dotfiles

Acid Genomics R package development conventions — per-project air.toml, global ~/.lintr only, roxygen2 8.x @importFrom split, S4 linter tuning, AcidDevTools::check() gate. Use when writing or checking an acidgenomics R package, configuring air/lintr, or fixing roxygen/lint failures.

Diagnose and recover from common git branch/state accidents — wrong-branch reset, git alias side effects, untracked-file checkout collisions, and stash cleanup. Use when a git command moved the wrong branch pointer, a checkout was blocked by untracked files, or stash noise is showing in the prompt.

Guide for maintaining and optimizing Claude Code configuration — CLAUDE.md, rules files, hooks, and skills. Use when auditing instruction bloat, deciding where a new rule belongs, or pruning stale content.

Workflow orchestration guidance — plan mode etiquette, subagent discipline, session hygiene, and git commit conventions. Use when asked about plan mode, how to structure multi-step work, when to use subagents, or when making a git commit.

Org-mode todo.org conventions for project task tracking. Use when the user pastes a `** TODO` heading, asks about project TODOs or plans, or when deciding where to track tasks or mark work complete.

Claude Code permission system internals — protected paths, permission modes, allow/ask/deny rule precedence, and the PreToolUse permissionDecision hook contract. Use when debugging unexpected permission prompts, understanding why Edit(.claude/**) or Bash(*) allow rules have no effect on .claude/ writes, or reasoning about acceptEdits vs plan vs bypassPermissions mode tradeoffs.

Rewrite git history safely with git filter-repo. Use when removing secrets or sensitive files from commits, rewriting author/committer emails across history, de-duplicating doubled commits, or any commit-level surgery.