Merge 15+ PRs: Security, Windows fixes, Knowledge files, Chat persistence, and more#117

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feat: Windows stability fixes, IDE integration, and API enhancements

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fix: add robust SQLite connection handling to prevent database corruption

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feat(ui): add custom theme override system

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feat: Twitter-style UI theme + Playwright optimization + documentation

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fix: SQLAlchemy PendingRollbackError + MCP support for Expand/Assistant

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fix: add engine caching to prevent file descriptor leaks

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fix: security vulnerabilities and race conditions from code review

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fix: UI TypeScript errors and missing dependencies

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feat: add attempt tracking, error logging, and code improvements

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fix: remove trailing whitespace from blank lines (lint)

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fix: update CI to use tests/ directory for security tests

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fix: address CodeRabbit review feedback

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fix: prevent agent subprocess blocking on Windows

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fix: kill process tree on agent completion to prevent zombies

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fix: improve rate limit handling with exponential backoff

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fix: address CodeRabbit review feedback

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fix: address CodeRabbit review - extract rate limit logic to shared module

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fix: remove unused RATE_LIMIT_PATTERNS import

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fix: add MCP server config to ExpandChatSession for feature creation

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feat: add least-tested-first regression testing

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fix: add row-level locking to prevent regression_count race condition

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fix: add diagnostic warnings for config loading failures (#91)

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fix: add diagnostic warnings for pkill_processes validation failures

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Add quality_gates.py from PR #110 - Quality gates for lint/type-check

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Add structured_logging.py from PR #113 - JSON structured logging for agent debugging

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Add knowledge files support from PR #48 - API endpoints, schemas, prompts, and frontend API

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cleanup: remove temp file

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feat: Add feature editing and deletion capabilities

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fix: Add retry limit to WebSocket connection polling

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fix: Address CodeRabbit feedback for useAssistantChat

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fix: Store connect polling timeout ID to prevent leaks on unmount

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docs: Add Project Assistant section with feature management capabilities

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docs: Clarify registry-driven project paths and remove New Chat reference

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docs: Address CodeRabbit feedback for README

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feat: Add assistant chat persistence and conversation management

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fix: Address PR review feedback

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fix: prevent coding agent from skipping refactoring features

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feat: Add project reset functionality

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fix: add venv activation to start_ui.sh

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feat(ui): Show setup wizard after full project reset

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fix: Prevent mock data implementations with infrastructure features

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fix: Address CodeRabbit review feedback

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fix: Address remaining CodeRabbit feedback

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fix: Health check now fails script on server startup failure

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fix: Address Leon's review - safer process killing and cross-platform support

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fix: Expand Map/Set grep search to entire src/ directory

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fix: use port-based process killing for cross-platform safety

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fix: add language tags to fenced code blocks per CodeRabbit/markdownlint

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fix: Update startAgent call to use options object

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fix: Resolve all ruff linting errors for CI

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Merge PR #114 and #115 from upstream leonvanzyl/autocoder

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fix: Address all CodeRabbit review feedback for PR #117

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Fix multiple issues: #106 DB corruption, #107 Ollama models, #44 Windows cmd, #73 denied commands, #38 hook bug, #40 project import

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Fix #49 Windows blank page and #69 test evidence storage

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Fix denied commands API - dict access and timestamp type

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fix(#32): Add optional HTTP Basic Auth for multi-user deployments

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docs: Add Basic Auth configuration to README

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Add migration for quality_result column

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fix: Resolve all ruff linting errors for CI

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docs: add critical security warnings to Web UI Authentication section

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fix: improve Feature model, MCP regression testing, and WebSocket cleanup

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Security and reliability fixes: rate limiting, auth error handling, cleanup scheduling, log redaction

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Fix deletion flow to cascade-update dependent features and add platform-safe process spawning for testing agents

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Updated project with new changes

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Apply CodeRabbit review fixes: null byte regex, start_ui.sh venv path, requirements version constraints

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Add health checks and GHCR deploy flow

heidi-dang
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Add readiness probe and extend deploy smoke tests

heidi-dang
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Add Gemini assistant chat support

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Add Gemini UI notice and improve Gemini error handling

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Add one-click VPS deploy script with Traefik, DuckDNS, and Let's Encrypt

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Ignore .code and add CI guard

heidi-dang
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Fix import order in health tests

heidi-dang
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Normalize import block spacing in health tests

heidi-dang
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Format imports in health tests

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Fix workflow expressions and add repo guard to PR checks

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Add DEVELOPMENT roadmap with phased plan

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Sort imports in assistant chat session

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Limit workflows to main branch

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Guard against tracked .env and .code

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Fix Traefik Docker API version mismatch

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Automate VPS deploy via deploy.sh

heidi-dang
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Fix Traefik routing and allow Docker access

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docs(fork): add FORK_README.md and FORK_CHANGELOG.md

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feat(config): add enhanced configuration system

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feat(error-recovery): add failure tracking and auto-clear stuck features

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feat(error-recovery): add MCP tools for failure tracking

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feat(import): add base analyzer abstract class

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feat(import): add stack detector orchestrator

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feat(import): add React/Next.js analyzer

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feat(import): add Node.js/Express/NestJS analyzer

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feat(import): add Python/FastAPI/Django/Flask analyzer

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feat(import): add Vue.js/Nuxt analyzer

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docs(fork): update changelog with Stack Detector feature

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feat(import): add feature extractor module

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feat(import): add import project REST API

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docs(fork): update changelog with Import Project API

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docs(fork): mark completed features in Planned Features section

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feat(logging): add structured logging module with SQLite storage

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docs(fork): update changelog with Enhanced Logging feature

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feat(security): add security scanning module

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docs(fork): update changelog with Security Scanning feature

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feat(git): add feature branches git workflow

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docs(fork): update changelog with Feature Branches feature

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feat(cicd): add CI/CD workflow generation

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docs(fork): update changelog with CI/CD Integration feature

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feat(templates): add project template library

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docs(fork): update changelog with Template Library feature

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feat(ui): add Import Wizard UI for importing existing projects

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docs(fork): update changelog with Import Wizard UI feature

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feat(review): add automatic code review agent

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docs(fork): update changelog with Review Agent feature

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feat(docs): add automatic documentation generator

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docs(fork): update changelog with Auto Documentation feature

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feat(design): add design tokens management system

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docs(fork): update changelog with Design Tokens feature

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feat(visual): add visual regression testing system

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docs(fork): update changelog with Visual Regression feature

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chore(ui): upgrade Vite to v7.3.1 and export API_BASE_URL

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fix: Fix features not appearing in Kanban "In Progress" column (parallel mode)

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feat: Add Infrastructure features to prevent mock data/dev-store implementations

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fix: prevent SQLite corruption in parallel mode with atomic operations

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fix: address ruff linting errors and connection leak

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feat: add Quality Gates to enforce lint/type-check before marking features

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fix: address CodeRabbit review feedback for PRs #95, #100, #108, #109, #110

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feat: integrate structured logging across agent system

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fix: resolve critical bugs causing agent failures

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fix: address CodeRabbit review feedback for structured logging

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fix: address CodeRabbit review feedback

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fix: use npx --no-install to prevent auto-download of tsc

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fix: resolve merge conflicts and linting issues

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fix: update verify_quality callers to use new parameter names

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fix: address CodeRabbit review issues

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fix: resolve all ruff lint errors

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fix: resolve agent errors from wp-translate logs analysis

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fix: address remaining CodeRabbit review issues for PR 119

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Apply CodeRabbit suggestions for PR #118

Agent-Planner
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Apply CodeRabbit suggestions for PR #119

Agent-Planner
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Apply remaining CodeRabbit suggestions for PR #119

Agent-Planner
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Fix syntax error in assistant_chat_session.py - malformed try/else block from merge

Agent-Planner
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fix: security, stability, and code quality improvements

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Fix CodeRabbit PR #117 issues and type annotations

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fix: resolve CI failures - syntax error and linting issues

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Apply CodeRabbit AI suggestions for code improvements and optimizations

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Fix all ruff linting errors

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security and validation fixes: error handling, path validation, type checking, and package constraints

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made all coderabbit edits and lint ruff

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Add startup warning when TEST_MODE is enabled

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Fix: Handle malformed Base64 input in auth

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Fix all ruff linting errors

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Update deploy.sh

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Update server/routers/git_workflow.py

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Update deploy.sh

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Update deploy.sh

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Update server/routers/git_workflow.py

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Update deploy.sh

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Fix code issues: confidence value handling, duckdns security, and blocked path validation

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Add .js file support to React/Next.js analyzer

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Update analyzers/react_analyzer.py

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Update api/migrations.py

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Update scripts/deploy.sh

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Update server/routers/import_project.py

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Fix security and validation issues

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feat: Add comprehensive project deletion cleanup across all systems

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fix: Update pywinpty version from 2.1 to 3.0

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Update server/routers/cicd.py

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Fix CodeRabbit AI issues and line endings

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