codetree-claude 1.4.7 → 1.5.1

package/README.md

@@ -1,47 +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.
 
-## The Problem
+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.
 
-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.
+> **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.
 
-## The Solution
+## Supported AI coding tools (multi-IDE)
 
-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.
+| 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 |
 
-### How it works
+**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.
+
+**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
 
@@ -50,29 +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:
@@ -92,79 +141,88 @@ Edit `.codetreerc.json` in your project root:
 }
 ```
 
-## MCP Tools
+## Built for real-world reliability
+
+### 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.
+
+### Cross-platform
+- **Windows `\r\n`** — `codetree_edit` normalizes for matching; preserves style on write.
+- **Paths** — forward slashes in MCP JSON strings for portability.
 
-CodeTree exposes 5 tools that Claude Code uses instead of native Read/Grep/Glob:
+### 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.
 
-| Tool | Replaces | What it does |
-|------|----------|-------------|
-| `codetree_read` | Read | Cached file read with symbol metadata |
-| `codetree_search` | Grep | Symbol index search (functions, classes, types) |
-| `codetree_structure` | Glob | Project tree browser with language stats |
-| `codetree_find_refs` | — | Cross-file reference finder |
-| `codetree_summary` | — | Full project overview for session start |
+### 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.
 
-## Supported Languages
+## MCP tools (all MCP hosts)
 
-Symbol extraction works for:
-- JavaScript / TypeScript (JSX, TSX)
-- Python
-- Java / Kotlin / C#
-- Go
-- All other files get indexed (content cached) but without symbol extraction
+These tools are registered for **Claude Code, Cursor, Codex, Antigravity**, and any compatible MCP client:
 
-## Architecture
+| 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. |
+
+## Supported languages (symbols)
+
+Symbol extraction: 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.
+
+## Architecture (conceptual)
 
 ```
-┌─────────────────────────────────────────────┐
-│  Claude Code                                │
-│  ┌───────────────────────────────────────┐  │
-│  │ PreToolUse Hook                       │  │
-│  │ Intercepts Read/Grep/Glob             │  │
-│  │ Queries IPC server (<30ms)            │  │
-│  │ Redirects to MCP tools if cached      │  │
-│  └─────────────┬─────────────────────────┘  │
-│                │                            │
-│  ┌─────────────▼─────────────────────────┐  │
-│  │ MCP Server (codetree)                 │  │
-│  │ ├── codetree_read                     │  │
-│  │ ├── codetree_search                   │  │
-│  │ ├── codetree_structure                │  │
-│  │ ├── codetree_find_refs                │  │
-│  │ └── codetree_summary                  │  │
-│  └─────────────┬─────────────────────────┘  │
-│                │                            │
-│  ┌─────────────▼─────────────────────────┐  │
-│  │ Indexer + File Watcher                │  │
-│  │ ├── SQLite database (persistent)      │  │
-│  │ ├── LRU in-memory cache (hot files)   │  │
-│  │ ├── Symbol extraction (regex-based)   │  │
-│  │ └── chokidar watcher (live updates)   │  │
-│  └───────────────────────────────────────┘  │
-└─────────────────────────────────────────────┘
+┌─────────────────────────────────────────────────────────────┐
+│  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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