fix: code quality improvements

.claude/commands/check.md

@@ -0,0 +1,30 @@
+# Quick Code Check
+
+> Fast code quality check for recent changes. Use `/refactor` for comprehensive analysis.
+
+## Run Checks
+
+```bash
+# Lint check
+uv run ruff check .
+
+# Format check
+uv run ruff format . --check && echo "Formatting OK" || echo "Formatting issues found"
+
+# Quick unit tests
+uv run pytest tests/unit -x -q --tb=short 2>/dev/null | tail -30
+```
+
+## Check Recent Changes
+
+```bash
+# Files changed vs main
+git diff --name-only main... 2>/dev/null || git diff --name-only HEAD~5
+```
+
+## Summary
+
+Provide a brief summary:
+1. Any lint/format issues found
+2. Test status
+3. Quick recommendations for the changed files

.claude/commands/prime.md

@@ -1,21 +1,52 @@
 # Prime
 
-> Execute the following sections to understand the codebase then summarize your understanding.
+> Quickly understand the pyplots codebase - structure, rules, and current state.
 
-## Run
+## Project Rules
 
-git ls-files
+@CLAUDE.md
 
-## Read
+## Project Config
 
-@README.md
 @pyproject.toml
-@docs/concepts/vision.md
-@docs/workflows/overview.md
-@docs/reference/repository.md
 
-## Read and Execute
+## Quick Stats
 
+```bash
+# Repository overview
+echo "=== Repository Stats ==="
+echo "Plot specifications: $(ls -d plots/*/ 2>/dev/null | wc -l)"
+echo "Python files: $(find api core automation tests -name '*.py' 2>/dev/null | wc -l)"
+echo "Frontend files: $(find app/src -name '*.tsx' -o -name '*.ts' 2>/dev/null | wc -l)"
+echo "Workflows: $(ls .github/workflows/*.yml 2>/dev/null | wc -l)"
+echo "Prompts: $(find prompts -name '*.md' 2>/dev/null | wc -l)"
+```
 
+## Structure
 
+```bash
+# Key directories
+ls -la api/ core/ app/src/ prompts/ .github/workflows/ 2>/dev/null | head -50
 
+# Documentation
+find docs -name "*.md" 2>/dev/null | sort
+```
+
+## Current State
+
+```bash
+# Git status
+git status --short
+
+# Recent activity
+git log --oneline -10
+```
+
+## Summarize
+
+After reading, provide:
+1. **Purpose**: What does this project do?
+2. **Architecture**: Key components and how they connect
+3. **Workflow**: How specs become implementations
+4. **Tech Stack**: Languages, frameworks, infrastructure
+5. **Key Rules**: Critical constraints from CLAUDE.md

.claude/commands/refactor.md

@@ -0,0 +1,217 @@
+# Code Quality Refactor
+
+> Comprehensive code quality analysis for the pyplots repository. Checks readability, performance, code smells, consistency, and modernization opportunities across all components.
+
+## Context
+
+@CLAUDE.md
+@pyproject.toml
+
+## Analysis Scope
+
+Analyze the following areas systematically. For each area, identify:
+- **Code Smells**: Dead code, duplication, overly complex functions, god classes
+- **Readability**: Unclear naming, missing/outdated comments, inconsistent formatting
+- **Performance**: Inefficient patterns, N+1 queries, unnecessary computations
+- **Modernization**: Deprecated APIs, old Python patterns, outdated dependencies
+- **Consistency**: Naming conventions, import styles, error handling patterns
+- **Type Safety**: Missing type hints, incorrect types, Any overuse
+- **Test Quality**: Missing tests, flaky tests, poor assertions
+
+## Discover Structure
+
+```bash
+# Overview of repository structure
+find . -type f -name "*.py" | grep -E "^\./(api|core|automation|tests)/" | head -80
+
+# Frontend structure
+find ./app/src -type f -name "*.ts" -o -name "*.tsx" 2>/dev/null | head -40
+
+# Workflow files
+ls -la .github/workflows/*.yml 2>/dev/null
+
+# Prompt files
+find ./prompts -type f -name "*.md" 2>/dev/null
+
+# Documentation
+find ./docs -type f -name "*.md" 2>/dev/null
+```
+
+## Run Quality Checks
+
+```bash
+# Linting issues
+uv run ruff check .
+
+# Format check (dry-run)
+uv run ruff format . --check --diff
+```
+
+## Analyze Backend (api/)
+
+Check for:
+- Router organization and REST conventions
+- Dependency injection patterns
+- Error handling consistency
+- Response schema completeness
+- Async/await correctness
+- Caching strategies
+
+```bash
+ls -la api/*.py api/**/*.py 2>/dev/null
+```
+
+## Analyze Core Logic (core/)
+
+Check for:
+- Repository pattern implementation
+- Database model design
+- Configuration management
+- Utility function organization
+- Type definitions
+
+```bash
+ls -la core/*.py core/**/*.py 2>/dev/null
+```
+
+## Analyze Automation (automation/)
+
+Check for:
+- Script modularity
+- Error handling in workflows
+- CLI argument parsing
+- Logging consistency
+
+```bash
+ls -la automation/**/*.py 2>/dev/null
+```
+
+## Analyze Frontend (app/src/)
+
+Check for:
+- Component structure and reusability
+- Hook patterns and custom hooks
+- TypeScript strictness (no `any`, proper interfaces)
+- Performance (memo, useCallback only where truly needed)
+- Accessibility (aria-labels, keyboard navigation, focus management)
+- Consistent error handling and error boundaries
+- Loading states and skeletons
+- Unused imports and dead code
+
+```bash
+ls -la app/src/**/*.tsx app/src/**/*.ts 2>/dev/null | head -30
+```
+
+## Analyze Tests (tests/)
+
+Check for:
+- Test coverage gaps
+- Fixture organization
+- Mock patterns
+- Assertion quality
+- Test naming conventions
+
+```bash
+find tests -name "*.py" -type f | head -30
+```
+
+## Analyze GitHub Workflows (.github/workflows/)
+
+Check for:
+- Workflow consistency and naming
+- Job dependencies and parallelization
+- Secret handling and security
+- Error handling and failure modes
+- Concurrency settings
+- Reusable workflows vs duplication
+- Environment variable consistency
+- Trigger conditions (labels, paths, branches)
+
+```bash
+ls -la .github/workflows/*.yml
+```
+
+## Analyze AI Prompts (prompts/)
+
+Check for:
+- Prompt clarity and structure
+- Consistency across prompt files
+- Outdated instructions or references
+- Missing edge cases
+- Template completeness
+- Library-specific rules alignment
+
+```bash
+find prompts -name "*.md" -o -name "*.yaml" | sort
+```
+
+## Analyze Documentation (docs/)
+
+Check for:
+- Outdated information vs actual code
+- Missing documentation for new features
+- Broken internal links
+- Inconsistent formatting
+- Sync with CLAUDE.md
+
+```bash
+find docs -name "*.md" | sort
+```
+
+## Cross-Check: Consistency
+
+Verify alignment across components:
+- Do workflows reference existing prompt files?
+- Are library names consistent across `prompts/library/`, `core/constants.py`, workflows?
+- Do workflow labels match documentation?
+- Are schema definitions in sync between API and frontend types?
+
+```bash
+# Check prompt references in workflows
+grep -r "prompts/" .github/workflows/ 2>/dev/null | head -20
+
+# Library definitions
+ls prompts/library/ 2>/dev/null | sed 's/.md//' | sort
+grep -E "SUPPORTED_LIBRARIES|LIBRARIES" core/constants.py 2>/dev/null | head -5
+```
+
+## Run Test Suite
+
+```bash
+# Quick test run to check for failures
+uv run pytest tests/unit -x -q --tb=no 2>/dev/null | tail -20
+```
+
+## Output Format
+
+After analysis, provide a structured report:
+
+### 1. Critical Issues (Must Fix)
+Issues that could cause bugs, security problems, or break functionality.
+
+### 2. High Priority (Should Fix)
+Code smells, performance issues, or maintainability concerns.
+
+### 3. Medium Priority (Consider)
+Modernization opportunities, style improvements, minor inconsistencies.
+
+### 4. Low Priority (Nice to Have)
+Minor improvements, documentation updates, cosmetic changes.
+
+### 5. Positive Patterns
+Good practices found that should be maintained or expanded.
+
+For each issue, provide:
+- **Location**: File path and line number
+- **Problem**: Clear description of the issue
+- **Impact**: Why this matters
+- **Solution**: Specific fix recommendation
+- **Effort**: Low/Medium/High
+
+## Exclusions
+
+Do NOT flag:
+- Plot implementations in `plots/` (AI-generated, different style rules)
+- Generated files or lock files (`uv.lock`, `yarn.lock`, etc.)
+- Third-party code
+- Issues already tracked in pyproject.toml exclusions