gitnexus 1.6.4-rc.60 → 1.6.4-rc.62

package/dist/core/run-analyze.js

@@ -14,7 +14,7 @@ import { runPipelineFromRepo } from './ingestion/pipeline.js';
 import { initLbug, loadGraphToLbug, getLbugStats, executeQuery, executeWithReusedStatement, closeLbug, loadCachedEmbeddings, } from './lbug/lbug-adapter.js';
 import { createSearchFTSIndexes } from './search/fts-indexes.js';
 import { getStoragePaths, saveMeta, loadMeta, ensureGitNexusIgnored, registerRepo, cleanupOldKuzuFiles, } from '../storage/repo-manager.js';
-import { getCurrentCommit, getRemoteUrl, hasGitDir, getInferredRepoName } from '../storage/git.js';
+import { getCurrentCommit, getRemoteUrl, hasGitDir, getInferredRepoName, resolveRepoIdentityRoot, } from '../storage/git.js';
 import { generateAIContextFiles } from '../cli/ai-context.js';
 import { EMBEDDING_TABLE_NAME } from './lbug/schema.js';
 import { STALE_HASH_SENTINEL } from './lbug/schema.js';
@@ -71,7 +71,12 @@ export async function runFullAnalysis(repoPath, options, callbacks) {
         if (currentCommit !== '') {
             await ensureGitNexusIgnored(repoPath);
             return {
-                repoName: options.registryName ?? getInferredRepoName(repoPath) ?? path.basename(repoPath),
+                // `resolveRepoIdentityRoot` collapses worktree roots to the
+                // canonical repo basename (#1259) but leaves arbitrary subdirs
+                // and `--skip-git` paths unchanged (#1232/#1233 intent preserved).
+                repoName: options.registryName ??
+                    getInferredRepoName(repoPath) ??
+                    path.basename(resolveRepoIdentityRoot(repoPath)),
                 repoPath,
                 stats: existingMeta.stats ?? {},
                 alreadyUpToDate: true,
@@ -219,7 +224,18 @@ export async function runFullAnalysis(repoPath, options, callbacks) {
                 }
             }
             const { readServerMapping } = await import('./embeddings/server-mapping.js');
-            const projectName = path.basename(repoPath);
+            // Mirror the registry's name-resolution chain so the server-mapping
+            // lookup key stays aligned with the final registry name (#1259):
+            //   --name → remote-derived → canonical-root basename
+            // (preserved-alias is intentionally NOT consulted here — server
+            // mappings are addressed by the operationally-meaningful name the
+            // user configures, not by a sticky registry-only alias they may not
+            // know about. The previous canonical-only logic ignored both --name
+            // and remote-derived names, silently breaking server-mapping for
+            // anyone with a `--name` alias or remote-named repo.)
+            const projectName = options.registryName ??
+                getInferredRepoName(repoPath) ??
+                path.basename(resolveRepoIdentityRoot(repoPath));
             const serverName = await readServerMapping(projectName);
             const embeddingResult = await runEmbeddingPipeline(executeQuery, executeWithReusedStatement, (p) => {
                 const scaled = 90 + Math.round((p.percent / 100) * 8);

package/dist/server/api.js

@@ -25,7 +25,7 @@ import { mountMCPEndpoints } from './mcp-http.js';
 import { fork } from 'child_process';
 import { fileURLToPath, pathToFileURL } from 'url';
 import { JobManager } from './analyze-job.js';
-import { assertString, escapeRegExp, BadRequestError } from './validation.js';
+import { assertString, escapeRegExp, BadRequestError, createRouteLimiter } from './validation.js';
 import { extractRepoName, getCloneDir, cloneOrPull } from './git-clone.js';
 const _require = createRequire(import.meta.url);
 const pkg = _require('../../package.json');
@@ -186,7 +186,19 @@ export const registerWebUI = (app, staticDir) => {
         // The regex excludes /api paths AND paths with file extensions (.js, .css, etc.)
         // so missing assets get real 404s instead of the SPA HTML.
         // Adding routes below this will be unreachable for non-API, non-asset paths.
-        app.get(SPA_FALLBACK_REGEX, (_req, res) => {
+        // Rate-limited (CodeQL js/missing-rate-limiting): the SPA fallback
+        // serves a constant index.html, but the FS access from a route handler
+        // is enough to trip the analyzer. The limit is generous (300 rpm/IP =
+        // 5 req/s sustained) so that multi-tab browser navigation, prefetch,
+        // and service-worker revalidation do not produce 429s for legitimate
+        // SPA users. At this rate, real browser navigation is extremely
+        // unlikely to hit the limit in practice, so the cosmetic issue of
+        // JSON-on-429 to a browser is a low-likelihood path. Content
+        // negotiation on the 429 (returning the SPA shell to HTML clients
+        // instead of `{ error: '...' }`) would require swapping
+        // express-rate-limit's `message` for a `handler` function and is
+        // deferred to keep this PR focused on closing the CodeQL alert.
+        app.get(SPA_FALLBACK_REGEX, createRouteLimiter({ limit: 300 }), (_req, res) => {
             res.sendFile(path.join(staticDir, 'index.html'));
         });
     }
@@ -524,6 +536,26 @@ export const handleFileRequest = async (req, res, repoPath) => {
 export const createServer = async (port, host = '127.0.0.1') => {
     const app = express();
     app.disable('x-powered-by');
+    // Trust X-Forwarded-* headers only when the connection comes from the
+    // local loopback or RFC1918 private/link-local addresses — exactly the
+    // origins the CORS allowlist accepts. Without this, every request behind
+    // any reverse proxy / Docker bridge counts as the same `req.ip` and a
+    // single user can trip the per-IP rate limiter for everyone.
+    //
+    // SCOPE: this setting is process-wide. Every middleware and route in this
+    // Express app sees req.ip resolved from X-Forwarded-For when the upstream
+    // hop is in the trusted set above — not just the rate-limited routes.
+    // Future IP-based middleware (audit logging, IP-bound authz) inherits this
+    // behavior.
+    //
+    // CLOUD-DEPLOY CAVEAT: a public cloud LB (AWS ALB, Cloudflare, Fly.io
+    // edge, CGNAT 100.64/10) is NOT in the trusted set. In those topologies
+    // req.ip will collapse to the LB hop IP for every request and the per-IP
+    // rate limiter degrades to per-server. Add an explicit env-var override
+    // and document the cloud-deploy story before binding to a non-loopback
+    // host in those topologies (tracked as a follow-up; not blocking for the
+    // local-bound default).
+    app.set('trust proxy', 'loopback, linklocal, uniquelocal');
     // CORS: allow localhost, private/LAN networks, and the deployed site.
     // Non-browser requests (curl, server-to-server) have no origin and are allowed.
     // Disallowed origins get the response without Access-Control-Allow-Origin,
@@ -716,7 +748,10 @@ export const createServer = async (port, host = '127.0.0.1') => {
         }
     });
     // Delete a repo — removes index, clone dir (if any), and unregisters it
-    app.delete('/api/repo', async (req, res) => {
+    // Rate-limited (CodeQL js/missing-rate-limiting): destructive operation
+    // doing fs.rm of clone + storage dirs. Default 60 rpm/IP is generous for
+    // delete; tighten if abuse is observed.
+    app.delete('/api/repo', createRouteLimiter(), async (req, res) => {
         try {
             const repoName = requestedRepo(req);
             if (!repoName) {
@@ -997,7 +1032,8 @@ export const createServer = async (port, host = '127.0.0.1') => {
         }
     });
     // Read file — with path traversal guard
-    app.get('/api/file', async (req, res) => {
+    // Rate-limited (CodeQL js/missing-rate-limiting): per-request fs.readFile.
+    app.get('/api/file', createRouteLimiter(), async (req, res) => {
         const entry = await resolveRepo(requestedRepo(req));
         if (!entry) {
             res.status(404).json({ error: 'Repository not found' });
@@ -1007,7 +1043,10 @@ export const createServer = async (port, host = '127.0.0.1') => {
     });
     // Grep — regex search across file contents in the indexed repo
     // Uses filesystem-based search for memory efficiency (never loads all files into memory)
-    app.get('/api/grep', async (req, res) => {
+    // Rate-limited (CodeQL js/missing-rate-limiting): scans every file in
+    // the indexed repo per request — heaviest I/O endpoint. Same default 60
+    // rpm/IP for now; consider tightening if real-world load shows abuse.
+    app.get('/api/grep', createRouteLimiter(), async (req, res) => {
         try {
             const entry = await resolveRepo(requestedRepo(req));
             if (!entry) {

package/dist/server/validation.d.ts

@@ -17,6 +17,7 @@
  * Helpers added in later units (U3 git-clone hardening, U4 rate-limiting) live
  * in this module too but are introduced with the dependency they require.
  */
+import { type RateLimitRequestHandler } from 'express-rate-limit';
 /**
  * Thrown by validation helpers when user input is rejected.
  * Routes catch via existing try/catch and convert with err.status / err.message.
@@ -58,3 +59,37 @@ export declare function assertSafePath(rawPath: string, root: string): string;
  * and any future endpoint that constructs a regex from caller input.
  */
 export declare function escapeRegExp(input: string): string;
+/**
+ * Project-specific subset of express-rate-limit options that callers may
+ * override. Intentionally narrow — `Partial<RateLimitOptions>` would let a
+ * caller pass `{ skip: () => true }` and silently disable limiting on a
+ * route. The two knobs below are sufficient for tests and any future
+ * legitimate per-route tuning.
+ */
+export interface RouteLimiterOverrides {
+    windowMs?: number;
+    /** Canonical name in express-rate-limit v8+. `max` is the deprecated alias. */
+    limit?: number;
+}
+/**
+ * Build a per-route rate-limit middleware with project-uniform defaults.
+ *
+ * Each call returns a NEW limiter instance — independent counters per route,
+ * so /api/file traffic doesn't push /api/grep into 429.
+ *
+ * Defaults:
+ *   - 60 requests per IP per minute
+ *   - draft-7 RateLimit-* response headers (no legacy X-RateLimit-* headers)
+ *   - 429 with a JSON body matching the project's `{ error: '...' }` shape
+ *   - passOnStoreError: store failures let the request through rather than
+ *     producing an HTML 500 from Express's default error handler
+ *   - keyGenerator: req.ip with a socket.remoteAddress fallback so abruptly
+ *     closed connections do not trigger ERR_ERL_UNDEFINED_IP_ADDRESS
+ *     (which would 500 the request via Express's default error handler).
+ *     Caller must wire `app.set('trust proxy', ...)` correctly — see
+ *     createServer in api.ts.
+ *
+ * Tests pass `{ windowMs: 100, limit: 3 }` to keep limiter tests fast and
+ * deterministic.
+ */
+export declare function createRouteLimiter(opts?: RouteLimiterOverrides): RateLimitRequestHandler;

package/dist/server/validation.js

@@ -18,6 +18,7 @@
  * in this module too but are introduced with the dependency they require.
  */
 import path from 'node:path';
+import rateLimit from 'express-rate-limit';
 /**
  * Thrown by validation helpers when user input is rejected.
  * Routes catch via existing try/catch and convert with err.status / err.message.
@@ -89,3 +90,47 @@ export function assertSafePath(rawPath, root) {
 export function escapeRegExp(input) {
     return input.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
 }
+/**
+ * Default rate-limit policy for FS-touching API routes (CodeQL
+ * js/missing-rate-limiting). Tuned for the local-bound HTTP server's expected
+ * traffic — interactive web UI use stays well under the limit; abusive loops
+ * trip 429.
+ *
+ * Module-internal — not exported. Tests assert the observable behavior
+ * (61st request returns 429), not the literal value, so callers don't grow
+ * a coupling on this number.
+ */
+const DEFAULT_RATE_LIMIT_RPM = 60;
+/**
+ * Build a per-route rate-limit middleware with project-uniform defaults.
+ *
+ * Each call returns a NEW limiter instance — independent counters per route,
+ * so /api/file traffic doesn't push /api/grep into 429.
+ *
+ * Defaults:
+ *   - 60 requests per IP per minute
+ *   - draft-7 RateLimit-* response headers (no legacy X-RateLimit-* headers)
+ *   - 429 with a JSON body matching the project's `{ error: '...' }` shape
+ *   - passOnStoreError: store failures let the request through rather than
+ *     producing an HTML 500 from Express's default error handler
+ *   - keyGenerator: req.ip with a socket.remoteAddress fallback so abruptly
+ *     closed connections do not trigger ERR_ERL_UNDEFINED_IP_ADDRESS
+ *     (which would 500 the request via Express's default error handler).
+ *     Caller must wire `app.set('trust proxy', ...)` correctly — see
+ *     createServer in api.ts.
+ *
+ * Tests pass `{ windowMs: 100, limit: 3 }` to keep limiter tests fast and
+ * deterministic.
+ */
+export function createRouteLimiter(opts) {
+    return rateLimit({
+        windowMs: 60 * 1000,
+        limit: DEFAULT_RATE_LIMIT_RPM,
+        standardHeaders: 'draft-7',
+        legacyHeaders: false,
+        passOnStoreError: true,
+        keyGenerator: (req) => req.ip ?? req.socket?.remoteAddress ?? 'unknown',
+        message: { error: 'Too many requests, please try again later.' },
+        ...opts,
+    });
+}

package/dist/storage/git.d.ts

@@ -28,6 +28,56 @@ export declare const getRemoteUrl: (repoPath: string) => string | undefined;
  * Find the git repository root from any path inside the repo
  */
 export declare const getGitRoot: (fromPath: string) => string | null;
+/**
+ * Get the *canonical* repository root, dereferencing git worktrees.
+ *
+ * Unlike `getGitRoot` (which uses `git rev-parse --show-toplevel` and
+ * returns the WORKTREE's root when called inside a linked worktree),
+ * this uses `git rev-parse --git-common-dir` — the shared `.git`
+ * directory, identical for the main checkout and every linked
+ * worktree — and returns its parent.
+ *
+ * Why it matters (#1259): when `gitnexus analyze` runs inside a
+ * worktree (e.g. `/repo/wt-feature/`), deriving `repoName` from
+ * `path.basename(getGitRoot(cwd))` registers the project under the
+ * worktree's directory slug (`wt-feature`) instead of the canonical
+ * repo's basename (`repo`). Each worktree then re-registers as a
+ * "different" project, AGENTS.md is rewritten with the wrong MCP URI,
+ * and Claude-Code-style worktree workflows silently accumulate
+ * duplicate registry entries.
+ *
+ * Returns `null` when the path is not inside a git repository or
+ * `git` is not available, so callers can chain safely:
+ * `getCanonicalRepoRoot(p) ?? getGitRoot(p) ?? p`.
+ *
+ * `--path-format=absolute` is required because `--git-common-dir`
+ * returns a path *relative to cwd* by default (e.g. `../.git` when
+ * called from a worktree), which would resolve to the wrong absolute
+ * path if the caller later resolved it from a different directory.
+ */
+export declare const getCanonicalRepoRoot: (fromPath: string) => string | null;
+/**
+ * Resolve `fromPath` to the directory whose basename should drive the
+ * registry name (#1259) — the *identity root*. Three outcomes:
+ *
+ *   1. `fromPath` IS the canonical checkout root → returns it unchanged.
+ *   2. `fromPath` is a linked-worktree root (has its own `.git` entry, but
+ *      `git rev-parse --git-common-dir` points at a different `.git`) →
+ *      returns the canonical repo root.
+ *   3. `fromPath` is anything else — an arbitrary subdir under a git repo,
+ *      a non-git folder, a `--skip-git` subdir of an unrelated parent
+ *      checkout — returns `fromPath` unchanged.
+ *
+ * Why not just use `getCanonicalRepoRoot` directly? Because `git rev-parse
+ * --git-common-dir` resolves the same canonical root for ANY path inside
+ * a git repo, including unrelated subdirs. Using it for registry-name
+ * derivation would silently re-key a `--skip-git` subdir analyze under
+ * the parent git's basename, defeating the user's `--skip-git` intent
+ * (regressing the #1232/#1233 fix). The "is this path a tree root"
+ * gate confines the canonical-root collapse to exactly the cases where
+ * #1259 matters: main checkouts and linked worktrees.
+ */
+export declare const resolveRepoIdentityRoot: (fromPath: string) => string;
 /**
  * Find a git root by checking only `.git` entries on the ancestor chain.
  *

package/dist/storage/git.js

@@ -91,6 +91,83 @@ export const getGitRoot = (fromPath) => {
         return null;
     }
 };
+/**
+ * Get the *canonical* repository root, dereferencing git worktrees.
+ *
+ * Unlike `getGitRoot` (which uses `git rev-parse --show-toplevel` and
+ * returns the WORKTREE's root when called inside a linked worktree),
+ * this uses `git rev-parse --git-common-dir` — the shared `.git`
+ * directory, identical for the main checkout and every linked
+ * worktree — and returns its parent.
+ *
+ * Why it matters (#1259): when `gitnexus analyze` runs inside a
+ * worktree (e.g. `/repo/wt-feature/`), deriving `repoName` from
+ * `path.basename(getGitRoot(cwd))` registers the project under the
+ * worktree's directory slug (`wt-feature`) instead of the canonical
+ * repo's basename (`repo`). Each worktree then re-registers as a
+ * "different" project, AGENTS.md is rewritten with the wrong MCP URI,
+ * and Claude-Code-style worktree workflows silently accumulate
+ * duplicate registry entries.
+ *
+ * Returns `null` when the path is not inside a git repository or
+ * `git` is not available, so callers can chain safely:
+ * `getCanonicalRepoRoot(p) ?? getGitRoot(p) ?? p`.
+ *
+ * `--path-format=absolute` is required because `--git-common-dir`
+ * returns a path *relative to cwd* by default (e.g. `../.git` when
+ * called from a worktree), which would resolve to the wrong absolute
+ * path if the caller later resolved it from a different directory.
+ */
+export const getCanonicalRepoRoot = (fromPath) => {
+    try {
+        const commonDir = execSync('git rev-parse --path-format=absolute --git-common-dir', {
+            cwd: fromPath,
+            stdio: ['ignore', 'pipe', 'ignore'],
+        })
+            .toString()
+            .trim();
+        if (!commonDir)
+            return null;
+        // Common dir is `<repo>/.git` for both the main checkout and all
+        // linked worktrees. Its parent is the canonical repo root.
+        return path.dirname(path.resolve(commonDir));
+    }
+    catch {
+        return null;
+    }
+};
+/**
+ * Resolve `fromPath` to the directory whose basename should drive the
+ * registry name (#1259) — the *identity root*. Three outcomes:
+ *
+ *   1. `fromPath` IS the canonical checkout root → returns it unchanged.
+ *   2. `fromPath` is a linked-worktree root (has its own `.git` entry, but
+ *      `git rev-parse --git-common-dir` points at a different `.git`) →
+ *      returns the canonical repo root.
+ *   3. `fromPath` is anything else — an arbitrary subdir under a git repo,
+ *      a non-git folder, a `--skip-git` subdir of an unrelated parent
+ *      checkout — returns `fromPath` unchanged.
+ *
+ * Why not just use `getCanonicalRepoRoot` directly? Because `git rev-parse
+ * --git-common-dir` resolves the same canonical root for ANY path inside
+ * a git repo, including unrelated subdirs. Using it for registry-name
+ * derivation would silently re-key a `--skip-git` subdir analyze under
+ * the parent git's basename, defeating the user's `--skip-git` intent
+ * (regressing the #1232/#1233 fix). The "is this path a tree root"
+ * gate confines the canonical-root collapse to exactly the cases where
+ * #1259 matters: main checkouts and linked worktrees.
+ */
+export const resolveRepoIdentityRoot = (fromPath) => {
+    const resolved = path.resolve(fromPath);
+    const canonical = getCanonicalRepoRoot(resolved);
+    if (!canonical)
+        return resolved; // non-git → use as-is
+    if (canonical === resolved)
+        return canonical; // canonical checkout
+    if (hasGitDir(resolved))
+        return canonical; // linked worktree (has .git file)
+    return resolved; // arbitrary subdir under a git repo → preserve as-is
+};
 /**
  * Find a git root by checking only `.git` entries on the ancestor chain.
  *

package/dist/storage/repo-manager.js

@@ -9,7 +9,7 @@ import fs from 'fs/promises';
 import { realpathSync } from 'fs';
 import path from 'path';
 import os from 'os';
-import { getInferredRepoName } from './git.js';
+import { getInferredRepoName, resolveRepoIdentityRoot } from './git.js';
 /**
  * Normalise a repo path for registry comparison across platforms
  * (#664 review feedback from @evander-wang).
@@ -296,6 +296,18 @@ const hasCustomAlias = (entry, inferredName) => {
     const resolved = path.resolve(entry.path);
     if (entry.name === path.basename(resolved))
         return false;
+    // Canonical-root-derived names are not user aliases either (#1259):
+    // a worktree registered under the canonical repo's basename
+    // (e.g. `{name: 'repo', path: '/repo/wt-feature'}`) must re-register
+    // cleanly without firing the duplicate-name collision guard. Without
+    // this check `entry.name = 'repo'` !== `path.basename('/repo/wt-feature') = 'wt-feature'`,
+    // so the prior check returns true → `isPreservedAlias = true` → guard
+    // throws `RegistryNameCollisionError` against the also-registered
+    // canonical checkout entry. The Claude-Code per-task worktree workflow
+    // — analyze canonical, then analyze worktree, then re-analyze worktree
+    // — would break on the third call.
+    if (entry.name === path.basename(resolveRepoIdentityRoot(resolved)))
+        return false;
     if (inferredName && entry.name === inferredName)
         return false;
     return true;
@@ -372,7 +384,13 @@ export const registerRepo = async (repoPath, meta, opts) => {
             isPreservedAlias = true;
         }
         else {
-            name = inferred ?? path.basename(resolved);
+            // Canonical-root fallback: when `resolved` is a worktree root,
+            // derive the registry name from the canonical repo's basename, not
+            // the worktree slug — see #1259. `resolveRepoIdentityRoot` confines
+            // the collapse to canonical checkouts and linked worktree roots only,
+            // so `--skip-git` subdirs of unrelated parent git repos keep using
+            // their own basename (preserves the #1232/#1233 fix's intent).
+            name = inferred ?? path.basename(resolveRepoIdentityRoot(resolved));
         }
     }
     // Duplicate-name guard: only fire when the user EXPLICITLY asked for

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.4-rc.60",
+  "version": "1.6.4-rc.62",
   "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",
@@ -60,6 +60,7 @@
     "commander": "^14.0.3",
     "cors": "^2.8.5",
     "express": "^4.19.2",
+    "express-rate-limit": "^8.4.1",
     "glob": "^13.0.6",
     "graphology": "^0.26.0",
     "graphology-indices": "^0.17.0",

package/web/assets/{agent-DSzTymIk.js → agent-C9r8n_cf.js}

@@ -1,4 +1,4 @@
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package/web/assets/architecture-YZFGNWBL-S5CXDPWN-CL__bSw6.js

@@ -0,0 +1 @@
+import"./index-BcZj1uBK.js";import"./chunk-H3VCZNTA-S6JCDFX6.js";import"./chunk-FXACKDTF-DDbh9iQA.js";import{n as e}from"./chunk-XGPFEOL4-C8lmtgql.js";export{e as createArchitectureServices};