chore: linting

.serena/.gitignore

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+/cache

.serena/memories/areas_for_improvement.md

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+# Areas for Improvement
+
+## Code Quality Enhancements
+
+### 1. Configuration Management
+
+- **Inconsistent indentation**: Mixed tabs/spaces across config files
+- **Line length management**: Need consistent enforcement of limits
+- **Template standardization**: Memory files need consistent formatting template
+
+### 2. Linting Configuration Improvements
+
+- **Shellcheck exclusions**: Add proper ignore patterns for submodules
+- **EditorConfig refinement**: Some rules too strict for generated/third-party content
+- **Prettier ignore patterns**: Better exclusion of binary/generated files
+
+### 3. Testing Infrastructure
+
+- **Bats test errors**: Tests failing due to missing `rm` command in PATH
+- **Test coverage**: Limited test coverage for shell functions
+- **CI/CD integration**: Need automated linting in GitHub Actions
+
+### 4. Documentation Gaps
+
+- **Onboarding docs**: Missing clear setup instructions for new contributors
+- **Troubleshooting guide**: Need common error resolution steps
+- **Architecture overview**: Missing high-level system architecture
+
+## Performance & Maintenance
+
+### 5. Submodule Management
+
+- **Large submodules**: Some submodules contain unnecessary files
+- **Update frequency**: Need systematic submodule update process
+- **Dependency tracking**: Better documentation of submodule purposes
+
+### 6. Cross-Platform Considerations
+
+- **Darwin-specific paths**: Some hardcoded macOS paths could be parameterized
+- **Shell compatibility**: More testing across bash/zsh/fish environments
+- **Tool availability**: Better fallbacks when optional tools missing
+
+### 7. Security & Privacy
+
+- **Secret management**: Better examples for secret configuration
+- **Permission handling**: Some scripts could use more restrictive permissions
+- **Audit trail**: Track configuration changes and their impact
+
+## Development Workflow
+
+### 8. Automation Opportunities
+
+- **Auto-formatting**: Pre-commit hooks for consistent formatting
+- **Dependency updates**: Automated updates for package.json dependencies
+- **Health checks**: Scripts to validate configuration integrity
+
+### 9. Error Handling
+
+- **Graceful degradation**: Better fallbacks when tools unavailable
+- **Error messages**: More informative error output
+- **Recovery procedures**: Automated recovery from common failures
+
+### 10. Modularity
+
+- **Configuration splitting**: Some large config files could be modularized
+- **Feature flags**: Optional components for minimal installations
+- **Host-specific configs**: Better organization of machine-specific settings

.serena/memories/code_style_conventions.md

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+# Code Style and Conventions
+
+## EditorConfig Rules (.editorconfig)
+
+- **Charset**: UTF-8
+- **Line endings**: LF
+- **Indent style**: Spaces (except for specific files)
+- **Indent size**: 2 spaces (default)
+- **Final newline**: Required
+- **Trailing whitespace**: Trimmed
+
+### Language-specific Rules
+
+- **Fish scripts**: 4-space indent, 80 char line limit
+- **PHP files**: 4-space indent
+- **Markdown**: 120 char line limit
+- **Lua**: 90 char line limit
+- **Git files**: Tab indentation
+- **Shell scripts**: 2-space indent with specific shfmt settings
+
+## Prettier Configuration
+
+- Extends `@ivuorinen/prettier-config`
+- **Trailing commas**: Always
+- **Markdown**: 120 char width, preserve prose wrapping
+
+## ESLint Configuration
+
+- Extends `@ivuorinen` base configuration
+- Applied to JavaScript/TypeScript files
+
+## Shell Script Standards (.shellcheckrc)
+
+- External sources following enabled
+- Disabled checks: SC2039, SC2166, SC2154, SC1091, SC2174, SC2016
+- Must include shebang or `# shellcheck shell=bash`
+
+## Formatting Tools
+
+- **Shell scripts**: shfmt with specific rules
+- **Markdown**: markdownlint + prettier
+- **JavaScript/TypeScript**: prettier + eslint
+- **YAML**: yamllint
+
+## Naming Conventions
+
+- **Shell functions**: Use `x-` prefix for cross-shell compatibility
+- **Environment variables**: UPPERCASE with underscores
+- **File names**: lowercase with hyphens for scripts
+- **Directory structure**: lowercase, organized by tool/purpose

.serena/memories/critical_linting_errors.md

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+# Critical Linting Errors That Must Be Fixed
+
+## Current Status: BLOCKING Issues Identified
+
+The linting system has revealed 150+ violations across multiple categories that must be addressed immediately.
+
+## EditorConfig Violations (High Priority)
+
+### Missing Final Newlines
+
+- All `.serena/memories/*.md` files missing final newlines
+- Multiple project configuration files affected
+- This is a BLOCKING issue per user instructions
+
+### Line Length Violations
+
+- Fish shell configs exceed 80-character limit (`.editorconfig` enforced)
+- Memory files have lines exceeding 120-character limit
+- WezTerm configuration files have long lines
+
+### Indentation Errors
+
+- Git configuration using tabs instead of spaces
+- WezTerm color scheme files using tabs vs spaces
+- Perl scripts with inconsistent indentation
+
+## Markdownlint Issues (Memory Files)
+
+### Systematic Problems Across All Memory Files
+
+- Missing blank lines around headings (MD022)
+- Lists not surrounded by blank lines (MD032)
+- Fenced code blocks not surrounded by blank lines (MD031)
+- Trailing punctuation in headings (MD026)
+- Missing language specification for fenced code blocks (MD040)
+- Missing final newlines (MD047)
+
+### Specific Files Affected
+
+- `areas_for_improvement.md`: 20+ violations
+- `code_style_conventions.md`: 15+ violations
+- `critical_linting_errors.md`: 25+ violations
+- `darwin_system_utilities.md`: 15+ violations
+- `immediate_action_items.md`: 25+ violations
+- `project_overview.md`: 15+ violations
+- `project_structure.md`: 20+ violations
+- `shellcheck_issues.md`: 15+ violations
+- `suggested_commands.md`: 25+ violations
+- `task_completion_checklist.md`: 10+ violations
+
+## Prettier Formatting Issues
+
+### JSON Configuration Files
+
+- `.commitlintrc.json`, `.eslintrc.json`, `.luarc.json`
+- `.releaserc.json`, `.github/renovate.json`
+- Host-specific configurations in `config/` directory
+
+### YAML Files
+
+- `.mega-linter.yml` formatting inconsistencies
+- Various configuration files needing formatting
+
+## Immediate Action Required
+
+1. **Fix memory files**: Apply markdown formatting rules
+2. **Run auto-fixers**: `yarn fix` to address automatic fixes
+3. **Manual corrections**: Address remaining EditorConfig violations
+4. **Validation**: Ensure `yarn lint` passes completely
+
+## Impact Assessment
+
+These violations prevent:
+
+- Successful CI/CD pipeline execution
+- Code quality standards compliance
+- Pre-commit hook success
+- Project maintainability standards
+
+Per user instructions: "Linting issues ARE NOT ACCEPTABLE" and "EditorConfig problems are blocking errors"

.serena/memories/darwin_system_utilities.md

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+# Darwin (macOS) System Utilities
+
+## Available Command Paths
+
+Based on the current system setup:
+
+### Core System Commands
+
+- `git`: `/opt/homebrew/bin/git` (Homebrew version)
+- `find`: `/usr/bin/find` (system version)
+- `cd`: shell built-in command
+- `ls`: aliased to `eza -h -s=type --git --icons --group-directories-first`
+- `grep`: aliased to `grep --color`
+
+### Modern Alternatives (Rust-based)
+
+- `fd`: `/Users/ivuorinen/.local/share/cargo/bin/fd` (modern find)
+- `rg`: `/Users/ivuorinen/.local/share/cargo/bin/rg` (ripgrep for text search)
+
+## Recommended Usage Patterns
+
+### File Search
+
+```bash
+# Use fd instead of find when possible
+fd "*.sh"                    # Find shell scripts
+fd -t f -e lua              # Find Lua files
+find . -name "*.sh"         # Fallback to system find
+```
+
+### Text Search
+
+```bash
+# Use rg (ripgrep) instead of grep when possible
+rg "function.*bash"         # Search for bash functions
+rg -t shell "export"        # Search in shell files only
+grep "pattern" file.txt     # Fallback to system grep
+```
+
+### Directory Navigation
+
+```bash
+# Use eza features via ls alias
+ls                          # Shows icons, git status, grouped directories
+ls -la                      # Long format with hidden files
+cd /full/path               # Always use full paths in scripts
+```
+
+## Path Configuration
+
+The system is configured with these PATH priorities:
+
+1. `~/.local/bin` (user scripts)
+2. `~/.dotfiles/local/bin` (dotfiles scripts)
+3. `~/.local/share/bob/nvim-bin` (Neovim)
+4. `~/.local/share/cargo/bin` (Rust tools like fd, rg)
+5. `/opt/homebrew/bin` (Homebrew packages)
+6. `/usr/local/bin` (system packages)
+
+## Shell Compatibility
+
+The dotfiles support multiple shells through `config/shared.sh`:
+
+- Functions prefixed with `x-` work across bash, zsh, and fish
+- Path management handled automatically per shell
+- Environment variables set appropriately per shell

.serena/memories/immediate_action_items.md

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+# Immediate Action Items - Priority Order
+
+## HIGH PRIORITY (Must Fix Before Any Development)
+
+### 1. Fix Memory File Formatting (BLOCKING)
+
+```bash
+# These files prevent any linting from passing:
+- .serena/memories/code_style_conventions.md
+- .serena/memories/darwin_system_utilities.md
+- .serena/memories/project_overview.md
+- .serena/memories/project_structure.md
+- .serena/memories/suggested_commands.md
+- .serena/memories/task_completion_checklist.md
+
+# Issues: Missing final newlines, markdown formatting, line length
+# Impact: Blocks all linting commands
+```
+
+### 2. Fix Fish Shell Line Length Violations (BLOCKING)
+
+```bash
+# Files exceeding 80-char limit:
+config/fish/alias.fish (4 violations)
+config/fish/exports.fish (15 violations)
+
+# These are CRITICAL - Fish config has strict limits
+# Must be fixed before any fish-related changes
+```
+
+### 3. Fix Git Configuration Indentation (BLOCKING)
+
+```bash
+# Files with tab/space mixing:
+config/git/shared (40+ violations)
+hosts/s/config/git/overrides/config
+hosts/s/config/git/local.d/work-git
+
+# Impact: Git configuration may not work correctly
+```
+
+## MEDIUM PRIORITY (Fix During Next Development Cycle)
+
+### 4. Prettier Formatting Issues
+
+```bash
+# 17 files need prettier formatting:
+yarn fix:prettier
+# Most are JSON/YAML configuration files
+```
+
+### 5. WezTerm Color Scheme Indentation
+
+```bash
+# All files in config/wezterm/colors/ using tabs instead of spaces
+# Affects terminal appearance configuration
+```
+
+### 6. Update Linting Configuration
+
+```bash
+# Add shellcheck exclusions for submodules:
+# - tools/antidote/
+# - config/tmux/plugins/
+# - config/vim/extra/fzf/
+# - config/cheat/cheatsheets/tldr/
+```
+
+## LOW PRIORITY (Future Improvements)
+
+### 7. Test Infrastructure
+
+```bash
+# Fix bats test PATH issues
+# Tests pass but show rm command not found errors
+```
+
+### 8. Documentation Updates
+
+```bash
+# Add troubleshooting section to AGENTS.md
+# Create shellcheck exclusion documentation
+```
+
+## Immediate Commands to Run
+
+### Step 1: Auto-fix What's Possible
+
+```bash
+yarn fix:prettier    # Fix 17 files
+yarn fix:markdown    # Attempt markdown fixes
+```
+
+### Step 2: Manual Fixes Required
+
+- Add final newlines to all memory files
+- Wrap long lines in Fish configuration files
+- Convert tabs to spaces in Git configuration files
+
+### Step 3: Verify Progress
+
+```bash
+yarn lint:ec         # Check EditorConfig compliance
+yarn lint:markdown   # Check markdown issues
+yarn lint:prettier   # Check remaining prettier issues
+```
+
+## Success Criteria
+
+✅ `yarn lint` passes without errors
+✅ All EditorConfig violations resolved
+✅ Memory files properly formatted
+✅ Fish configuration under line limits
+✅ Git configuration uses consistent indentation

.serena/memories/project_overview.md

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+# .dotfiles Project Overview
+
+## Purpose
+
+This is a comprehensive personal dotfiles repository for managing development
+environment configurations across macOS systems. The project uses **Dotbot** as
+the primary installation framework to manage symlinks and setup configurations.
+
+## Key Features
+
+- Automated configuration management using Dotbot
+- Support for multiple development tools and applications
+- Host-specific configurations in `/hosts/` directory
+- Comprehensive testing and linting setup with pre-commit hooks
+- Cross-shell compatibility (bash, zsh, fish)
+- Large collection of custom utility scripts in `local/bin/`
+- Git submodules for external tools (dotbot, antidote, tmux plugins)
+- Environment-specific configurations (secrets management)
+
+## Recent Notable Changes (from git status)
+
+- New everforest color theme configurations added
+- Multiple temporary fish configuration files present
+- Updates to various configuration files (.commitlintrc.json, .eslintrc.json, etc.)
+- New x-pr-comments script and documentation added
+- Various tmux plugin updates
+- Husky configuration relocated from base/ to config/husky/
+
+## Tech Stack
+
+- **Shell**: Bash (primary), with Fish and Zsh support
+- **Configuration Manager**: Dotbot with plugins (asdf, brew, include, pip)
+- **Package Manager**: Yarn 1.22.22 (Node.js), Homebrew (macOS), pipx (Python)
+- **Testing**: Bats test framework, custom test-all.sh script
+- **Linting**: MegaLinter, Prettier, ESLint, Markdownlint, ShellCheck, EditorConfig
+- **Automation**: Pre-commit hooks, GitHub Actions, Renovate
+
+## Project Structure Highlights
+
+- `/config/` - Main configuration directory (74+ subdirectories)
+- `/local/bin/` - Custom utility scripts (100+ scripts with documentation)
+- `/hosts/` - Host-specific configurations
+- `/tools/` - Git submodules for external tools
+- `/base/` - Base configuration files
+- `/secrets/` - Secret management configurations
+- `/scripts/` - Installation and setup scripts
+- `/.github/` - GitHub Actions workflows and configurations
+
+## Target System
+
+- **Platform**: Darwin (macOS) - Version 24.6.0
+- **Architecture**: Universal (Intel/Apple Silicon via Homebrew)
+- **Dependencies**: Git, Homebrew, Yarn, various CLI tools managed via asdf/aqua
+
+## Development Environment
+
+- Node.js managed via nvm/asdf
+- Go version specified (.go-version)
+- Python version specified (.python-version)
+- Package management via Yarn with lockfile
+- TypeScript support for configuration files

.serena/memories/project_structure.md

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+# Project Structure
+
+## Root Directory
+
+```text
+.dotfiles/
+├── install                 # Main installation script (Dotbot runner)
+├── install.conf.yaml      # Dotbot configuration
+├── package.json           # Node.js dependencies for linting/testing (Yarn managed)
+├── AGENTS.md              # Project documentation and guidelines
+├── test-all.sh            # Bats test runner
+├── add-submodules.sh      # Git submodule management
+└── .serena/               # Claude Code/Serena analysis cache (new)
+```
+
+## Main Directories
+
+### `config/` (74+ subdirectories)
+
+Configuration files for development tools and applications:
+
+- `git/` - Git configuration with delta integration and everforest theme
+- `nvim/` - Neovim configuration with Lua plugins
+- `tmux/` - Tmux configuration with multiple plugins (dark-notify, window-name, etc.)
+- `fish/` - Fish shell configuration with completions and functions
+- `zsh/` - Zsh configuration with antidote plugin manager
+- `fzf/` - Fuzzy finder configuration with everforest theme
+- `wezterm/` - WezTerm terminal configuration
+- `homebrew/` - Homebrew environment configuration
+- `starship.toml` - Starship prompt configuration
+- `shared.sh` - Cross-shell compatibility functions
+- `aerospace/`, `amethyst/`, `yabai/`, `skhd/` - Window managers
+- `direnv/`, `asdf/`, `aqua/` - Development environment tools
+- `gpg-tui/`, `op/`, `gh/` - Security and CLI tools
+- Theme configurations: everforest color schemes across multiple tools
+
+### `base/`
+
+Dotfiles that get symlinked to home directory with `.` prefix:
+
+- Contains traditional dotfiles like `.bashrc`, `.zshrc`, etc.
+- `plan` - Planning/note-taking configuration
+- `shellcheckrc` - ShellCheck rules
+
+### `local/`
+
+- `bin/` - 100+ custom scripts with comprehensive documentation
+  - Homegrown utilities (dfm, git tools, backup scripts, etc.)
+  - Sourced utilities (from skx/sysadmin-util, mvdan/dotfiles)
+  - Each script has corresponding .md documentation
+  - Recent additions: x-pr-comments for GitHub PR analysis
+- `share/fonts/` - JetBrains Mono font files
+- `man/` - Manual pages
+
+### `ssh/`
+
+SSH configuration files (mode 0600/0700)
+
+- `shared.d/` - Shared SSH configurations for specific hosts
+
+### `tools/` (Git submodules)
+
+External tools and Dotbot plugins:
+
+- `dotbot/` - Dotbot installation framework
+- `dotbot-*` - Dotbot plugins (asdf, brew, include, pip)
+- `antidote/` - Zsh plugin manager
+- Various tmux plugins (continuum, resurrect, yank, etc.)
+
+### `hosts/`
+
+Host-specific configurations:
+
+- `air/`, `s/`, `v/` - Individual host configurations
+- Applied after main configuration
+
+### `secrets/`
+
+Secret and credential management configuration
+
+### `scripts/`
+
+Installation and setup automation scripts
+
+### `.github/`
+
+- GitHub Actions workflows
+- Renovate configuration
+- Issue templates and documentation
+
+### Development Configuration Files
+
+- `.editorconfig` - Editor configuration rules
+- `.prettierrc.js` - Prettier formatting rules
+- `.eslintrc.json` - ESLint linting rules
+- `.commitlintrc.json` - Commit message linting
+- `.shellcheckrc` - ShellCheck configuration
+- `.mega-linter.yml` - MegaLinter configuration
+- `.luarc.json` - Lua language server configuration
+- `.nvmrc`, `.go-version`, `.python-version` - Version management
+- Various ignore files (.gitignore, .prettierignore, .yamlignore, etc.)
+
+## Testing Infrastructure
+
+- `tests/` - Bats test files
+- `test-all.sh` - Main test runner
+- Pre-commit hooks for automated testing
+- GitHub Actions for CI/CD
+
+## Recent Structural Changes
+
+- Husky configuration moved from `base/huskyrc` to `config/husky/init.sh`
+- Addition of everforest theme configurations across multiple tools
+- New .serena directory for AI analysis caching
+- Multiple temporary fish configuration files (everforest themes)
+- Enhanced git configuration with delta and everforest theming

.serena/memories/shellcheck_issues.md

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+# ShellCheck Issues Analysis
+
+## Critical Shell Script Problems
+
+### Missing Shebangs (SC2148)
+
+Multiple shell scripts missing proper shebang lines:
+
+- `tools/antidote/tests/` - Test scripts
+- `config/vim/*/test/lib/common.sh` - FZF test libraries
+- `config/tmux/plugins/*/scripts/helpers.sh` - Plugin helper scripts
+- Various submodule scripts
+
+### Syntax Errors (SC1036, SC1088, SC1073)
+
+- `config/vim/fzf/test/lib/common.sh` - Invalid ERB template syntax
+- `config/cheat/cheatsheets/tldr/` - Markdown files incorrectly parsed as shell
+- `tmux-sessionist/scripts/list_sessions.sh` - Brace parsing errors
+
+### Variable Assignment Issues (SC1007, SC2155)
+
+- `config/vim/extra/fzf/test/lib/common.sh` - Incorrect empty variable assignments
+- Multiple tmux plugin scripts - Declare and assign should be separate
+
+### Quoting Problems (SC2086, SC2006)
+
+- Unquoted variable expansions in tmux plugin scripts
+- Legacy backtick usage instead of $(...) syntax
+- Missing quotes around variable expansions
+
+## Third-Party Code Issues
+
+### Submodule Problems
+
+Most shellcheck errors are in **third-party submodules**:
+
+- `tools/antidote/` - Zsh plugin manager
+- `config/tmux/plugins/` - Tmux plugins
+- `config/vim/extra/fzf/` - FZF integration
+- `config/cheat/cheatsheets/tldr/` - Cheat sheet collection
+
+### Recommendation
+
+- These should be **excluded from shellcheck** via configuration
+- Focus linting only on **project-owned scripts**
+- Add shellcheck ignore patterns for submodule directories
+
+## Project-Owned Script Issues
+
+### Main Scripts Status
+
+- `install` - ✅ Clean (no shellcheck errors)
+- `test-all.sh` - ✅ Clean
+- `add-submodules.sh` - ✅ Clean
+- `config/shared.sh` - ✅ Clean
+- Scripts in `local/bin/` - ✅ Mostly clean
+
+### Minor Issues Found
+
+- Some scripts could benefit from stricter quoting
+- Consistent shebang usage across all scripts
+- Consider adding `set -euo pipefail` to more scripts

.serena/memories/suggested_commands.md

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+# Essential Commands for .dotfiles Development
+
+## Installation & Setup
+
+```bash
+# Initial setup - install linting tools and dependencies
+yarn install
+
+# Install/update all dotfiles configurations
+./install
+
+# Update git submodules (multiple approaches)
+git submodule update --remote --merge
+git submodule update --init --recursive --force
+bash add-submodules.sh
+```
+
+## Development Commands
+
+```bash
+# Linting (run all linters - ALWAYS fix all issues)
+yarn lint
+
+# Individual linting commands
+yarn lint:markdown    # Markdownlint
+yarn lint:prettier    # Prettier check
+yarn lint:ec          # EditorConfig checker
+
+# Auto-fixing (use these BEFORE manual linting)
+yarn fix              # Fix all format issues
+yarn fix:markdown     # Fix markdown formatting
+yarn fix:prettier     # Fix prettier formatting
+
+# Testing
+yarn test             # Run all Bats tests
+bash test-all.sh      # Alternative test runner
+```
+
+## Pre-commit Hooks (Comprehensive)
+
+Current pre-commit configuration includes:
+
+- **Security**: detect-aws-credentials, detect-private-key
+- **File integrity**: check-case-conflict, check-merge-conflict, check-symlinks
+- **Shell scripts**: shellcheck, shfmt (formatting)
+- **YAML/JSON**: yamllint, check-yaml, check-toml, pretty-format-json
+- **Markdown**: markdownlint with auto-fix
+- **Lua**: stylua formatting for Neovim configs
+- **Fish**: fish_syntax, fish_indent for shell configs
+- **GitHub Actions**: actionlint validation
+- **Renovate**: renovate-config-validator
+- **General**: trailing-whitespace, end-of-file-fixer, mixed-line-ending
+
+```bash
+# Run pre-commit manually
+pre-commit run --all-files
+```
+
+## Version Management
+
+```bash
+# Check current versions
+node --version        # Managed by nvm (.nvmrc: v20.18.1)
+go version           # Managed by asdf (.go-version)
+python --version     # Managed by asdf (.python-version)
+```
+
+## System Utilities (Darwin-specific)
+
+```bash
+# Modern CLI tools available
+ls                   # aliased to eza with icons and git info
+grep                 # aliased to grep --color
+fd pattern           # modern find alternative
+rg pattern           # ripgrep for text search
+bat file            # modern cat with syntax highlighting
+```
+
+## Project-specific Scripts (100+ available)
+
+```bash
+# Dotfiles management
+bash local/bin/dfm install all
+
+# Git utilities
+git-dirty            # Check for dirty git repositories
+git-fsck-dirs        # Run fsck on git directories
+git-update-dirs      # Update multiple git directories
+
+# Development utilities
+x-pr-comments <pr>   # Analyze GitHub PR comments (NEW)
+x-set-php-aliases    # Generate PHP version aliases
+x-env-list          # List environment variables
+x-open-ports        # Check open network ports
+
+# Backup utilities
+x-backup-folder     # Backup directories
+x-backup-mysql-with-prefix  # MySQL backup with prefix
+```
+
+## Configuration Management
+
+```bash
+# Load shell configurations
+source config/shared.sh      # Cross-shell compatibility functions
+source x-set-php-aliases     # PHP version management
+
+# Host-specific configurations
+# Automatically applied: hosts/{hostname}/
+```
+
+## Quality Assurance (CRITICAL)
+
+**All linting errors are BLOCKING and must be fixed:**
+
+- EditorConfig violations are considered blocking errors
+- ShellCheck warnings must be addressed
+- Prettier formatting must be consistent
+- Markdownlint rules must be followed
+- NEVER use --no-verify with git operations
+- ALWAYS run autofixers before manual intervention

.serena/memories/task_completion_checklist.md

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+# Task Completion Checklist
+
+When completing any development task in this dotfiles repository, follow this
+checklist to ensure compliance with project standards.
+
+## Required Steps (BLOCKING)
+
+### 1. Code Quality Checks
+
+```bash
+# Run all linting tools - MUST PASS with zero errors
+yarn lint
+
+# Individual checks if needed:
+yarn lint:markdown    # Markdownlint validation
+yarn lint:prettier    # Prettier formatting check
+yarn lint:ec          # EditorConfig compliance verification
+```
+
+### 2. Shell Script Validation (if applicable)
+
+```bash
+# All shell scripts must pass shellcheck without warnings
+find . -path ./node_modules -prune -o -name '*.sh' -print0 | xargs -0 shellcheck
+
+# For individual scripts:
+shellcheck path/to/script.sh
+```
+
+### 3. Testing Infrastructure
+
+```bash
+# Run all tests - MUST PASS completely
+yarn test
+# OR alternative runner
+bash test-all.sh
+
+# For specific test categories:
+# Bats tests in tests/ directory
+# Individual script functionality tests
+```
+
+### 4. EditorConfig Compliance (CRITICAL)
+
+- **BLOCKING REQUIREMENT**: EditorConfig violations prevent completion
+- All code must follow `.editorconfig` rules exactly:
+  - UTF-8 charset
+  - LF line endings
+  - Final newline required
+  - Trailing whitespace removal
+  - Language-specific indentation (2-space default, 4-space for Fish)
+- Use autofixers before attempting manual fixes
+- Never modify linting configuration to bypass errors
+
+## Auto-fixing Protocol
+
+```bash
+# ALWAYS run auto-fixers first, in this order:
+yarn fix              # Fix all auto-fixable issues
+yarn fix:markdown     # Fix markdown formatting violations
+yarn fix:prettier     # Fix code formatting issues
+
+# Verify fixes applied correctly:
+yarn lint             # Should show reduced error count
+```
+
+## Pre-commit Hook Integration
+
+Current pre-commit configuration enforces:
+
+- Security checks (credentials, private keys)
+- Shell script validation (shellcheck, shfmt)
+- Markdown formatting (markdownlint with auto-fix)
+- YAML/JSON validation and formatting
+- Lua formatting (stylua for Neovim configs)
+- Fish shell syntax validation
+- GitHub Actions validation (actionlint)
+- Renovate configuration validation
+
+## Memory File Maintenance
+
+When updating memory files:
+
+1. Follow markdown best practices (blank lines around headings/lists)
+2. Specify language for fenced code blocks
+3. Ensure final newline exists
+4. Respect line length limits (120 chars for markdown)
+5. Use proper heading hierarchy
+
+## Critical Success Criteria
+
+✅ **REQUIRED FOR TASK COMPLETION:**
+
+- `yarn lint` exits with code 0 (no errors)
+- `yarn test` passes all test suites
+- EditorConfig compliance verified
+- No trailing whitespace or missing final newlines
+- Shell scripts have proper shebangs and pass shellcheck
+- All temporary/cache files cleaned up
+
+❌ **BLOCKING ISSUES:**
+
+- Any linting errors or warnings
+- EditorConfig violations of any kind
+- Test failures or incomplete test coverage
+- Use of `--no-verify` flag with git operations
+- Modified linting configurations to bypass errors
+
+## Quality Assurance Notes
+
+- **Use `which command`** to get full paths in scripts
+- **Prefer modern tools**: `rg` over `grep`, `fd` over `find`, `bat` over `cat`
+- **Test cross-shell compatibility**: bash, zsh, fish
+- **Validate host-specific configurations** don't break general setup
+- **Document any new utilities** in `local/bin/README.md`

.serena/project.yml

@@ -0,0 +1,90 @@
+# language of the project (csharp, python, rust, java, typescript, go, cpp, or ruby)
+#  * For C, use cpp
+#  * For JavaScript, use typescript
+# Special requirements:
+#  * csharp: Requires the presence of a .sln file in the project folder.
+language: bash
+
+# whether to use the project's gitignore file to ignore files
+# Added on 2025-04-07
+ignore_all_files_in_gitignore: true
+# list of additional paths to ignore
+# same syntax as gitignore, so you can use * and **
+# Was previously called `ignored_dirs`, please update your config if you are using that.
+# Added (renamed) on 2025-04-07
+ignored_paths:
+  - '*.swp'
+  - '*.tmp'
+  - '*.tmp.*'
+  - '.DS_Store'
+  - '.git/**'
+  - /config/cheat/cheatsheets/community/**
+  - /config/cheat/cheatsheets/pure-bash-bible/**
+  - /config/cheat/cheatsheets/tldr/**
+  - /config/fish/cheatsheets/community/**
+  - /config/fzf/**
+  - /config/nvim/snippets/**
+  - /config/nvim/spell/**
+  - /config/op/plugins/**
+  - /config/tmux/plugins/**
+  - /config/vim/extra/**
+  - /config/zsh/completions/**
+  - /config/zsh/plugins/**
+  - /local/man/fzf
+  - /local/share/fonts
+  - /tools/antidote
+  - /tools/dotbot
+  - /tools/dotbot-*/**
+  - node_modules/**
+
+# whether the project is in read-only mode
+# If set to true, all editing tools will be disabled and attempts to use them will result in an error
+# Added on 2025-04-18
+read_only: false
+
+# list of tool names to exclude. We recommend not excluding any tools, see the readme for more details.
+# Below is the complete list of tools for convenience.
+# To make sure you have the latest list of tools, and to view their descriptions,
+# execute `uv run scripts/print_tool_overview.py`.
+#
+#  * `activate_project`: Activates a project by name.
+#  * `check_onboarding_performed`: Checks whether project onboarding was already performed.
+#  * `create_text_file`: Creates/overwrites a file in the project directory.
+#  * `delete_lines`: Deletes a range of lines within a file.
+#  * `delete_memory`: Deletes a memory from Serena's project-specific memory store.
+#  * `execute_shell_command`: Executes a shell command.
+#  * `find_referencing_code_snippets`: Finds code snippets in which the symbol at the given location is referenced.
+#  * `find_referencing_symbols`: Finds symbols that reference the symbol at the given location (optionally filtered by type).
+#  * `find_symbol`: Performs a global (or local) search for symbols with/containing a given name/substring (optionally filtered by type).
+#  * `get_current_config`: Prints the current configuration of the agent, including the active and available projects, tools, contexts, and modes.
+#  * `get_symbols_overview`: Gets an overview of the top-level symbols defined in a given file.
+#  * `initial_instructions`: Gets the initial instructions for the current project.
+#     Should only be used in settings where the system prompt cannot be set,
+#     e.g. in clients you have no control over, like Claude Desktop.
+#  * `insert_after_symbol`: Inserts content after the end of the definition of a given symbol.
+#  * `insert_at_line`: Inserts content at a given line in a file.
+#  * `insert_before_symbol`: Inserts content before the beginning of the definition of a given symbol.
+#  * `list_dir`: Lists files and directories in the given directory (optionally with recursion).
+#  * `list_memories`: Lists memories in Serena's project-specific memory store.
+#  * `onboarding`: Performs onboarding (identifying the project structure and essential tasks, e.g. for testing or building).
+#  * `prepare_for_new_conversation`: Provides instructions for preparing for a new conversation (in order to continue with the necessary context).
+#  * `read_file`: Reads a file within the project directory.
+#  * `read_memory`: Reads the memory with the given name from Serena's project-specific memory store.
+#  * `remove_project`: Removes a project from the Serena configuration.
+#  * `replace_lines`: Replaces a range of lines within a file with new content.
+#  * `replace_symbol_body`: Replaces the full definition of a symbol.
+#  * `restart_language_server`: Restarts the language server, may be necessary when edits not through Serena happen.
+#  * `search_for_pattern`: Performs a search for a pattern in the project.
+#  * `summarize_changes`: Provides instructions for summarizing the changes made to the codebase.
+#  * `switch_modes`: Activates modes by providing a list of their names
+#  * `think_about_collected_information`: Thinking tool for pondering the completeness of collected information.
+#  * `think_about_task_adherence`: Thinking tool for determining whether the agent is still on track with the current task.
+#  * `think_about_whether_you_are_done`: Thinking tool for determining whether the task is truly completed.
+#  * `write_memory`: Writes a named memory (for future reference) to Serena's project-specific memory store.
+excluded_tools: []
+
+# initial prompt for the project. It will always be given to the LLM upon activating the project
+# (contrary to the memories, which are loaded on demand).
+initial_prompt: ''
+
+project_name: '.dotfiles'