diff --git a/.env.example b/.env.example
index aff166c..e1e10a4 100644
--- a/.env.example
+++ b/.env.example
@@ -1,9 +1,6 @@
 # Copy this file to .env and fill in your credentials
 # The .env file will be baked into the Docker image during build
 
-# Required for Claude Code if not using via subscription.
-ANTHROPIC_API_KEY=your_anthropic_api_key_here
-
 # Optional: Twilio credentials for SMS notifications
 TWILIO_ACCOUNT_SID=your_twilio_account_sid
 TWILIO_AUTH_TOKEN=your_twilio_auth_token
@@ -11,7 +8,7 @@ TWILIO_FROM_NUMBER=+1234567890
 TWILIO_TO_NUMBER=+0987654321
 
 # Optional: Custom conda installation (for academic/lab environments)
-# Example: CONDA_PREFIX=/vol/biomedic3/username/miniconda3
+# Example: CONDA_PREFIX=/path/to/miniconda3
 CONDA_PREFIX=
 
 # Optional: Additional conda directories (space-separated list)
@@ -19,7 +16,7 @@ CONDA_PREFIX=
 # Automatic detection:
 #   - Paths with "*env*" are added to CONDA_ENVS_DIRS (for environments)
 #   - Paths with "*pkg*" are added to CONDA_PKGS_DIRS (for package cache)
-# Example: CONDA_EXTRA_DIRS="/vol/biomedic3/username/.conda/envs /vol/biomedic3/username/conda_envs /vol/biomedic3/username/.conda/pkgs /vol/biomedic3/username/conda_pkgs /homes/username/.conda/envs"
+# Example: CONDA_EXTRA_DIRS="/vol/lab/username/.conda/envs /vol/lab/username/conda_envs /vol/lab/username/.conda/pkgs /vol/lab/username/conda_pkgs"
 CONDA_EXTRA_DIRS=
 
 # Optional: System packages to install in Docker container (space-separated)
diff --git a/scratchpad.md b/scratchpad.md
deleted file mode 100644
index 547bd87..0000000
--- a/scratchpad.md
+++ /dev/null
@@ -1,77 +0,0 @@
-# Claude Docker Project Scratchpad
-
-## Project Overview
-Docker container for Claude Code with full autonomous permissions, authentication persistence, and Twilio SMS notifications.
-
-## ✅ COMPLETED PHASES
-
-### Phase 1 - MVP (Complete)
-- Docker setup with Claude Code + Twilio MCP integration
-- Wrapper script for easy invocation
-- Auto .claude directory setup 
-- Full autonomous permissions with --dangerously-skip-permissions
-- Context persistence via scratchpad.md files
-
-### Phase 2 - Authentication Persistence (Complete) 
-- **SOLVED**: Authentication files copied during Docker build
-- **SOLVED**: MCP servers persist with user scope
-- **SOLVED**: No unnecessary rebuilds
-- **RESULT**: Zero-friction experience - no login prompts, SMS ready instantly
-
-## 🎯 CURRENT FOCUS
-**CRITICAL ISSUE TO RESOLVE NEXT SESSION:**
-
-### CLAUDE.md Template Not Being Copied to Container
-**Problem:** The CLAUDE.md template file is not appearing in `~/.claude/CLAUDE.md` inside the container, so Claude doesn't read the project instructions.
-
-**Root Cause Identified:** In Dockerfile line 65, the cleanup command `rm -rf /tmp/.claude*` is deleting `/tmp/CLAUDE.md` BEFORE it can be copied to the final location.
-
-**Solution Applied (needs testing):**
-- Fixed order: copy CLAUDE.md BEFORE cleanup in same RUN block
-- Line 64: `cp /tmp/CLAUDE.md /home/claude-user/.claude/CLAUDE.md &&`
-- Line 65: `rm -rf /tmp/.claude* /tmp/CLAUDE.md`
-
-**Test Command:** 
-```bash
-docker rmi claude-docker:latest && claude-docker
-# Then: ls -la ~/.claude/CLAUDE.md
-```
-
-**Impact:** Without this file, Claude doesn't know:
-- How to use conda environments properly
-- When/how to send SMS notifications  
-- Context persistence guidelines
-- Available tools and capabilities
-
-## 📚 KEY INSIGHTS FROM AUTHENTICATION JOURNEY
-
-### Critical Discovery: ~/.claude.json + MCP Scope
-- Claude Code requires BOTH `~/.claude.json` (user profile) AND `~/.claude/.credentials.json` (tokens)
-- MCP servers default to "local" scope (project-specific) - need "user" scope for persistence
-- Authentication can be baked into Docker image during build
-- Simple rebuild logic (only if image missing) prevents unnecessary rebuilds
-
-### Technical Implementation 
-- Copy auth files during Docker build, not runtime mounting
-- Use `-s user` flag for MCP persistence across sessions
-- Files placed at correct locations before user switch in Dockerfile
-
-## 🔮 FUTURE ENHANCEMENTS
-- Network security with firewall (iptables + ipset)
-- Shell history persistence between sessions
-- Git configuration persistence
-
-## 📋 DECISIONS LOG
-- MCP integration using user scope for persistence
-- Authentication files baked into Docker image at build time
-- Single container approach (no Docker Compose)
-- Simplified rebuild logic (only when image missing)
-- SMS via `@yiyang.1i/sms-mcp-server` with Auth Token
-
-## 🔗 QUICK REFERENCES
-- **Install:** `./scripts/install.sh`
-- **Usage:** `claude-docker` (from any project directory)
-- **Config:** `~/.claude-docker/.env` 
-- **Force rebuild:** `docker rmi claude-docker:latest`
-- **SMS command:** `twilio__send_text`
-- **Repository:** https://github.com/VishalJ99/claude-docker
\ No newline at end of file
diff --git a/scripts/setup-env.sh b/scripts/setup-env.sh
deleted file mode 100644
index 7a2f603..0000000
--- a/scripts/setup-env.sh
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/bin/bash
-# ABOUTME: Setup script to create ~/.claude-docker/.env with Twilio credentials
-# ABOUTME: Run this once on your host machine to configure Twilio for all projects
-
-CLAUDE_DOCKER_DIR="$HOME/.claude-docker"
-ENV_FILE="$CLAUDE_DOCKER_DIR/.env"
-
-# Create directory if it doesn't exist
-mkdir -p "$CLAUDE_DOCKER_DIR"
-
-# Check if .env already exists
-if [ -f "$ENV_FILE" ]; then
-    echo "⚠️  $ENV_FILE already exists!"
-    read -p "Do you want to update it? (y/N) " -n 1 -r
-    echo
-    if [[ ! $REPLY =~ ^[Yy]$ ]]; then
-        exit 0
-    fi
-fi
-
-echo "Setting up Twilio credentials for Claude Docker..."
-echo "You'll need your Twilio account information."
-echo
-
-# Collect Twilio credentials
-read -p "Enter your Twilio Account SID: " TWILIO_ACCOUNT_SID
-read -sp "Enter your Twilio Auth Token: " TWILIO_AUTH_TOKEN
-echo
-read -p "Enter your Twilio phone number (with country code, e.g., +1234567890): " TWILIO_FROM_NUMBER
-read -p "Enter the phone number to receive SMS (with country code): " TWILIO_TO_NUMBER
-
-# Create .env file
-cat > "$ENV_FILE" << EOF
-# Twilio credentials for Claude Docker
-TWILIO_ACCOUNT_SID=$TWILIO_ACCOUNT_SID
-TWILIO_AUTH_TOKEN=$TWILIO_AUTH_TOKEN
-TWILIO_FROM_NUMBER=$TWILIO_FROM_NUMBER
-TWILIO_TO_NUMBER=$TWILIO_TO_NUMBER
-EOF
-
-# Set restrictive permissions
-chmod 600 "$ENV_FILE"
-
-echo
-echo "✅ Twilio credentials saved to $ENV_FILE"
-echo "These credentials will be available to all Claude Docker sessions."
-echo
-echo "To test, run claude-docker from any project directory and use:"
-echo "  node /workspace/test-twilio.js"
\ No newline at end of file