Merge 15+ PRs: Security, Windows fixes, Knowledge files, Chat persistence, and more

[getworken]

Summary

This PR consolidates and merges 15+ open PRs from the community, resolving conflicts and ensuring compatibility with the current codebase.

PRs Included:

Security & Stability:

• fix: Security vulnerabilities and race conditions from code review #112 - Security vulnerabilities and race conditions
• fix: prevent agent subprocess blocking on Windows #89 - Windows subprocess blocking fix
• fix: improve rate limit handling with exponential backoff #109 - Rate limit handling with exponential backoff
• fix: add diagnostic warnings for config loading failures #100 - Diagnostic warnings for config loading

New Features:

• feat: add knowledge files support for additional project context #48 - Knowledge files support (API, schemas, prompts)
• feat: Add feature editing and deletion capabilities #29 - Feature editing and deletion (MCP tools)
• feat: Add assistant chat persistence and conversation management #45 - Chat persistence with conversation history
• feat: Add project reset functionality #4 - Project reset functionality
• fix: prevent coding agent from skipping refactoring features #52 - Refactoring feature guidance in prompts
• Fix: Fix expanding project from the ui by adding new features #114 - Fix expanding project from UI by adding new features
• Fix latest build issues from master #115 - Fix latest build issues from master

Infrastructure:

• fix: add MCP server config to ExpandChatSession for feature creation #88 - MCP server config for ExpandChatSession
• feat: add Quality Gates to enforce lint/type-check before marking features #110 - Quality gates module (quality_gates.py)
• feat: add structured logging system for agent debugging #113 - Structured logging module (structured_logging.py)
• fix: Prevent mock data implementations with infrastructure features #95 - UI polish, health checks, cross-platform fixes

Skipped (Already in HEAD):

• fix: Use least-tested-first selection for regression testing #47, feat: Add parallel subagent execution support #6, fix: Windows command line length limit errors #7, fix: handle 404 errors for deleted assistant conversations #105 - Features already exist in current codebase

Additional Fixes:

• Fixed TypeScript build error in ProjectSetupRequired.tsx
• Fixed all ruff linting errors (17 errors resolved, all ruff checks now pass)
• Converted UTF-16 encoded files to UTF-8
• Removed duplicate function definitions

Testing:

• npm run build passes (2245 modules)
• ruff check passes (0 errors)
• UI server starts and runs correctly

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Note: This PR includes everything manageable and best working changes up until PR #123. PR #123 has NOT been added to this merge.

Summary by CodeRabbit

• New Features

  • Project registry/import, per-project assistant chat, knowledge files, templates, "Open in IDE" + IDE preference, design tokens, visual regression, auto-generated docs, CI/workflow generation, security scanner, code review agent, structured logging, project reset/export, health/readiness endpoints, Gemini provider support.

• Improvements

  • Mandatory infrastructure checks included in feature counts, quality-gate enforcement, HTTP Basic Auth and rate limiting, safer Windows/process handling, improved persistence verification.

• Bug Fixes

  • Robust lock/process cleanup, stuck-feature recovery, DB concurrency and retry resilience.

• Tests

  • Expanded test suites and pytest configuration.

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