codetree-claude 1.5.0 → 1.5.1

package/README.md

@@ -1,49 +1,65 @@
-# CodeTree
+# CodeTree (`codetree-claude`)
 
-**Reduce Claude Code token usage by 60-70%** by caching codebase reads in a persistent index.
+**Persistent codebase index + MCP tools for AI coding assistants** — cut redundant **Read / Grep / Glob** token use by routing work through a **cached SQLite index** and **symbol-aware** APIs.
 
-> **v1.5** — Now with real-time cache integrity, Windows `\r\n` support, git branch awareness, and full session tracking across all tools.
+Works with **Anthropic Claude Code**, **Cursor**, **OpenAI Codex**, **Google Antigravity / Gemini-oriented flows**, and any **MCP-compatible** editor or CLI — not only Claude. One **`codetree init`** wires the **same MCP server** into each tool’s config format your repo uses.
 
-## The Problem
+> **v1.5** — Real-time cache integrity, Windows `\r\n` support, git branch awareness, session tracking, and **multi-editor setup** (Claude + Cursor + Codex + Antigravity) from a single CLI.
 
-When your team uses Claude Code, **~70% of tokens** go to re-reading the same files across conversations — Glob, Grep, and Read calls that scan the same codebase over and over.
+## Supported AI coding tools (multi-IDE)
 
-## The Solution
+| Product | What CodeTree configures | How you save tokens |
+|--------|---------------------------|---------------------|
+| **Claude Code** (Anthropic) | Root `.mcp.json`, `.claude/settings.json` **hooks**, `CLAUDE.md`, `.claude/rules` | **Hooks** can redirect native Read/Grep/Glob/Edit/Write to `codetree_*` when safe |
+| **Cursor** | `.cursor/mcp.json`, `.cursor/rules/codetree.mdc` | MCP tools + rules steer the agent toward CodeTree |
+| **OpenAI Codex** | `.codex/config.toml` `[mcp_servers.codetree]`, `AGENTS.md` | MCP tools + agent instructions (merge-safe TOML) |
+| **Google Antigravity** | `.antigravity/mcp.json`, **`AGENTS.md`**, **`GEMINI.md`** | MCP + portable docs (Gemini / Antigravity steering) |
+| **VS Code** | Marketplace extension **“CodeTree — Cache for Claude Code”** | Helps activate / discover setup in the editor |
+| **Any MCP host** | Same `node …/mcp-server.js` entry as above | Register **Model Context Protocol** server manually if your stack reads custom paths |
 
-CodeTree indexes your codebase into a persistent SQLite database and intercepts Claude Code's file operations. When a file hasn't changed since the last read, Claude uses the cached version. Every read is validated against disk — you'll never get stale content, even after git branch switches, VS Code edits, or external file changes.
+**Important:** **Token-saving hooks** (PreToolUse interception) are a **Claude Code** feature. **Cursor, Codex, and Antigravity** use **MCP + project rules/docs** — the model is steered to call `codetree_read`, `codetree_search`, etc., instead of only native tools. The **indexer, cache, and MCP tool surface** are shared for everyone.
 
-### How it works
+**Search keywords (ecosystem):** MCP server, Model Context Protocol, AI coding agent, AI pair programmer, codebase RAG alternative, repo indexer, Claude Code cache, Cursor MCP, OpenAI Codex MCP, Google Antigravity MCP, Gemini coding, VS Code extension, developer productivity, LLM tools, context window optimization.
+
+## The problem
+
+Teams using **AI coding assistants** spend a large share of **context / tokens** on **re-reading** the same files — repeated Glob, Grep, and Read calls across chats and tasks.
+
+## The solution
+
+CodeTree **indexes** the repo into a **local SQLite** database and exposes **MCP tools** (`codetree_read`, `codetree_search`, `codetree_structure`, …). **Claude Code** can additionally **intercept** native tool calls via **hooks** and redirect when the index can answer. **Other IDEs** rely on **MCP + rules** so agents prefer CodeTree. Reads stay **mtime-validated** so content is not silently stale after edits, branch switches, or merges.
+
+### How it works (Claude Code with hooks)
 
 ```
-Developer asks Claude to work on a feature
+Developer asks the assistant to work on a feature
     │
-    ├── Claude calls Read("src/api/auth.ts")
-    │     └── Hook intercepts → file cached? YES → redirect to codetree_read
-    │           └── Returns cached content + symbols metadata
+    ├── Read("src/api/auth.ts")
+    │     └── Hook (Claude Code) → cached? YES → codetree_read
+    │           └── Cached content + symbol metadata
     │
-    ├── Claude calls Grep("handleAuth")  
-    │     └── Hook intercepts → symbol indexed? YES → redirect to codetree_search
-    │           └── Returns indexed symbol locations instantly
+    ├── Grep("handleAuth")
+    │     └── Hook → indexed? YES → codetree_search
     │
-    └── Claude calls Glob("src/**/*.ts")
-          └── Hook intercepts → tree indexed? YES → redirect to codetree_structure
-                └── Returns file tree from index
+    └── Glob("src/**/*.ts")
+          └── Hook → tree indexed? YES → codetree_structure
 ```
 
+For **Cursor / Codex / Antigravity**, the same tools are available over **MCP**; steering is via **rules** and **`AGENTS.md` / `GEMINI.md`** instead of hooks.
+
 ## Install
 
-### Option 1: npm package (any project)
+### Option 1: npm package (global — any project)
 
 ```bash
 npm install -g codetree-claude
 
-# In your project root:
 codetree init
 ```
 
-### Option 2: VS Code Extension
+### Option 2: VS Code extension
 
-Install "CodeTree — Cache for Claude Code" from the VS Code marketplace. It auto-activates when you open a project.
+Install **“CodeTree — Cache for Claude Code”** from the VS Code Marketplace. It helps you use CodeTree when the project is open in VS Code.
 
 ### Option 3: Per-project dev dependency
 
@@ -52,29 +68,60 @@ npm install --save-dev codetree-claude
 npx codetree init
 ```
 
-## What gets created
+## What `codetree init` creates (multi-tool)
+
+`codetree init` configures **Claude Code** (hooks + root `.mcp.json`) and, in the same run, adds **Cursor**, **Antigravity**, **OpenAI Codex**, and portable agent docs — **without changing** the established Claude behavior.
 
 ```
 your-project/
-  .codetreerc.json          # Config (ignore patterns, cache size, etc.)
-  .claude/settings.json     # PreToolUse hook registration  
-  .mcp.json                 # MCP server registration
-  .codetree/                # Index database (gitignored)
+  .codetreerc.json              # Config (ignore patterns, cache size, …)
+  .claude/settings.json         # Hooks (Claude Code): PreToolUse, PostToolUse, SessionStart, compaction, …
+  .mcp.json                     # MCP — Claude Code convention
+  .cursor/mcp.json              # MCP — Cursor IDE
+  .cursor/rules/codetree.mdc    # Cursor: prefer CodeTree MCP tools
+  .antigravity/mcp.json         # MCP — Google Antigravity (project-level)
+  .codex/config.toml            # MCP — OpenAI Codex (trusted projects; merged safely)
+  CLAUDE.md                     # Claude Code instructions
+  AGENTS.md                     # Portable (Cursor, Codex, Antigravity, …)
+  GEMINI.md                     # Short pointer for Antigravity / Gemini
+  .codetree/                    # Index database (gitignored)
     index.db
     ipc.port
     stats.json
 ```
 
-## CLI Commands
+Commit `.codetreerc.json`, `.mcp.json`, `.cursor/`, `.antigravity/`, `.codex/`, `AGENTS.md`, and `GEMINI.md` as your team prefers; keep `.codetree/` gitignored.
+
+### Where rules & config live per tool
+
+| Tool | MCP config | Instructions / rules |
+|------|------------|----------------------|
+| **Claude Code** | Root `.mcp.json` | Hooks in `.claude/settings.json` + `CLAUDE.md` + `.claude/rules/codetree.md` |
+| **Cursor** | `.cursor/mcp.json` | `.cursor/rules/codetree.mdc` (alwaysApply) |
+| **OpenAI Codex** | `.codex/config.toml` | `AGENTS.md` (and Codex trust settings) |
+| **Google Antigravity** | `.antigravity/mcp.json` | **`AGENTS.md`** (full table) + **`GEMINI.md`** (short Gemini pointer). Antigravity loads these; there is no extra Antigravity-only rules file in this package. |
+
+### Bundled templates (npm package)
+
+Instruction text ships under **`templates/`** in the published package (see `templates/README.md`). `codetree init` copies from those files into your repo. Customize locally; re-run `codetree init` to refresh from the bundled templates.
+
+## CLI commands
 
 ```bash
-codetree init       # Set up CodeTree in current project
+codetree init       # Set up CodeTree + Claude + Cursor + Antigravity + Codex configs
 codetree status     # Check if running + index health
-codetree stats      # View cache hit rate + token savings
+codetree stats      # Cache hit rate + estimated token savings (see output for assumptions)
 codetree reindex    # Force full re-index
+codetree doctor     # Verify MCP paths, hook scripts, IPC (after Node/npm changes)
 codetree help       # Show help
 ```
 
+### Dev dependency vs global, and AI tools
+
+- With **`npm install --save-dev codetree-claude`**, `.mcp.json` points at `node_modules/codetree-claude/dist/...`. The **MCP server runs** as usual; some assistants **skip `node_modules`** in search context — that is expected.
+- The **indexer** skips **`node_modules`** for speed. To hack on **CodeTree source**, open a **git clone** of this repo as the project root.
+- After **`nvm use`**, switching Node, or changing **npm prefix**, run **`codetree doctor`** and **`codetree init`** again if paths are wrong.
+
 ## Configuration
 
 Edit `.codetreerc.json` in your project root:
@@ -94,119 +141,88 @@ Edit `.codetreerc.json` in your project root:
 }
 ```
 
-## Built for Real-World Reliability
+## Built for real-world reliability
 
-CodeTree isn't just a cache — it's designed for the messy reality of daily development.
+### Never stale
+- **External edits** — mtime validation; fresh content after VS Code saves, merges, etc.
+- **Git branch aware** — branch switches invalidate relevant cache.
+- **Any process** that changes files on disk is reflected on next read.
 
-### Never Stale
-- **External edits detected** — Edit a file in VS Code, save, immediately ask Claude about it. CodeTree validates disk mtime every 5 seconds per file and serves fresh content automatically.
-- **Git branch aware** — Switch branches with `git checkout` and CodeTree instantly invalidates its cache. No stale content from the old branch, no manual cache clearing.
-- **Works with any tool** — git merge, rebase, stash, sed, vim — any process that modifies files on disk is detected on the next read.
+### Cross-platform
+- **Windows `\r\n`** — `codetree_edit` normalizes for matching; preserves style on write.
+- **Paths** — forward slashes in MCP JSON strings for portability.
 
-### Cross-Platform
-- **Windows `\r\n` handled** — `codetree_edit` normalizes line endings for matching and preserves the original style on write. No more "old_string not found" on Windows projects.
-- **Path normalization** — Forward slashes everywhere internally, regardless of OS.
+### Safe at scale
+- **Large files** — truncation with offset/limit guidance.
+- **Large repos** — structure view can collapse top-level for 500+ files.
+- **Hooks (Claude)** — redirect only when CodeTree can serve; otherwise native tools run.
+- **Graceful degradation** — non-critical failures wrapped so core reads do not break.
 
-### Safe at Scale
-- **Large files** — Reads over 100KB are auto-truncated with guidance to use offset/limit. No blown context windows.
-- **Large repos** — Project structure auto-collapses to top-level directories for repos with 500+ files.
-- **Smart redirects** — The hook only blocks native Read/Edit/Write/Grep/Glob when CodeTree can actually serve the request. If the file isn't cached, native tools proceed normally.
-- **Graceful degradation** — Session logging, cache validation, and all non-critical operations are wrapped in try/catch. A failure in telemetry never breaks your read or edit.
+### Full session memory (Claude Code path)
+Session logging and compaction-related behavior are strongest where **hooks** run; MCP-only clients still get the full **tool set** on the server.
 
-### Full Session Memory
-Every CodeTree tool logs its activity — not just native Read/Grep/Glob. Hot files, search patterns, and modification history are complete across both native and CodeTree tools, giving you accurate session context and compaction restores.
+## MCP tools (all MCP hosts)
 
-## MCP Tools
+These tools are registered for **Claude Code, Cursor, Codex, Antigravity**, and any compatible MCP client:
 
-CodeTree exposes 8 tools that Claude Code uses instead of native Read/Grep/Glob:
+| Tool | Replaces / complements | What it does |
+|------|------------------------|--------------|
+| `codetree_read` | Read | Cached read + symbols; mtime-validated. |
+| `codetree_edit` | Edit | Edit without prior Read; `\r\n`-safe on Windows. |
+| `codetree_write` | Write | Write without prior Read; creates parent dirs. |
+| `codetree_search` | Grep | Symbol index + optional content search. |
+| `codetree_structure` | Glob | Project tree; auto-collapse on huge repos. |
+| `codetree_find_refs` | — | Cross-file references. |
+| `codetree_summary` | — | Project overview for session start. |
+| `codetree_memory` | — | Save / recall insights across sessions. |
 
-| Tool | Replaces | What it does |
-|------|----------|-------------|
-| `codetree_read` | Read | Cached file read with symbol metadata. Mtime-validated, never stale. |
-| `codetree_edit` | Edit | File edit without prior Read. Handles `\r\n` line endings on Windows. |
-| `codetree_write` | Write | File write without prior Read. Auto-creates parent directories. |
-| `codetree_search` | Grep | Symbol index search + optional content search with fast pre-filtering. |
-| `codetree_structure` | Glob | Project tree browser. Auto-collapses large repos to top-level directories. |
-| `codetree_find_refs` | — | Cross-file reference finder with fast file-skip for common symbols. |
-| `codetree_summary` | — | Full project overview for session start. |
-| `codetree_memory` | — | Persistent session memory — save and recall insights across conversations. |
+## Supported languages (symbols)
 
-## Supported Languages
+Symbol extraction: JavaScript, TypeScript (JSX/TSX), Python, Java/Kotlin/C#, Go.
 
-Symbol extraction works for:
-- JavaScript / TypeScript (JSX, TSX)
-- Python
-- Java / Kotlin / C#
-- Go
+Indexing and text caching: Prisma, GraphQL, Protobuf, SQL, YAML, TOML, JSON, Markdown, HTML, CSS/SCSS, shell, Docker, Terraform, `.env`, and more.
 
-Content caching and indexing works for all text files, including:
-- Prisma, GraphQL, Protobuf
-- SQL, YAML, TOML, JSON
-- Markdown, HTML, CSS/SCSS
-- Shell scripts, Dockerfiles, Terraform
-- `.env` and config files
-
-## Architecture
+## Architecture (conceptual)
 
 ```
-┌───────────────────────────────────────────────────┐
-│  Claude Code                                      │
-│  ┌─────────────────────────────────────────────┐  │
-│  │ Hooks (5 lifecycle events)                  │  │
-│  │ ├── PreToolUse: redirect Read/Grep/Glob/    │  │
-│  │ │   Edit/Write → CodeTree if cached         │  │
-│  │ ├── PostToolUse: log session activity       │  │
-│  │ ├── SessionStart: inject prior knowledge    │  │
-│  │ ├── PreCompact: save context snapshot        │  │
-│  │ └── PostCompact: restore context from cache │  │
-│  └──────────────┬──────────────────────────────┘  │
-│                 │                                 │
-│  ┌──────────────▼──────────────────────────────┐  │
-│  │ MCP Server (8 tools)                        │  │
-│  │ ├── codetree_read    (mtime-validated)      │  │
-│  │ ├── codetree_edit    (\r\n-safe)             │  │
-│  │ ├── codetree_write                          │  │
-│  │ ├── codetree_search  (pre-filtered)         │  │
-│  │ ├── codetree_structure (auto-collapse)      │  │
-│  │ ├── codetree_find_refs                      │  │
-│  │ ├── codetree_summary                        │  │
-│  │ └── codetree_memory  (cross-session)        │  │
-│  └──────────────┬──────────────────────────────┘  │
-│                 │                                 │
-│  ┌──────────────▼──────────────────────────────┐  │
-│  │ Indexer + Cache Layer                       │  │
-│  │ ├── SQLite database (persistent index)      │  │
-│  │ ├── LRU cache (hot files, mtime-checked)    │  │
-│  │ ├── Symbol extraction (JS/TS/Py/Java/Go)    │  │
-│  │ ├── File watcher (chokidar, live updates)   │  │
-│  │ ├── Git HEAD watcher (branch switch detect) │  │
-│  │ ├── Session memory (reads/edits/insights)   │  │
-│  │ └── Disk manager (space monitoring)         │  │
-│  └─────────────────────────────────────────────┘  │
-└───────────────────────────────────────────────────┘
+┌─────────────────────────────────────────────────────────────┐
+│  AI client (Claude Code / Cursor / Codex / Antigravity / …) │
+│  ┌───────────────────────────────────────────────────────┐  │
+│  │ Claude Code: hooks (optional redirects)               │  │
+│  │ Others: MCP + rules / AGENTS.md / GEMINI.md           │  │
+│  └───────────────────────────┬───────────────────────────┘  │
+│                              │                               │
+│  ┌───────────────────────────▼───────────────────────────┐  │
+│  │ MCP server — codetree_read, codetree_search, …          │  │
+│  └───────────────────────────┬───────────────────────────┘  │
+│                              │                               │
+│  ┌───────────────────────────▼───────────────────────────┐  │
+│  │ Indexer + cache (SQLite, LRU, watcher, git HEAD, …)    │  │
+│  └─────────────────────────────────────────────────────────┘  │
+└─────────────────────────────────────────────────────────────┘
 ```
 
-## Org-wide Rollout
+## Org-wide rollout
 
-1. Add `codetree-claude` as a dev dependency in your repos
-2. Commit `.codetreerc.json` and `.mcp.json` to version control
-3. Add `.codetree/` to `.gitignore` (done automatically by `codetree init`)
-4. Each developer runs `npx codetree init` once (or use the VS Code extension)
+1. Add `codetree-claude` as a dev dependency (or document global install).
+2. Commit `.codetreerc.json`, `.mcp.json`, `.cursor/`, `.antigravity/`, `.codex/`, `AGENTS.md`, `GEMINI.md` as policy allows.
+3. Add `.codetree/` to `.gitignore` (init does this).
+4. Each developer runs `npx codetree init` once (or uses the VS Code extension).
 
-The index database is local to each machine — it rebuilds automatically on first run.
+The index is **local per machine** and rebuilds on demand.
 
-## Token Savings Estimate
+## Token savings (illustrative)
 
-For a typical session on a 10K-file TypeScript project:
+Typical session on a large TypeScript repo — **your** numbers may differ; run **`codetree stats`** for real metrics.
 
 | Without CodeTree | With CodeTree |
-|-----------------|---------------|
-| ~50 Read calls per task | ~10 Read calls (rest cached) |
-| ~20 Grep calls per task | ~5 Grep calls (rest from index) |
-| ~15 Glob calls per task | ~3 Glob calls (rest from tree) |
-| **~800K tokens/task** | **~250K tokens/task** |
+|------------------|---------------|
+| Many Read / Grep / Glob calls | Fewer, more cache/index hits |
+| Higher token use on repetition | Lower repetition via index + MCP |
+
+## npm discovery
 
-Run `codetree stats` to see actual savings for your project.
+This package is published as **`codetree-claude`**. **Keywords** in `package.json` (e.g. `mcp`, `claude-code`, `cursor`, `codex`, `antigravity`, `gemini`, `codebase-index`) help **npmjs.com** search. They are not read from `.npmrc` — `.npmrc` is for **registry and install** settings.
 
 ## License
 

package/dist/cli.js

@@ -1,8 +1,10 @@
 #!/usr/bin/env node
 import { resolve, join, dirname } from "node:path";
-import { existsSync, readFileSync, readdirSync } from "node:fs";
+import { existsSync, readFileSync } from "node:fs";
 import { fileURLToPath } from "node:url";
-import { installHook, installMcpServer, createDefaultConfig, updateGitignore, installClaudeMd, installClaudeRules } from "./setup/install.js";
+import { installHook, installMcpServer, createDefaultConfig, updateGitignore, installClaudeMd, installClaudeRules, installCursorMcp, installCursorRules, installAntigravityMcp, installCodexMcp, installAgentsMd, installGeminiMd, } from "./setup/install.js";
+import { runDoctor } from "./doctor.js";
+import { findGitRepos, findPackageRoot, formatNumber } from "./utils.js";
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = dirname(__filename);
 const args = process.argv.slice(2);
@@ -21,48 +23,15 @@ async function main() {
         case "reindex":
             await handleReindex();
             break;
+        case "doctor":
+            await runDoctor();
+            break;
         case "help":
         default:
             printHelp();
             break;
     }
 }
-// ─── Find all git repos ──────────────────────────────────────
-function findGitRepos(startDir, maxDepth = 3) {
-    const repos = [];
-    const visited = new Set();
-    function walk(dir, depth) {
-        if (depth > maxDepth)
-            return;
-        const resolved = resolve(dir);
-        if (visited.has(resolved))
-            return;
-        visited.add(resolved);
-        // Is this a git repo?
-        if (existsSync(join(resolved, ".git"))) {
-            repos.push(resolved);
-            return; // Don't recurse into git repos
-        }
-        // Scan subdirectories
-        let entries;
-        try {
-            entries = readdirSync(resolved, { withFileTypes: true });
-        }
-        catch {
-            return;
-        }
-        const skip = new Set(["node_modules", ".git", "dist", "build", ".next", "__pycache__", ".codetree", ".cache"]);
-        for (const entry of entries) {
-            if (!entry.isDirectory())
-                continue;
-            if (skip.has(entry.name) || entry.name.startsWith("."))
-                continue;
-            walk(join(resolved, entry.name), depth + 1);
-        }
-    }
-    walk(startDir, 0);
-    return repos;
-}
 // ─── Init ────────────────────────────────────────────────────
 async function handleInit() {
     const cwd = resolve(process.cwd());
@@ -83,45 +52,76 @@ async function handleInit() {
         console.log(`    - ${repo}`);
     }
     console.log();
-    const packageRoot = findPackageRoot();
+    const packageRoot = findPackageRootFromDir();
     const hookScript = join(packageRoot, "dist", "hook", "pre-tool-use.js");
     const serverScript = join(packageRoot, "dist", "server", "mcp-server.js");
     let totalSetup = 0;
     for (const repo of repos) {
         const repoName = dirname(repo) === repo ? repo : repo.split(/[/\\]/).pop();
         console.log(`  ── Setting up: ${repoName} ──`);
-        // 1. Config
-        const configResult = createDefaultConfig(repo);
-        console.log(`    [1/5] Config: ${existsSync(join(repo, ".codetreerc.json")) ? "exists" : "created"}`);
-        // 2. Gitignore
-        updateGitignore(repo);
-        console.log(`    [2/5] .gitignore: updated`);
-        // 3. Hooks
-        const hookResult = installHook(repo, hookScript);
-        console.log(`    [3/5] Hooks: ${hookResult.message}`);
-        // 4. MCP server
-        const mcpResult = installMcpServer(repo, serverScript);
-        console.log(`    [4/5] MCP: ${mcpResult.message}`);
-        // 5. CLAUDE.md — instructs Claude to use CodeTree MCP tools
-        installClaudeMd(repo);
-        console.log(`    [5/6] CLAUDE.md: updated`);
-        // 6. .claude/rules/ — mandatory rules Claude MUST follow
-        installClaudeRules(repo);
-        console.log(`    [6/6] Rules: .claude/rules/codetree.md`);
-        totalSetup++;
+        try {
+            // 1. Config
+            createDefaultConfig(repo);
+            console.log(`    [1/12] Config: ${existsSync(join(repo, ".codetreerc.json")) ? "exists" : "created"}`);
+            // 2. Gitignore
+            updateGitignore(repo);
+            console.log(`    [2/12] .gitignore: updated`);
+            // 3. Hooks
+            const hookResult = installHook(repo, hookScript);
+            console.log(`    [3/12] Hooks: ${hookResult.message}`);
+            // 4. MCP server (Claude Code — root .mcp.json)
+            const mcpResult = installMcpServer(repo, serverScript);
+            console.log(`    [4/12] MCP: ${mcpResult.message}`);
+            // 5. CLAUDE.md — instructs Claude to use CodeTree MCP tools
+            installClaudeMd(repo);
+            console.log(`    [5/12] CLAUDE.md: updated`);
+            // 6. .claude/rules/ — mandatory rules Claude MUST follow
+            installClaudeRules(repo);
+            console.log(`    [6/12] Rules: .claude/rules/codetree.md`);
+            // 7–12. Cursor, Antigravity, Codex, AGENTS.md, GEMINI.md (do not change Claude paths above)
+            const cursorMcp = installCursorMcp(repo, serverScript);
+            console.log(`    [7/12] ${cursorMcp.message}`);
+            installCursorRules(repo);
+            console.log(`    [8/12] Cursor rules: .cursor/rules/codetree.mdc`);
+            const agMcp = installAntigravityMcp(repo, serverScript);
+            console.log(`    [9/12] ${agMcp.message}`);
+            const codexMcp = installCodexMcp(repo, serverScript);
+            console.log(`    [10/12] ${codexMcp.message}`);
+            installAgentsMd(repo);
+            console.log(`    [11/12] AGENTS.md: CodeTree block`);
+            installGeminiMd(repo);
+            console.log(`    [12/12] GEMINI.md: CodeTree pointer`);
+            totalSetup++;
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            console.error(`    ✗ Failed for ${repoName}: ${msg}`);
+        }
         console.log();
     }
     // Also install at workspace root (cwd) if it's different from repos
     if (!repos.includes(cwd)) {
-        installClaudeMd(cwd);
-        installClaudeRules(cwd);
-        console.log(`  Workspace root: CLAUDE.md + rules added`);
+        try {
+            installClaudeMd(cwd);
+            installClaudeRules(cwd);
+            installCursorMcp(cwd, serverScript);
+            installCursorRules(cwd);
+            installAntigravityMcp(cwd, serverScript);
+            installCodexMcp(cwd, serverScript);
+            installAgentsMd(cwd);
+            installGeminiMd(cwd);
+            console.log(`  Workspace root: CLAUDE.md, rules, Cursor, Antigravity, Codex, AGENTS.md, GEMINI.md`);
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            console.error(`  ✗ Workspace root setup failed: ${msg}`);
+        }
         console.log();
     }
     console.log(`  ✓ ${totalSetup} project${totalSetup > 1 ? "s" : ""} configured.`);
     console.log();
     console.log(`  What happens now:`);
-    console.log(`    1. Reload VS Code (Ctrl+Shift+P → Developer: Reload Window)`);
+    console.log(`    1. Reload the editor (VS Code / Cursor: Cmd/Ctrl+Shift+P → Developer: Reload Window)`);
     console.log(`    2. Claude Code will auto-start the MCP server per project`);
     console.log(`    3. Hooks intercept Read/Grep/Glob and serve from cache`);
     console.log(`    4. Check the CodeTree sidebar for live stats`);
@@ -132,6 +132,9 @@ async function handleInit() {
     console.log(`    codetree reindex  — Force re-index all projects`);
     console.log();
 }
+function findPackageRootFromDir() {
+    return findPackageRoot(__dirname);
+}
 // ─── Status (aggregated) ─────────────────────────────────────
 async function handleStatus() {
     const cwd = resolve(process.cwd());
@@ -223,7 +226,8 @@ async function handleStats() {
         }
     }
     const totalHitRate = totalQueries > 0 ? ((totalHits / totalQueries) * 100).toFixed(1) : "0.0";
-    const costSaved = ((totalTokensSaved / 1_000_000) * 3).toFixed(2);
+    // Blended avg: Opus $15/M input, Sonnet $3/M input, weighted ~$10/M
+    const costSaved = ((totalTokensSaved / 1_000_000) * 10).toFixed(2);
     console.log(`\n  ── Totals ──`);
     console.log(`  Active repos:     ${activeRepos}`);
     console.log(`  Total files:      ${formatNumber(totalFiles)}`);
@@ -232,7 +236,7 @@ async function handleStats() {
     console.log(`  Cache misses:     ${formatNumber(totalMisses)}`);
     console.log(`  Hit rate:         ${totalHitRate}%`);
     console.log(`  Tokens saved:     ~${formatNumber(totalTokensSaved)}`);
-    console.log(`  Cost saved:       ~$${costSaved} (at $3/MTok)`);
+    console.log(`  Cost saved (est.): ~${costSaved} USD (blended avg ~$10/M input tokens: Opus $15, Sonnet $3)`);
     console.log();
 }
 async function handleReindex() {
@@ -270,31 +274,13 @@ function printHelp() {
     codetree status    Check all projects
     codetree stats     Aggregated cache hit rates and token savings
     codetree reindex   Force re-index all projects
+    codetree doctor    Verify MCP paths, hooks, and IPC (after Node/npm changes)
     codetree help      Show this help
 
   Run 'codetree init' from your workspace root — it auto-discovers
   all git repos underneath and sets up each one.
 `);
 }
-function findPackageRoot() {
-    let dir = resolve(__dirname);
-    for (let i = 0; i < 10; i++) {
-        if (existsSync(join(dir, "package.json")))
-            return dir;
-        const parent = resolve(dir, "..");
-        if (parent === dir)
-            break;
-        dir = parent;
-    }
-    return resolve(__dirname, "..");
-}
-function formatNumber(n) {
-    if (n < 1_000)
-        return String(n);
-    if (n < 1_000_000)
-        return `${(n / 1_000).toFixed(1)}K`;
-    return `${(n / 1_000_000).toFixed(1)}M`;
-}
 main().catch((err) => {
     console.error(`Error: ${err.message}`);
     process.exit(1);

package/dist/cli.js.map

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