feat: Add comprehensive Jules setup support with Docker installation

[manavgup]

• Add .jules/ directory with complete configuration files

  • config-with-docker.yaml: Jules config for Docker installation
  • config.yaml: Jules config for remote infrastructure
  • setup-with-docker.sh: Automated Docker installation script
  • setup.sh: Basic setup without Docker
  • DOCKER_SETUP.md: Detailed Docker installation guide
  • SECRETS_GUIDE.md: Security best practices for Jules
  • README.md: Jules configuration overview

• Add comprehensive documentation

  • JULES_SETUP.md: Quick start guide for Jules
  • JULES_DOCKER_COMPARISON.md: Remote vs Docker setup comparison
  • docs/deployment/jules-setup.md: Detailed deployment guide
  • env.jules.example: Environment template for Jules

• Update Makefile with verify-remote-connections target

• Update README.md with Jules setup reference

This enables RAG Modulo to run in Google's Jules environment with both remote infrastructure and local Docker options, complete with automated Docker Hub authentication and comprehensive setup guides.

[github-actions]

🚀 Development Environment Options

This repository supports Dev Containers for a consistent development environment.

Option 1: GitHub Codespaces (Recommended)

Create a cloud-based development environment:

1. Click the green Code button above
2. Select the Codespaces tab
3. Click Create codespace on feat/jules-setup-clean
4. Wait 2-3 minutes for environment setup
5. Start coding with all tools pre-configured!

Option 2: VS Code Dev Containers (Local)

Use Dev Containers on your local machine:

1. Install Docker Desktop
2. Install VS Code
3. Install the Dev Containers extension
4. Clone this PR branch locally
5. Open in VS Code and click "Reopen in Container" when prompted

Option 3: Traditional Local Setup

Set up the development environment manually:

# Clone the repository
git clone https://github.com/manavgup/rag_modulo.git
cd rag_modulo
git checkout feat/jules-setup-clean

# Initialize development environment
make dev-init
make dev-build
make dev-up
make dev-validate

Available Commands

Once in your development environment:

make help           # Show all available commands
make dev-validate   # Validate environment setup
make test-atomic    # Run atomic tests
make test-unit      # Run unit tests
make lint          # Run linting

Services Available

When running make dev-up:

• Backend API: http://localhost:8000
• Frontend: http://localhost:3000
• MLflow: http://localhost:5001

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This automated message helps reviewers quickly set up the development environment.

[claude]

PR Review: Jules Setup Support with Docker Installation

📊 Overview

This PR adds comprehensive Jules environment support with two setup approaches: remote infrastructure (recommended) and Docker installation (advanced). The implementation is well-documented and provides clear guidance for users.

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✅ Strengths

1. Excellent Documentation 🌟

• Comprehensive guides for multiple deployment scenarios
• Clear decision matrices (remote vs Docker)
• Step-by-step troubleshooting sections
• Well-organized with visual formatting (emojis, tables, sections)

2. Good Architecture Decisions

• Two-path approach: simple remote setup + advanced Docker option
• Sensible defaults (remote infrastructure recommended)
• Proper separation of concerns (config files, scripts, docs)
• Good use of environment variables for configuration

3. Security Considerations

• Placeholder credentials in config files (not hardcoded secrets) ✅
• SECRETS_GUIDE.md provides token rotation guidance
• Warnings about Docker group permissions
• Proper handling of sensitive data

4. DevEx Improvements

• verify-remote-connections Makefile target for quick debugging
• Clear error messages in setup scripts
• Multiple fallback options (systemctl vs service, Docker Compose V1/V2)
• Helpful success/failure indicators in scripts

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🔍 Issues & Concerns

High Priority Issues

1. Security: Docker Socket Permissions (Line 131 in setup-with-docker.sh)

sudo chmod 666 /var/run/docker.sock

• ⚠️ Issue: This gives world-writable access to Docker socket, equivalent to root access
• Risk: Any user on the system can run Docker commands with root privileges
• Recommendation: Remove this line or make it a last-resort option with warnings. Better to rely on group membership (usermod -aG docker)

2. Error Handling: Setup Script Continues on Docker Failure

• Lines 92-97 in setup-with-docker.sh: Docker login failure continues silently
• Issue: If authentication fails, setup continues but may hit rate limits later
• Recommendation: Consider failing fast if Docker Hub credentials are provided but authentication fails

3. Resource Management: No Disk Space Check

• Docker installation requires significant disk space (~20GB recommended)
• Issue: Setup may fail mid-way if disk space runs out
• Recommendation: Add disk space check before starting Docker pulls

Medium Priority Issues

4. Permission Issues Not Fully Resolved

• Lines 118-126: Adding user to docker group, but warns "may need to log out"
• Issue: The script continues but Docker commands may still fail without re-login
• Recommendation: After adding to group, either use newgrp docker automatically, or explicitly run remaining commands with sudo, or fail with clear instructions to restart session

5. Volume Directory Permissions (Line 191)

chmod -R 777 volumes/

• ⚠️ Issue: World-writable/executable directories are a security risk
• Recommendation: Use more restrictive permissions (755 or 775) or set proper ownership

6. Missing Validation in verify-remote-connections

• Makefile lines 396+: Connection verification script exists but not comprehensive
• Issue: Only tests basic connectivity, not authentication or write permissions
• Recommendation: Add checks for database authentication, schema/collection creation permissions, vector DB index creation, and object storage write/read operations

Low Priority Issues

7. Documentation: Hardcoded Docker Hub References

• Multiple references to Docker Hub in SECRETS_GUIDE.md
• Issue: Does not cover alternative registries (GHCR, ECR, etc.)
• Recommendation: Mention alternatives for enterprise users

8. Script Portability

• setup-with-docker.sh uses Bash-specific features
• Shebang is #!/bin/bash but some systems may not have bash at that path
• Recommendation: Consider #!/usr/bin/env bash for better portability

9. Missing Rollback Mechanism

• If setup fails mid-way, no cleanup or rollback
• Issue: Failed installations leave partial state
• Recommendation: Add cleanup function with trap for failure cases

10. Environment File Handling

• Lines 164-171 in setup-with-docker.sh: Creates .env from env.example
• Issue: Should use env.jules.example for Jules environments
• Recommendation: Check environment and use appropriate template

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🚀 Performance Considerations

1. Docker Image Pulls: Large images (Milvus ~2GB) - documented well in resource requirements ✅
2. Concurrent Setup: Could parallelize dependency installs (Poetry + npm), but current sequential approach is safer
3. No caching considerations: Docker login persists, which is good

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🧪 Test Coverage

Missing Tests:

• No automated tests for setup scripts
• No integration tests for Jules-specific configurations
• No validation that both config paths work end-to-end

Recommendations:

• Add shellcheck/bash unit tests for setup scripts
• Add CI job to test setup scripts in container environment
• Test verify-remote-connections target in CI

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📝 Code Quality

Positive:

• Consistent formatting and style
• Good use of comments and section headers
• Clear variable naming
• Proper use of set -e for error propagation

Areas for Improvement:

• Some repeated code between setup.sh and setup-with-docker.sh
• Could extract common functions to shared utility script
• Magic numbers (ports, timeouts) could be variables

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🔒 Security Assessment

Critical:

• ✅ No actual secrets committed
• ⚠️ Docker socket permissions too permissive (chmod 666)
• ⚠️ Volume permissions too permissive (chmod 777)

Recommendations:

1. Review and tighten file permissions
2. Add security warnings in documentation
3. Consider rootless Docker as alternative
4. Add note about Jules environment isolation

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📋 Recommendations Summary

Must Fix Before Merge:

1. ❌ Remove or restrict chmod 666 /var/run/docker.sock (security risk)
2. ❌ Change chmod -R 777 volumes/ to more restrictive permissions
3. ❌ Fix .env template selection (use env.jules.example for Jules)

Should Fix Before Merge:

4. Add disk space check before Docker installation
5. Handle docker group membership better (use newgrp or require restart)
6. Add rollback/cleanup mechanism for failed setups
7. Improve error handling for Docker Hub authentication

Nice to Have:

8. Add shellcheck validation to CI
9. Extract common functions from setup scripts
10. Add integration tests for setup scripts
11. Document alternative container registries

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🎯 Overall Assessment

Score: 7/10

Pros:

• Excellent documentation and user guidance
• Well-thought-out dual-path approach
• Good separation of concerns
• Clear and helpful error messages

Cons:

• Security issues with file permissions
• Missing error handling in critical paths
• No automated testing for setup scripts
• Some edge cases not handled

Verdict: Good foundation with some security and reliability concerns that should be addressed. The documentation is exemplary, but the implementation needs hardening for production use.

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📚 Additional Notes

• Consider adding a --dry-run flag to setup scripts for testing
• Add telemetry/logging to track setup success rates
• Consider containerizing the setup process itself for consistency
• Great work on the comprehensive documentation! 🎉

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Reviewed by: Claude Code
Date: 2025-10-09
Commit: [Latest]

[claude]

Pull Request Review: Jules Setup Support

Overall Assessment

Quality: 4/5 | Complexity: High (+2616 lines) | Risk: Medium | Recommendation: Approve with changes

Strengths

1. Excellent documentation quality with comprehensive guides
2. Well-structured architecture with clean separation of concerns
3. Good user experience with clear setup scripts
4. Follows project standards from CLAUDE.md

Critical Security Issues

1. Hardcoded Credentials (High Risk)

File: .jules/config-with-docker.yaml:34-35

• Credentials in plaintext version control
• Placeholder values teach bad security practices
• Risk of users committing real tokens
  Recommendation: Replace with comments pointing to Jules Secrets UI

2. Overly Permissive File Permissions (Medium Risk)

File: .jules/setup-with-docker.sh:191
chmod -R 777 volumes/

• Grants world-writable access (security risk)
• Could enable privilege escalation
  Recommendation: Use chmod -R 775 instead

3. Docker Socket Permissions (Medium Risk)

File: .jules/setup-with-docker.sh:131
sudo chmod 666 /var/run/docker.sock

• Grants root-equivalent access
• Risk not emphasized enough
  Recommendation: Add prominent security warning in output

Code Quality Issues

4. Shell Script Error Handling

• Script continues after Docker auth fails
• No validation of required environment variables
• Missing cleanup on failure
  Recommendation: Add validation and cleanup trap

5. Makefile verify-remote-connections

File: Makefile:396-424

• Silently suppresses errors
• Doesn't fail on connection failures
  Recommendation: Track failures and exit with non-zero status

6. Missing Input Validation

• No validation of Docker Hub token format
• Doesn't verify credentials before use

Minor Issues

7. Documentation has some inconsistencies
8. Missing test coverage for shell scripts
9. Resource requirements inconsistent (4GB vs 2-3GB)

Security Summary

• No SQL/command injection risks
• Overly permissive file permissions
• Credentials in config files
• Root-equivalent Docker socket access

Testing Recommendations

1. Add shellcheck to CI
2. Add config validation tests
3. Test verify-remote-connections failure cases

Final Recommendations

Must Fix (Before Merge):

1. Remove/obfuscate Docker Hub credentials in config examples
2. Change file permissions from 777 to 775
3. Add prominent security warnings in script output

Should Fix (Soon After Merge):
4. Add shellcheck to CI pipeline
5. Add tests for configuration validation
6. Improve verify-remote-connections error handling
7. Consolidate duplicate documentation

Conclusion

Well-executed feature that significantly improves RAG Modulo deployment flexibility. Documentation is excellent, code is generally well-structured. Main concerns are security best practices (file permissions, credential handling) which should be addressed before merge.

Overall: APPROVE with requested changes

Great work on this comprehensive Jules integration!

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Reviewer: Claude Code | Date: 2025-10-09 | PR: #356