('-c, --coding-agent <agents>', 'Configure only these coding agents (comma-separated or repeatable)', collectCodingAgents)
     .action(createLazyAction(() => import('./setup.js'), 'setupCommand'));
 program

package/dist/cli/setup.js

@@ -14,7 +14,7 @@ import { promisify } from 'util';
 import { fileURLToPath } from 'url';
 import { parseTree, modify, applyEdits, parse as parseJsonc } from 'jsonc-parser';
 import { getGlobalDir } from '../storage/repo-manager.js';
-import { getEditorTargets, mcpTarget, skillTarget, hookTarget, detectIndentation, } from './editor-targets.js';
+import { getEditorTargets, mcpTarget, skillTarget, hookTarget, detectIndentation, isEnoent, } from './editor-targets.js';
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
 const execFileAsync = promisify(execFile);
@@ -66,6 +66,8 @@ const CODING_AGENT_IDS = {
     claude: 'claude',
     antigravity: 'antigravity',
     opencode: 'opencode',
+    codebuddy: 'codebuddy',
+    qoder: 'qoder',
     codex: 'codex',
 };
 const SUPPORTED_CODING_AGENTS = Object.values(CODING_AGENT_IDS);
@@ -173,7 +175,13 @@ async function mergeJsoncFile(filePath, keyPath, value) {
     try {
         raw = await fs.readFile(filePath, 'utf-8');
     }
-    catch {
+    catch (err) {
+        // Only an absent file means "start fresh". Any other read failure (EACCES,
+        // EIO, cloud-placeholder faults) must not be treated as empty — the write
+        // below would replace the user's existing config with a gitnexus-only
+        // document and report success. Rethrow into the per-editor catch instead.
+        if (!isEnoent(err))
+            throw err;
         raw = '';
     }
     if (raw.trim().length === 0) {
@@ -207,6 +215,35 @@ async function dirExists(dirPath) {
         return false;
     }
 }
+/**
+ * Detection probe: is there a non-empty regular file at this path?
+ * Swallows ALL errors (like dirExists) — detection gates run outside the
+ * per-editor try blocks, so a rethrowing probe would abort setup for every
+ * remaining editor. Size > 0 keeps detection aligned with the config-chain
+ * resolver: an empty config file is not evidence of an install, and treating
+ * it as one would route the write to a fresh file whose mkdir manufactures
+ * the editor's directory.
+ */
+async function isNonEmptyFile(filePath) {
+    try {
+        const stat = await fs.stat(filePath);
+        return stat.isFile() && stat.size > 0;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Detection probe: does any file in the target's MCP config chain look like an
+ * install trace? Always walks [file, ...legacyFiles] so an editor gaining
+ * legacyFiles later is automatically covered (CodeBuddy and Qoder share this —
+ * a per-editor copy is how the root-config-only detection gap crept in, see
+ * PR #2368 review I4).
+ */
+async function anyChainConfigFile(target) {
+    const hits = await Promise.all([target.file, ...(target.legacyFiles ?? [])].map(isNonEmptyFile));
+    return hits.includes(true);
+}
 // ─── Editor-specific setup ─────────────────────────────────────────
 async function setupCursor(result) {
     const cursorDir = path.join(os.homedir(), '.cursor');
@@ -287,7 +324,12 @@ async function mergeHooksJsonc(filePath, entries) {
     try {
         raw = await fs.readFile(filePath, 'utf-8');
     }
-    catch {
+    catch (err) {
+        // Same contract as mergeJsoncFile: an unreadable (non-ENOENT) settings
+        // file must not be rewritten as hooks-only — that would destroy every
+        // user setting in it. Rethrow into the hook installer's catch.
+        if (!isEnoent(err))
+            throw err;
         raw = '';
     }
     if (raw.trim().length === 0) {
@@ -660,6 +702,118 @@ async function setupOpenCode(result) {
         result.errors.push(`OpenCode: ${err.message}`);
     }
 }
+/**
+ * Resolve which config file in a target's [file, ...legacyFiles] priority
+ * chain setup should write into: the first that exists, else the recommended
+ * `file`. CodeBuddy reads only the first existing file in its chain, so
+ * creating the recommended file above a populated deprecated one would shadow
+ * the user's existing MCP servers.
+ */
+async function resolveMcpConfigFile(target) {
+    for (const candidate of [target.file, ...(target.legacyFiles ?? [])]) {
+        try {
+            const stat = await fs.stat(candidate);
+            // Non-empty regular files only: a 0-byte recommended file must not
+            // shadow a populated deprecated one (mergeJsoncFile treats empty as a
+            // fresh document anyway), and directories are never config candidates.
+            if (stat.isFile() && stat.size > 0)
+                return candidate;
+        }
+        catch (err) {
+            // ENOENT = candidate absent — try the next one. Anything else (EACCES
+            // on the file or a parent) is surfaced: silently skipping could route
+            // the write to a lower-priority file the editor never reads.
+            if (!isEnoent(err))
+                throw err;
+        }
+    }
+    return target.file;
+}
+async function setupCodeBuddy(result) {
+    const codebuddyDir = path.join(os.homedir(), '.codebuddy');
+    const target = mcpTarget('codebuddy');
+    // Installed = the config dir exists OR any registered MCP config file does.
+    // A user whose only trace is a root-level config (e.g. a legacy
+    // ~/.codebuddy.json) still gets configured — uninstall already handles that
+    // shape, so setup skipping it was an asymmetry (PR #2368 review I4).
+    if (!(await dirExists(codebuddyDir)) && !(await anyChainConfigFile(target))) {
+        result.skipped.push('CodeBuddy (not installed)');
+        return;
+    }
+    try {
+        const configFile = await resolveMcpConfigFile(target);
+        const ok = await mergeJsoncFile(configFile, target.keyPath, getMcpEntry());
+        if (ok) {
+            result.configured.push('CodeBuddy');
+        }
+        else {
+            result.errors.push(`CodeBuddy: ${path.basename(configFile)} is corrupt — skipping to preserve existing content`);
+        }
+    }
+    catch (err) {
+        result.errors.push(`CodeBuddy: ${err instanceof Error ? err.message : String(err)}`);
+    }
+}
+async function setupQoder(result) {
+    const qoderDir = path.join(os.homedir(), '.qoder');
+    const target = mcpTarget('qoder');
+    const { file: mcpPath, keyPath } = target;
+    // Same chain-aware detection as CodeBuddy: ~/.qoder.json alone counts.
+    if (!(await dirExists(qoderDir)) && !(await anyChainConfigFile(target))) {
+        result.skipped.push('Qoder (not installed)');
+        return;
+    }
+    try {
+        const ok = await mergeJsoncFile(mcpPath, keyPath, getMcpEntry());
+        if (ok) {
+            result.configured.push('Qoder');
+        }
+        else {
+            result.errors.push('Qoder: .qoder.json is corrupt — skipping to preserve existing content');
+        }
+    }
+    catch (err) {
+        result.errors.push(`Qoder: ${err instanceof Error ? err.message : String(err)}`);
+    }
+}
+/**
+ * Install global CodeBuddy skills to ~/.codebuddy/skills/
+ * (https://www.codebuddy.ai/docs/cli/skills — same SKILL.md layout as Claude Code).
+ */
+async function installCodeBuddySkills(result) {
+    const codebuddyDir = path.join(os.homedir(), '.codebuddy');
+    if (!(await dirExists(codebuddyDir)))
+        return;
+    const skillsDir = skillTarget('codebuddy').dir;
+    try {
+        const installed = await installSkillsTo(skillsDir);
+        if (installed.length > 0) {
+            result.configured.push(`CodeBuddy skills (${installed.length} skills → ~/.codebuddy/skills/)`);
+        }
+    }
+    catch (err) {
+        result.errors.push(`CodeBuddy skills: ${err instanceof Error ? err.message : String(err)}`);
+    }
+}
+/**
+ * Install global Qoder skills to ~/.qoder/skills/
+ * (https://docs.qoder.com/extensions/skills — same SKILL.md layout as Claude Code).
+ */
+async function installQoderSkills(result) {
+    const qoderDir = path.join(os.homedir(), '.qoder');
+    if (!(await dirExists(qoderDir)))
+        return;
+    const skillsDir = skillTarget('qoder').dir;
+    try {
+        const installed = await installSkillsTo(skillsDir);
+        if (installed.length > 0) {
+            result.configured.push(`Qoder skills (${installed.length} skills → ~/.qoder/skills/)`);
+        }
+    }
+    catch (err) {
+        result.errors.push(`Qoder skills: ${err instanceof Error ? err.message : String(err)}`);
+    }
+}
 /**
  * Build a TOML section for Codex MCP config (~/.codex/config.toml).
  */
@@ -677,7 +831,12 @@ async function upsertCodexConfigToml(configPath) {
     try {
         existing = await fs.readFile(configPath, 'utf-8');
     }
-    catch {
+    catch (err) {
+        // TOML variant of the mergeJsoncFile contract: treating a non-ENOENT read
+        // failure as an empty config would rewrite config.toml with only the
+        // gitnexus section. Rethrow into setupCodex's catch.
+        if (!isEnoent(err))
+            throw err;
         existing = '';
     }
     if (existing.includes(`[${getEditorTargets().codex.tomlSection}]`)) {
@@ -885,6 +1044,10 @@ export const setupCommand = async (options) => {
         await setupAntigravity(result);
     if (selected.has('opencode'))
         await setupOpenCode(result);
+    if (selected.has('codebuddy'))
+        await setupCodeBuddy(result);
+    if (selected.has('qoder'))
+        await setupQoder(result);
     if (selected.has('codex'))
         await setupCodex(result);
     // Install global skills for platforms that support them
@@ -900,6 +1063,10 @@ export const setupCommand = async (options) => {
         await installCursorSkills(result);
     if (selected.has('opencode'))
         await installOpenCodeSkills(result);
+    if (selected.has('codebuddy'))
+        await installCodeBuddySkills(result);
+    if (selected.has('qoder'))
+        await installQoderSkills(result);
     if (selected.has('codex'))
         await installCodexSkills(result);
     // Print results

package/dist/cli/uninstall.js

@@ -33,7 +33,7 @@ import { execFile } from 'child_process';
 import { promisify } from 'util';
 import { fileURLToPath } from 'url';
 import { parseTree, modify, applyEdits, findNodeAtLocation, parse as parseJsonc, } from 'jsonc-parser';
-import { getEditorTargets, detectIndentation } from './editor-targets.js';
+import { getEditorTargets, detectIndentation, isEnoent } from './editor-targets.js';
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
 const execFileAsync = promisify(execFile);
@@ -50,7 +50,13 @@ async function removeJsoncKey(filePath, keyPath, dryRun) {
     try {
         raw = await fs.readFile(filePath, 'utf-8');
     }
-    catch {
+    catch (err) {
+        // ENOENT = genuinely not configured. Any other read failure (EACCES,
+        // locks) must not report 'missing' — the file may hold a real gitnexus
+        // entry the dry-run would then deny exists. Rethrow into the caller's
+        // per-file catch.
+        if (!isEnoent(err))
+            throw err;
         return 'missing';
     }
     if (raw.trim().length === 0)
@@ -88,7 +94,12 @@ async function removeHookEntries(filePath, eventNames, commandNeedle, dryRun) {
     try {
         raw = await fs.readFile(filePath, 'utf-8');
     }
-    catch {
+    catch (err) {
+        // Masking a non-ENOENT read failure as 'missing' would also let the
+        // caller delete the hook scriptDir while the unreadable settings file
+        // still references it. Rethrow into the hook uninstaller's catch.
+        if (!isEnoent(err))
+            throw err;
         return { status: 'missing', count: 0 };
     }
     if (raw.trim().length === 0)
@@ -323,8 +334,15 @@ async function uninstallCodex(result, dryRun, configPath, tomlSection) {
     try {
         raw = await fs.readFile(configPath, 'utf-8');
     }
-    catch {
-        result.skipped.push('Codex MCP (not configured)');
+    catch (err) {
+        // Catch locally: this call site has no surrounding try, so a rethrow
+        // would abort the hooks/skills cleanup that runs after Codex.
+        if (isEnoent(err)) {
+            result.skipped.push('Codex MCP (not configured)');
+        }
+        else {
+            result.errors.push(`Codex: ${err instanceof Error ? err.message : String(err)}`);
+        }
         return;
     }
     if (!raw.includes(`[${tomlSection}]`)) {
@@ -369,20 +387,50 @@ export const uninstallCommand = async (options) => {
         console.log('  Dry run — nothing will be changed. Re-run with --force to apply.');
         console.log('');
     }
-    const result = { removed: [], skipped: [], errors: [] };
+    const result = { removed: [], skipped: [], errors: [], corruptLegacy: false };
     // ─── MCP server entries (JSONC editors) ──────────────────────────
+    // Sweep legacyFiles too: setup writes into the first existing file of the
+    // editor's priority chain, so the gitnexus entry may live in a deprecated
+    // location (e.g. CodeBuddy's ~/.codebuddy/mcp.json).
     for (const target of targets.mcpJsonc) {
-        try {
-            const status = await removeJsoncKey(target.file, target.keyPath, dryRun);
-            if (status === 'removed')
-                result.removed.push(`${target.label} MCP server — ${target.keyPath.join('.')} in ${target.file}`);
-            else if (status === 'corrupt')
-                result.errors.push(`${target.label}: ${path.basename(target.file)} is corrupt — left untouched`);
-            else
-                result.skipped.push(`${target.label} MCP (not configured)`);
+        let removedAny = false;
+        let erroredAny = false;
+        let corruptLegacyAny = false;
+        for (const file of [target.file, ...(target.legacyFiles ?? [])]) {
+            try {
+                const status = await removeJsoncKey(file, target.keyPath, dryRun);
+                if (status === 'removed') {
+                    removedAny = true;
+                    result.removed.push(`${target.label} MCP server — ${target.keyPath.join('.')} in ${file}`);
+                }
+                else if (status === 'corrupt') {
+                    if (file === target.file) {
+                        // The primary path is where gitnexus itself writes — corruption
+                        // there is an error worth failing the command over.
+                        erroredAny = true;
+                        result.errors.push(`${target.label}: ${path.basename(file)} is corrupt — left untouched`);
+                    }
+                    else {
+                        // Legacy chain files are vendor locations gitnexus may never have
+                        // touched (e.g. a corrupt ~/.codebuddy.json from an old install).
+                        // Report informationally without failing uninstall. Deliberate
+                        // asymmetry: an UNREADABLE (non-ENOENT) legacy file still errors —
+                        // that's an environmental problem worth surfacing, while corrupt-
+                        // but-readable proves there is no removable gitnexus entry.
+                        corruptLegacyAny = true;
+                        result.corruptLegacy = true;
+                        result.skipped.push(`${target.label} MCP (legacy ${path.basename(file)} is corrupt — left untouched)`);
+                    }
+                }
+            }
+            catch (err) {
+                erroredAny = true;
+                result.errors.push(`${target.label}: ${err instanceof Error ? err.message : String(err)}`);
+            }
         }
-        catch (err) {
-            result.errors.push(`${target.label}: ${err.message}`);
+        // A corrupt legacy file makes "not configured" unknowable — suppress it.
+        if (!removedAny && !erroredAny && !corruptLegacyAny) {
+            result.skipped.push(`${target.label} MCP (not configured)`);
         }
     }
     await uninstallCodex(result, dryRun, targets.codex.configFile, targets.codex.tomlSection);
@@ -425,6 +473,12 @@ export const uninstallCommand = async (options) => {
         for (const name of result.removed)
             console.log(`    - ${name}`);
     }
+    else if (result.errors.length > 0 || result.corruptLegacy) {
+        // Errors (corrupt primary files, unreadable configs) or corrupt legacy
+        // configs make "not configured" unknowable — claiming it right above an
+        // Errors block would be a contradiction users learn to distrust.
+        console.log('  Nothing removed.');
+    }
     else {
         console.log('  Nothing to remove — GitNexus is not configured in any detected editor.');
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.9",
+  "version": "1.6.10-rc.1",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",

package/scripts/cross-platform-tests.ts

@@ -30,6 +30,7 @@ const PLATFORM_LOGIC = [
   'test/unit/setup-jsonc.test.ts',
   'test/unit/setup-codex.test.ts',
   'test/unit/setup-antigravity.test.ts',
+  'test/integration/setup-uninstall-roundtrip.test.ts',
   'test/unit/resolve-invocation.test.ts',
   'test/unit/platform-capabilities.test.ts',
   'test/unit/worker-pool-windows-quarantine.test.ts',