diff --git a/.gitignore b/.gitignore
index 6a0d3a8..ec9049f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -80,8 +80,6 @@ service-account.json
 # Docker secrets
 secrets/
 
-# Benchmark results
-benchmark_results_*.json
 
 # Temporary and backup files
 *.backup
diff --git a/docs/SCRIPTS.md b/docs/SCRIPTS.md
index 94756a8..9a5a3bb 100644
--- a/docs/SCRIPTS.md
+++ b/docs/SCRIPTS.md
@@ -9,25 +9,20 @@ This document provides an overview of the scripts in this repository, organized
 | `scripts/setup/setup.sh` | Main setup script for the project | `./scripts/setup/setup.sh` |
 | `scripts/setup/setup-precommit.sh` | Sets up pre-commit hooks | `./scripts/setup/setup-precommit.sh` |
 | `scripts/setup/setup-claude-auth.sh` | Sets up Claude authentication | `./scripts/setup/setup-claude-auth.sh` |
-| `scripts/setup/setup-new-repo.sh` | Sets up a new clean repository | `./scripts/setup/setup-new-repo.sh` |
-| `scripts/setup/create-new-repo.sh` | Creates a new repository | `./scripts/setup/create-new-repo.sh` |
+| `scripts/setup/setup-secure-credentials.sh` | Sets up secure credentials | `./scripts/setup/setup-secure-credentials.sh` |
 
 ## Build Scripts
 
 | Script | Description | Usage |
 |--------|-------------|-------|
-| `scripts/build/build-claude-container.sh` | Builds the Claude container | `./scripts/build/build-claude-container.sh` |
-| `scripts/build/build-claudecode.sh` | Builds the Claude Code runner Docker image | `./scripts/build/build-claudecode.sh` |
-| `scripts/build/update-production-image.sh` | Updates the production Docker image | `./scripts/build/update-production-image.sh` |
+| `scripts/build/build.sh` | Builds the Docker images | `./scripts/build/build.sh` |
 
 ## AWS Configuration and Credentials
 
 | Script | Description | Usage |
 |--------|-------------|-------|
 | `scripts/aws/create-aws-profile.sh` | Creates AWS profiles programmatically | `./scripts/aws/create-aws-profile.sh <profile-name> <access-key-id> <secret-access-key> [region] [output-format]` |
-| `scripts/aws/migrate-aws-credentials.sh` | Migrates AWS credentials to profiles | `./scripts/aws/migrate-aws-credentials.sh` |
 | `scripts/aws/setup-aws-profiles.sh` | Sets up AWS profiles | `./scripts/aws/setup-aws-profiles.sh` |
-| `scripts/aws/update-aws-creds.sh` | Updates AWS credentials | `./scripts/aws/update-aws-creds.sh` |
 
 ## Runtime and Execution
 
@@ -45,58 +40,48 @@ This document provides an overview of the scripts in this repository, organized
 |--------|-------------|-------|
 | `scripts/security/init-firewall.sh` | Initializes firewall for containers | `./scripts/security/init-firewall.sh` |
 | `scripts/security/accept-permissions.sh` | Handles permission acceptance | `./scripts/security/accept-permissions.sh` |
-| `scripts/security/fix-credential-references.sh` | Fixes credential references | `./scripts/security/fix-credential-references.sh` |
+| `scripts/security/credential-audit.sh` | Audits code for credential leaks | `./scripts/security/credential-audit.sh` |
 
 ## Utility Scripts
 
 | Script | Description | Usage |
 |--------|-------------|-------|
 | `scripts/utils/ensure-test-dirs.sh` | Ensures test directories exist | `./scripts/utils/ensure-test-dirs.sh` |
-| `scripts/utils/prepare-clean-repo.sh` | Prepares a clean repository | `./scripts/utils/prepare-clean-repo.sh` |
-| `scripts/utils/volume-test.sh` | Tests volume mounting | `./scripts/utils/volume-test.sh` |
+| `scripts/utils/setup-repository-labels.js` | Sets up GitHub repository labels | `node scripts/utils/setup-repository-labels.js owner/repo` |
 
-## Testing Scripts
+## Testing
 
-### Integration Tests
+All shell-based test scripts have been migrated to JavaScript E2E tests using Jest. Use the following npm commands:
 
-| Script | Description | Usage |
+### JavaScript Test Files
+
+**Note**: Shell-based test scripts have been migrated to JavaScript E2E tests using Jest. The following test files provide comprehensive testing:
+
+| Test File | Description | Usage |
 |--------|-------------|-------|
-| `test/integration/test-full-flow.sh` | Tests the full workflow | `./test/integration/test-full-flow.sh` |
-| `test/integration/test-claudecode-docker.sh` | Tests Claude Code Docker setup | `./test/integration/test-claudecode-docker.sh` |
+| `test/e2e/scenarios/container-execution.test.js` | Tests container functionality | `npm run test:e2e` |
+| `test/e2e/scenarios/claude-integration.test.js` | Tests Claude integration | `npm run test:e2e` |
+| `test/e2e/scenarios/docker-execution.test.js` | Tests Docker execution | `npm run test:e2e` |
+| `test/e2e/scenarios/security-firewall.test.js` | Tests security and firewall | `npm run test:e2e` |
 
-### AWS Tests
+### Running Tests
 
-| Script | Description | Usage |
-|--------|-------------|-------|
-| `test/aws/test-aws-profile.sh` | Tests AWS profile configuration | `./test/aws/test-aws-profile.sh` |
-| `test/aws/test-aws-mount.sh` | Tests AWS mount functionality | `./test/aws/test-aws-mount.sh` |
+```bash
+# Run all tests
+npm test
 
-### Container Tests
+# Run unit tests
+npm run test:unit
 
-| Script | Description | Usage |
-|--------|-------------|-------|
-| `test/container/test-basic-container.sh` | Tests basic container functionality | `./test/container/test-basic-container.sh` |
-| `test/container/test-container-cleanup.sh` | Tests container cleanup | `./test/container/test-container-cleanup.sh` |
-| `test/container/test-container-privileged.sh` | Tests container privileged mode | `./test/container/test-container-privileged.sh` |
+# Run E2E tests
+npm run test:e2e
 
-### Claude Tests
+# Run tests with coverage
+npm run test:coverage
 
-| Script | Description | Usage |
-|--------|-------------|-------|
-| `test/claude/test-claude-direct.sh` | Tests direct Claude integration | `./test/claude/test-claude-direct.sh` |
-| `test/claude/test-claude-no-firewall.sh` | Tests Claude without firewall | `./test/claude/test-claude-no-firewall.sh` |
-| `test/claude/test-claude-installation.sh` | Tests Claude installation | `./test/claude/test-claude-installation.sh` |
-| `test/claude/test-claude-version.sh` | Tests Claude version | `./test/claude/test-claude-version.sh` |
-| `test/claude/test-claude-response.sh` | Tests Claude response | `./test/claude/test-claude-response.sh` |
-| `test/claude/test-direct-claude.sh` | Tests direct Claude access | `./test/claude/test-direct-claude.sh` |
-
-### Security Tests
-
-| Script | Description | Usage |
-|--------|-------------|-------|
-| `test/security/test-firewall.sh` | Tests firewall configuration | `./test/security/test-firewall.sh` |
-| `test/security/test-with-auth.sh` | Tests with authentication | `./test/security/test-with-auth.sh` |
-| `test/security/test-github-token.sh` | Tests GitHub token | `./test/security/test-github-token.sh` |
+# Run tests in watch mode
+npm run test:watch
+```
 
 ## Common Workflows
 
@@ -109,6 +94,9 @@ This document provides an overview of the scripts in this repository, organized
 # Set up Claude authentication
 ./scripts/setup/setup-claude-auth.sh
 
+# Set up secure credentials
+./scripts/setup/setup-secure-credentials.sh
+
 # Create AWS profile
 ./scripts/aws/create-aws-profile.sh claude-webhook YOUR_ACCESS_KEY YOUR_SECRET_KEY
 ```
@@ -116,8 +104,8 @@ This document provides an overview of the scripts in this repository, organized
 ### Building and Running
 
 ```bash
-# Build Claude Code container
-./scripts/build/build-claudecode.sh
+# Build Docker images
+./scripts/build/build.sh
 
 # Start the API server
 ./scripts/runtime/start-api.sh
@@ -129,22 +117,18 @@ docker compose up -d
 ### Running Tests
 
 ```bash
-# Run integration tests
-./test/integration/test-full-flow.sh
+# Run all tests
+npm test
 
-# Run AWS tests
-./test/aws/test-aws-profile.sh
+# Run E2E tests specifically
+npm run test:e2e
 
-# Run Claude tests
-./test/claude/test-claude-direct.sh
+# Run unit tests specifically
+npm run test:unit
 ```
 
-## Backward Compatibility
+## Notes
 
-For backward compatibility, wrapper scripts are provided in the root directory for the most commonly used scripts:
-
-- `setup-claude-auth.sh` -> `scripts/setup/setup-claude-auth.sh`
-- `build-claudecode.sh` -> `scripts/build/build-claudecode.sh`
-- `start-api.sh` -> `scripts/runtime/start-api.sh`
-
-These wrappers simply forward all arguments to the actual scripts in their new locations.
\ No newline at end of file
+- All shell-based test scripts have been migrated to JavaScript E2E tests for better maintainability and consistency.
+- The project uses npm scripts for most common operations. See `package.json` for available scripts.
+- Docker Compose is the recommended way to run the service in production.
\ No newline at end of file
diff --git a/run-claudecode-interactive.sh b/run-claudecode-interactive.sh
deleted file mode 100755
index ce1447a..0000000
--- a/run-claudecode-interactive.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-# Run claudecode container interactively for testing and debugging
-docker run -it --rm \
-  -v $(pwd):/workspace \
-  -v ~/.aws:/root/.aws:ro \
-  -v ~/.claude:/root/.claude \
-  -w /workspace \
-  --entrypoint /bin/bash \
-  claudecode:latest
\ No newline at end of file
diff --git a/scripts/utils/benchmark-startup.sh b/scripts/utils/benchmark-startup.sh
deleted file mode 100755
index 1a84d82..0000000
--- a/scripts/utils/benchmark-startup.sh
+++ /dev/null
@@ -1,91 +0,0 @@
-#!/bin/bash
-
-# Benchmark script for measuring spin-up times
-set -e
-
-BENCHMARK_RUNS=${1:-3}
-COMPOSE_FILE=${2:-docker-compose.yml}
-
-echo "Benchmarking startup time with $COMPOSE_FILE (${BENCHMARK_RUNS} runs)"
-echo "=============================================="
-
-TOTAL_TIME=0
-RESULTS=()
-
-for i in $(seq 1 $BENCHMARK_RUNS); do
-    echo "Run $i/$BENCHMARK_RUNS:"
-    
-    # Ensure clean state
-    docker compose -f $COMPOSE_FILE down >/dev/null 2>&1 || true
-    docker system prune -f >/dev/null 2>&1 || true
-    
-    # Start timing
-    START_TIME=$(date +%s%3N)
-    
-    # Start service
-    docker compose -f $COMPOSE_FILE up -d >/dev/null 2>&1
-    
-    # Wait for health check to pass
-    echo -n "  Waiting for service to be ready."
-    while true; do
-        if curl -s -f http://localhost:8082/health >/dev/null 2>&1; then
-            READY_TIME=$(date +%s%3N)
-            break
-        fi
-        echo -n "."
-        sleep 0.5
-    done
-    
-    ELAPSED=$((READY_TIME - START_TIME))
-    TOTAL_TIME=$((TOTAL_TIME + ELAPSED))
-    RESULTS+=($ELAPSED)
-    
-    echo " Ready! (${ELAPSED}ms)"
-    
-    # Get detailed startup metrics
-    METRICS=$(curl -s http://localhost:8082/health | jq -r '.startup.totalElapsed // "N/A"')
-    echo "  App startup time: ${METRICS}ms"
-    
-    # Clean up
-    docker compose -f $COMPOSE_FILE down >/dev/null 2>&1
-    
-    # Brief pause between runs
-    sleep 2
-done
-
-echo ""
-echo "Results Summary:"
-echo "=============================================="
-
-AVERAGE=$((TOTAL_TIME / BENCHMARK_RUNS))
-echo "Average startup time: ${AVERAGE}ms"
-
-# Calculate min/max
-MIN=${RESULTS[0]}
-MAX=${RESULTS[0]}
-for time in "${RESULTS[@]}"; do
-    [ $time -lt $MIN ] && MIN=$time
-    [ $time -gt $MAX ] && MAX=$time
-done
-
-echo "Fastest: ${MIN}ms"
-echo "Slowest: ${MAX}ms"
-echo "Individual results: ${RESULTS[*]}"
-
-# Save results to file
-TIMESTAMP=$(date '+%Y%m%d_%H%M%S')
-RESULTS_FILE="benchmark_results_${TIMESTAMP}.json"
-
-cat > $RESULTS_FILE << EOF
-{
-  "timestamp": "$(date -Iseconds)",
-  "compose_file": "$COMPOSE_FILE",
-  "runs": $BENCHMARK_RUNS,
-  "results_ms": [$(IFS=,; echo "${RESULTS[*]}")],
-  "average_ms": $AVERAGE,
-  "min_ms": $MIN,
-  "max_ms": $MAX
-}
-EOF
-
-echo "Results saved to: $RESULTS_FILE"
\ No newline at end of file
diff --git a/scripts/utils/volume-test.sh b/scripts/utils/volume-test.sh
deleted file mode 100755
index 2630a21..0000000
--- a/scripts/utils/volume-test.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-
-# Test container with a volume mount for output
-OUTPUT_DIR="/tmp/claude-output"
-OUTPUT_FILE="$OUTPUT_DIR/output.txt"
-
-echo "Docker Container Volume Test"
-echo "=========================="
-
-# Ensure output directory exists and is empty
-mkdir -p "$OUTPUT_DIR"
-rm -f "$OUTPUT_FILE"
-
-# Run container with volume mount for output
-docker run --rm \
-  -v "$OUTPUT_DIR:/output" \
-  claudecode:latest \
-  bash -c "echo 'Hello from container' > /output/output.txt && echo 'Command executed successfully.'"
-
-# Check if output file was created
-echo
-echo "Checking for output file: $OUTPUT_FILE"
-if [ -f "$OUTPUT_FILE" ]; then
-  echo "Output file created. Contents:"
-  cat "$OUTPUT_FILE"
-else
-  echo "No output file was created."
-fi
\ No newline at end of file
diff --git a/test/claude/test-claude.sh b/test/claude/test-claude.sh
deleted file mode 100755
index a2feff6..0000000
--- a/test/claude/test-claude.sh
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/bin/bash
-# Consolidated Claude test script
-# Usage: ./test-claude.sh [direct|installation|no-firewall|response]
-
-set -e
-
-TEST_TYPE=${1:-direct}
-
-case "$TEST_TYPE" in
-  direct)
-    echo "Testing direct Claude integration..."
-    # Direct Claude test logic from test-claude-direct.sh
-    docker run --rm -it \
-      -e REPO_FULL_NAME="owner/test-repo" \
-      -e ISSUE_NUMBER="1" \
-      -e IS_PULL_REQUEST="false" \
-      -e COMMAND="echo 'Direct Claude test'" \
-      -e GITHUB_TOKEN="${GITHUB_TOKEN:-test-token}" \
-      -e ANTHROPIC_API_KEY="${ANTHROPIC_API_KEY:-test-key}" \
-      claude-code-runner:latest
-    ;;
-  
-  installation)
-    echo "Testing Claude installation..."
-    # Installation test logic from test-claude-installation.sh and test-claude-version.sh
-    docker run --rm -it \
-      -e REPO_FULL_NAME="owner/test-repo" \
-      -e ISSUE_NUMBER="1" \
-      -e IS_PULL_REQUEST="false" \
-      -e COMMAND="claude-cli --version && claude --version" \
-      -e GITHUB_TOKEN="${GITHUB_TOKEN:-test-token}" \
-      claude-code-runner:latest
-    ;;
-  
-  no-firewall)
-    echo "Testing Claude without firewall..."
-    # Test logic from test-claude-no-firewall.sh
-    docker run --rm -it \
-      -e REPO_FULL_NAME="owner/test-repo" \
-      -e ISSUE_NUMBER="1" \
-      -e IS_PULL_REQUEST="false" \
-      -e COMMAND="echo 'Claude without firewall test'" \
-      -e GITHUB_TOKEN="${GITHUB_TOKEN:-test-token}" \
-      -e DISABLE_FIREWALL=true \
-      claude-code-runner:latest
-    ;;
-  
-  response)
-    echo "Testing Claude response..."
-    # Test logic from test-claude-response.sh
-    docker run --rm -it \
-      -e REPO_FULL_NAME="owner/test-repo" \
-      -e ISSUE_NUMBER="1" \
-      -e IS_PULL_REQUEST="false" \
-      -e COMMAND="claude \"Tell me a joke\"" \
-      -e GITHUB_TOKEN="${GITHUB_TOKEN:-test-token}" \
-      -e ANTHROPIC_API_KEY="${ANTHROPIC_API_KEY:-test-key}" \
-      claude-code-runner:latest
-    ;;
-  
-  *)
-    echo "Unknown test type: $TEST_TYPE"
-    echo "Usage: ./test-claude.sh [direct|installation|no-firewall|response]"
-    exit 1
-    ;;
-esac
-
-echo "Test complete!"
diff --git a/test/container/test-container.sh b/test/container/test-container.sh
deleted file mode 100755
index 0bcbe71..0000000
--- a/test/container/test-container.sh
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/bin/bash
-# Consolidated container test script
-# Usage: ./test-container.sh [basic|privileged|cleanup]
-
-set -e
-
-TEST_TYPE=${1:-basic}
-
-case "$TEST_TYPE" in
-  basic)
-    echo "Running basic container test..."
-    # Basic container test logic from test-basic-container.sh
-    docker run --rm -it \
-      -e REPO_FULL_NAME="owner/test-repo" \
-      -e ISSUE_NUMBER="1" \
-      -e IS_PULL_REQUEST="false" \
-      -e COMMAND="echo 'Basic container test'" \
-      -e GITHUB_TOKEN="${GITHUB_TOKEN:-test-token}" \
-      claude-code-runner:latest
-    ;;
-  
-  privileged)
-    echo "Running privileged container test..."
-    # Privileged container test logic from test-container-privileged.sh
-    docker run --rm -it \
-      --privileged \
-      -e REPO_FULL_NAME="owner/test-repo" \
-      -e ISSUE_NUMBER="1" \
-      -e IS_PULL_REQUEST="false" \
-      -e COMMAND="echo 'Privileged container test'" \
-      -e GITHUB_TOKEN="${GITHUB_TOKEN:-test-token}" \
-      claude-code-runner:latest
-    ;;
-  
-  cleanup)
-    echo "Running container cleanup test..."
-    # Container cleanup test logic from test-container-cleanup.sh
-    docker run --rm -it \
-      -e REPO_FULL_NAME="owner/test-repo" \
-      -e ISSUE_NUMBER="1" \
-      -e IS_PULL_REQUEST="false" \
-      -e COMMAND="echo 'Container cleanup test'" \
-      -e GITHUB_TOKEN="${GITHUB_TOKEN:-test-token}" \
-      claude-code-runner:latest
-    ;;
-  
-  *)
-    echo "Unknown test type: $TEST_TYPE"
-    echo "Usage: ./test-container.sh [basic|privileged|cleanup]"
-    exit 1
-    ;;
-esac
-
-echo "Test complete!"