gitnexus 1.6.13-rc.75 → 1.6.13-rc.77

package/README.md

@@ -36,6 +36,8 @@ To configure MCP for your editor, run `npx gitnexus setup` once — or set it up
 
 `gitnexus setup` auto-detects your editors and writes the correct global MCP config. You only need to run it once. To configure only selected integrations, pass `--coding-agent`/`-c` with a comma-separated list or repeat the option, for example `gitnexus setup -c cursor,codex`.
 
+For Claude Code, Cursor, and Codex, setup keeps an existing URL-based `gitnexus` MCP entry and its authentication settings. Skills are still installed; setup installs Claude Code and Codex hooks, while Cursor hooks require [manual installation](../gitnexus-cursor-integration/README.md#hook-install).
+
 ### Editor Support
 
 | Editor                   | MCP | Skills | Hooks (auto-augment)                                                                       | Support      |
@@ -398,7 +400,7 @@ An operation must name a protocol, either through its own `bindings` or through
 
 Like Actuator snapshots, documents are external to git freshness — replacing one moves no commit and dirties no file — so an enabled run always rebuilds, and the first later run without the option rebuilds once to remove document-derived evidence. There is no glob-based auto-discovery, and the option is unsupported with `--watch`.
 
-> **`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.
+> **`gitnexus uninstall`** removes the named GitNexus MCP entries, hooks, and skill directories from detected editors. This includes a URL-based MCP entry you configured yourself, even if setup preserved it. 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.
 
 ## Remote Embeddings
 

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

@@ -42,7 +42,7 @@ export interface McpJsoncTarget {
 export interface CodexMcpTarget {
     id: 'codex';
     label: string;
-    /** Absolute path to ~/.codex/config.toml. */
+    /** Absolute path to CODEX_HOME/config.toml (default ~/.codex/config.toml). */
     configFile: string;
     /** The TOML table header (without brackets) setup writes / uninstall strips. */
     tomlSection: string;

package/dist/cli/editor-targets.js

@@ -24,6 +24,9 @@ import path from 'path';
  * `process.env.HOME` before invoking sees the right locations.
  */
 export function getEditorTargets(home = os.homedir()) {
+    const codexHome = process.env.CODEX_HOME
+        ? path.resolve(process.env.CODEX_HOME)
+        : path.join(home, '.codex');
     const mcpJsonc = [
         {
             id: 'cursor',
@@ -89,7 +92,7 @@ export function getEditorTargets(home = os.homedir()) {
     const codex = {
         id: 'codex',
         label: 'Codex',
-        configFile: path.join(home, '.codex', 'config.toml'),
+        configFile: path.join(codexHome, 'config.toml'),
         tomlSection: 'mcp_servers.gitnexus',
     };
     const skills = [
@@ -126,10 +129,10 @@ export function getEditorTargets(home = os.homedir()) {
             // Codex hooks use Claude Code's exact {hooks: {Event: [...]}} JSON shape
             // and hookSpecificOutput response contract, in a dedicated hooks.json
             // (https://developers.openai.com/codex/hooks).
-            settingsFile: path.join(home, '.codex', 'hooks.json'),
+            settingsFile: path.join(codexHome, 'hooks.json'),
             events: ['PreToolUse', 'PostToolUse'],
             needle: 'gitnexus-hook',
-            scriptDir: path.join(home, '.codex', 'hooks', 'gitnexus'),
+            scriptDir: path.join(codexHome, 'hooks', 'gitnexus'),
         },
         {
             id: 'antigravity',

package/dist/cli/setup.js

@@ -11,7 +11,8 @@ import os from 'os';
 import { execFile, execFileSync } from 'child_process';
 import { promisify } from 'util';
 import { fileURLToPath } from 'url';
-import { parseTree, modify, applyEdits, parse as parseJsonc } from 'jsonc-parser';
+import { parseTree, findNodeAtLocation, getNodeValue, modify, applyEdits, parse as parseJsonc, } from 'jsonc-parser';
+import { parse as parseToml, TomlError } from 'smol-toml';
 import { packageVersion } from '../core/package-version.js';
 import { getGlobalDir } from '../storage/repo-manager.js';
 import { getEditorTargets, mcpTarget, skillTarget, hookTarget, detectIndentation, isEnoent, } from './editor-targets.js';
@@ -172,7 +173,7 @@ function getOpenCodeMcpEntry() {
  * Merge a key/value pair into a JSONC config file, preserving comments and formatting.
  * If the file is genuinely corrupt (not valid JSONC), leaves it untouched.
  */
-async function mergeJsoncFile(filePath, keyPath, value) {
+async function mergeJsoncFile(filePath, keyPath, value, options) {
     let raw;
     try {
         raw = await fs.readFile(filePath, 'utf-8');
@@ -197,6 +198,13 @@ async function mergeJsoncFile(filePath, keyPath, value) {
     const parseErrors = [];
     const tree = parseTree(raw, parseErrors);
     if (tree && tree.type === 'object' && parseErrors.length === 0) {
+        const existingNode = options?.preserveHttpEntry ? findNodeAtLocation(tree, keyPath) : undefined;
+        const existingEntry = existingNode === undefined ? undefined : getNodeValue(existingNode);
+        if (existingEntry !== null &&
+            typeof existingEntry === 'object' &&
+            typeof existingEntry.url === 'string') {
+            return 'preserved-http';
+        }
         const formattingOptions = detectIndentation(raw);
         const edits = modify(raw, keyPath, value, { formattingOptions });
         const result = applyEdits(raw, edits);
@@ -255,8 +263,13 @@ async function setupCursor(result) {
     }
     const { file: mcpPath, keyPath } = mcpTarget('cursor');
     try {
-        const ok = await mergeJsoncFile(mcpPath, keyPath, getMcpEntry());
-        if (ok) {
+        const ok = await mergeJsoncFile(mcpPath, keyPath, getMcpEntry(), {
+            preserveHttpEntry: true,
+        });
+        if (ok === 'preserved-http') {
+            result.configured.push('Cursor (existing HTTP MCP entry kept)');
+        }
+        else if (ok) {
             result.configured.push('Cursor');
         }
         else {
@@ -276,8 +289,13 @@ async function setupClaudeCode(result) {
     // Claude Code stores MCP config in ~/.claude.json
     const { file: mcpPath, keyPath } = mcpTarget('claude');
     try {
-        const ok = await mergeJsoncFile(mcpPath, keyPath, getMcpEntry());
-        if (ok) {
+        const ok = await mergeJsoncFile(mcpPath, keyPath, getMcpEntry(), {
+            preserveHttpEntry: true,
+        });
+        if (ok === 'preserved-http') {
+            result.configured.push('Claude Code (existing HTTP MCP entry kept)');
+        }
+        else if (ok) {
             result.configured.push('Claude Code');
         }
         else {
@@ -907,12 +925,44 @@ async function upsertCodexConfigToml(configPath) {
     await fs.mkdir(path.dirname(configPath), { recursive: true });
     await fs.writeFile(configPath, `${nextContent.trimEnd()}\n`, 'utf-8');
 }
+async function codexHasHttpMcpEntry(configPath) {
+    let raw;
+    try {
+        raw = await fs.readFile(configPath, 'utf-8');
+    }
+    catch (err) {
+        if (isEnoent(err))
+            return false;
+        throw err;
+    }
+    const config = parseToml(raw);
+    const servers = config.mcp_servers;
+    if (servers === null || typeof servers !== 'object')
+        return false;
+    const entry = servers.gitnexus;
+    return (entry !== null &&
+        typeof entry === 'object' &&
+        typeof entry.url === 'string');
+}
 async function setupCodex(result) {
-    const codexDir = path.join(os.homedir(), '.codex');
-    if (!(await dirExists(codexDir))) {
+    const configPath = getEditorTargets().codex.configFile;
+    const codexDir = path.dirname(configPath);
+    if (!process.env.CODEX_HOME && !(await dirExists(codexDir))) {
         result.skipped.push('Codex (not installed)');
         return;
     }
+    try {
+        if (await codexHasHttpMcpEntry(configPath)) {
+            result.configured.push('Codex (existing HTTP MCP entry kept)');
+            return;
+        }
+    }
+    catch (err) {
+        result.errors.push(err instanceof TomlError
+            ? `Codex: invalid config.toml (line ${err.line}, column ${err.column}); MCP entry unchanged`
+            : `Codex: ${err instanceof Error ? err.message : String(err)}`);
+        return;
+    }
     try {
         const entry = getMcpEntry();
         await execFileAsync('codex', ['mcp', 'add', 'gitnexus', '--', entry.command, ...entry.args], {
@@ -926,9 +976,8 @@ async function setupCodex(result) {
         // Fallback for environments where `codex` binary isn't on PATH.
     }
     try {
-        const configPath = getEditorTargets().codex.configFile;
         await upsertCodexConfigToml(configPath);
-        result.configured.push('Codex (MCP added to ~/.codex/config.toml)');
+        result.configured.push('Codex (MCP added to active config.toml)');
     }
     catch (err) {
         result.errors.push(`Codex: ${err.message}`);
@@ -1110,7 +1159,7 @@ async function installOpenCodeSkills(result) {
  * Install global Codex skills to ~/.agents/skills/gitnexus/
  */
 async function installCodexSkills(result) {
-    const codexDir = path.join(os.homedir(), '.codex');
+    const codexDir = path.dirname(getEditorTargets().codex.configFile);
     if (!(await dirExists(codexDir)))
         return;
     const skillsDir = skillTarget('codex').dir;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.13-rc.75",
+  "version": "1.6.13-rc.77",
   "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",
@@ -52,6 +52,7 @@
     "serve": "tsx src/cli/index.ts serve",
     "dev": "tsx watch src/cli/index.ts",
     "test": "vitest run",
+    "typecheck:tests": "tsc --noEmit -p tsconfig.test.json",
     "test:unit": "vitest run test/unit",
     "pretest:integration": "node scripts/build.js",
     "test:integration": "vitest run test/integration",