nocodo feat: implement project command management with LLM-enhanced discovery

Summary

This PR implements a comprehensive project command management system with LLM-enhanced command discovery across the desktop app and manager components.

Key Features

Command Discovery System: Implements a 3-phase LLM-enhanced command discovery workflow that analyzes project files and repository metadata to intelligently identify install, build, run, and test commands
Desktop App UI: Complete command management interface with command cards, execution history, branch/worktree selector, and real-time status updates
API Integration: New project commands API endpoints for discovery, listing, execution, and history management
Database Layer: SQLite-backed storage for project commands with proper schema management
E2E Testing: Comprehensive test coverage for LLM-enhanced command discovery workflow

Changes

Manager (Backend)

Added command_discovery.rs with LLM-enhanced detection logic (782 lines)
Added database/project_commands.rs for command persistence (382 lines)
Added handlers/project_commands.rs with API endpoints (732 lines)
Implemented schema_provider.rs for automatic JSON schema generation (174 lines)
Enhanced LLM agent with better tool-calling and recursion handling
Added comprehensive E2E tests for command discovery

Desktop App (Frontend)

Implemented command discovery UI with build/dependency management fixes
Added CommandCard component for displaying commands (113 lines)
Enhanced project detail page with commands list and execution history (864 lines)
Added branch/worktree selector for Git repository navigation
Implemented API client methods for command operations
Added configurable SSH and HTTP client logging

Documentation & Specs

Added DESKTOP_APP_UI_CONVENTIONS.md (577 lines)
Multiple task documentation files for implementation guidance
Enhanced README with debugging instructions

Testing

E2E tests for LLM-enhanced command discovery
Integration tests for command API endpoints
Manual testing across multiple project types

Technical Improvements

Replaced hardcoded Claude model IDs with constants
Modularized database code with proper separation of concerns
Fixed state management issues in desktop app (project detail state clearing, favorites persistence)
Improved error handling and logging throughout

Breaking Changes

None - this is a new feature addition that doesn't affect existing functionality.

🤖 Generated with Claude Code

Dec 02 '25 07:12 brainless

📊 Code Complexity Analysis

Lines added: 7514
Lines removed: 547
Net change: 6967

💡 Suggestion: This is a large PR with 7514 added lines. Consider:

Breaking it into smaller, focused PRs
Adding comprehensive tests for the new functionality
Updating documentation as needed

Automated analysis by GitHub Actions

Dec 02 '25 07:12 github-actions[bot]

🤖 Automated Code Review Summary

This automated review was generated to help ensure code quality and security standards.

Rust Code Analysis

⚠️ Code formatting: Some Rust files are not formatted according to rustfmt standards.
- Run cargo fmt to fix formatting issues.
⚠️ Linting: Clippy found potential issues in Rust code.
- Run cargo clippy --workspace --all-targets -- --deny warnings to see detailed warnings.

Security Analysis

⚠️ Potential secrets: Found references to passwords, secrets, or tokens.
- Please verify no hardcoded credentials are present.
ℹ️ Debug output: Found debug print statements.
- Consider removing or replacing with proper logging.

Recommendations

Run the full CI pipeline to ensure all tests pass
Consider adding tests for any new functionality
Update documentation if API changes are involved
Follow the development workflow described in CLAUDE.md

This review was automatically generated. Please address any issues before merging.

Dec 02 '25 07:12 github-actions[bot]

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Dec 03 '25 04:12 cloudflare-workers-and-pages[bot]

📊 Code Complexity Analysis

Lines added: 7542
Lines removed: 547
Net change: 6995

💡 Suggestion: This is a large PR with 7542 added lines. Consider:

Breaking it into smaller, focused PRs
Adding comprehensive tests for the new functionality
Updating documentation as needed

Automated analysis by GitHub Actions

Dec 03 '25 04:12 github-actions[bot]

🤖 Automated Code Review Summary

This automated review was generated to help ensure code quality and security standards.

Rust Code Analysis

⚠️ Code formatting: Some Rust files are not formatted according to rustfmt standards.
- Run cargo fmt to fix formatting issues.
⚠️ Linting: Clippy found potential issues in Rust code.
- Run cargo clippy --workspace --all-targets -- --deny warnings to see detailed warnings.

Security Analysis

⚠️ Potential secrets: Found references to passwords, secrets, or tokens.
- Please verify no hardcoded credentials are present.
ℹ️ Debug output: Found debug print statements.
- Consider removing or replacing with proper logging.

Recommendations

Run the full CI pipeline to ensure all tests pass
Consider adding tests for any new functionality
Update documentation if API changes are involved
Follow the development workflow described in CLAUDE.md

This review was automatically generated. Please address any issues before merging.

Dec 03 '25 04:12 github-actions[bot]

📊 Code Complexity Analysis

Lines added: 7652
Lines removed: 547
Net change: 7105

💡 Suggestion: This is a large PR with 7652 added lines. Consider:

Breaking it into smaller, focused PRs
Adding comprehensive tests for the new functionality
Updating documentation as needed

Automated analysis by GitHub Actions

Dec 03 '25 04:12 github-actions[bot]

🤖 Automated Code Review Summary

This automated review was generated to help ensure code quality and security standards.

Rust Code Analysis

⚠️ Code formatting: Some Rust files are not formatted according to rustfmt standards.
- Run cargo fmt to fix formatting issues.
⚠️ Linting: Clippy found potential issues in Rust code.
- Run cargo clippy --workspace --all-targets -- --deny warnings to see detailed warnings.

Security Analysis

⚠️ Potential secrets: Found references to passwords, secrets, or tokens.
- Please verify no hardcoded credentials are present.
ℹ️ Debug output: Found debug print statements.
- Consider removing or replacing with proper logging.

Recommendations

Run the full CI pipeline to ensure all tests pass
Consider adding tests for any new functionality
Update documentation if API changes are involved
Follow the development workflow described in CLAUDE.md

This review was automatically generated. Please address any issues before merging.

Dec 03 '25 04:12 github-actions[bot]