acidgenomics

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.

koopa R package release — cloud-native S3 + CloudFront, acidgenomics profile, koopa app r publish/reindex/archive, sonoma-arm64 binaries, pre-release AcidDevTools::check() gate. Use when releasing, publishing, reindexing, or archiving an Acid Genomics R package.

PowerShell (pwsh 7+) activation architecture, starship integration, and color-mode sync in koopa. Use when writing or debugging lang/powershell/ files, editing activate-*.ps1 functions, adding prompt-tool support (starship, zoxide), integrating OS appearance detection, or porting shell logic from bash/zsh/fish to PowerShell.

koopa AWS environment configuration — the gitignored <koopa-root>/.env, load_dotenv()/aws_account_id()/koopa_s3_bucket() helpers in aws.py, required vars, bucket naming, lazy-eval rule. Use when adding an AWS secret, wiring a bucket/CloudFront ID, or debugging a missing AWS env var in release tooling.

How koopa manages home dotfiles via chezmoi — source-of-truth layout, the explicit --source flag, template-vs-generator ordering, XDG path derivation in templates, symlink_ source files for App Support bridges, diagnosing chezmoi status contamination from stale env, and the correct re-run command. Use when editing a dotfile, working in opt/dotfiles/chezmoi/, debugging a file that reverts on chezmoi apply, wiring a chezmoi template, or bridging XDG paths to macOS Library/Application Support.

How koopa propagates and applies dark/light color mode across SSH, tmux, shells, and chezmoi-rendered theme files. Use when debugging wrong-palette or stale-theme symptoms after a dark↔light flip, working on color-mode sync jobs or watchers, editing the chezmoi color-mode apply path, or investigating why bat/starship/delta renders the wrong theme while fzf/LS_COLORS look correct.

Acid Genomics Python package release — python.acidgenomics.com PEP 503 S3+CloudFront index, koopa app python publish/reindex, quality gate, CHANGELOG format, smoke test. Use when releasing or publishing an Acid Genomics Python package.

VS Code terminal font configuration, Nerd Font glyph debugging, and Quarto/LuaLS setup for koopa. Use when debugging missing terminal glyphs (tofu), changing the VS Code terminal or editor font, understanding the App Support symlink bridge for editor settings, editing .luarc.json, or making VS Code config portable across machines.

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.