koopa

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.

Apache-2.0 LICENSE file conventions (Acid Genomics) — canonical sources per repo type, how GitHub licensee detection works (>=98% match), corruption history, badge wiring. Use when adding or repairing a LICENSE file or a repo shows NOASSERTION.

koopa command syntax, app.json registry semantics, tool-inclusion scope, and installer/version-check machinery. Use when composing koopa commands, reasoning about successor/default/completions semantics, importing atuin history, deciding whether a tool belongs in koopa, writing a new installer, or wiring auto-update for apps with non-version metadata (build IDs, per-platform hashes).

How `koopa update` works end to end — the pull→apps→system-apps sequence and the admin-gated automatic system updates (Homebrew, system R/Python, TeX). Use when reasoning about what `koopa update` does, why system updates run (or silently skip) on macOS, the is_admin() gate vs has_sudo(), the "System R is out of date" warning, or the update-system platform matrix. For update_koopa() git merge/rebase recovery see koopa-shell-internals.

Internals of koopa shell activation and update recovery. Use when optimizing shell startup, editing activation-path functions, caching plugin init output, debugging lazy-load wrappers, or fixing update_koopa() merge/rebase recovery.

koopa shell completion architecture — generator, flag extraction, bash/zsh/PowerShell/elvish emitters, lazy-load mechanism, compdump freshness, and known bug patterns. Use when debugging missing completions, editing generate_completion.py, or adding flags to a CLI handler that need to appear in TAB completion.

Notable git features and flags introduced in git 2.55 — new builtins (history, format-rev, url-parse), checkout -m autostash, config set advice, --graph-lane-limit, push to remote groups, --max-count-oldest, Linux fsmonitor. Use when reaching for a recent git command/flag, or unsure whether a 2.55 feature exists. For koopa's PR/tag/release workflow use koopa-git; for history rewriting use git-history-surgery.

koopa git workflow — develop→main PR pattern, merge conflict resolution, tag management, and how to avoid rebase hell. Use when dealing with PR conflicts, moving tags, or pushing a release branch.

Reference for koopa theme synthesis across editors and terminals — Dracula Pro runtime pipeline, fish color architecture (fish_frozen_theme.fish override, _FISH_COLOR_ROLES generator, live sync hook), JetBrains/IntelliJ scheme delivery, atuin and mcfly color config, and macOS sandboxed-app theme installation. Use when generating or fixing editor/terminal color schemes, debugging a theme that renders incorrectly, or writing theme-install code. For the "never hardcode Pro hex" guardrail see the path-scoped theme-colors rule.

Google AI CLI installer management for koopa — Antigravity CLI (agy) and Gemini CLI transition, versioned GCS download mechanics, self-update gate, manifest structure, and settings.json config path. Use when bumping the antigravity-cli version, debugging the installer, or managing the gemini-cli successor relationship.

koopa release procedure — CHANGELOG authoring, bumpver contract, pre-release gate, and what stays with the user. Use when preparing a release, writing release notes, or understanding what "prepare the release" entails.

Managing the opt/dotfiles standalone git clone — git state, committing changes, and license/metadata updates. Use when making changes to opt/dotfiles/ that need to be committed, or when the clone is in a detached HEAD state.

atuin configuration, bash hook architecture, installer patterns, and DB maintenance for koopa. Use when debugging atuin history recording, editing activation functions, working on the bash-preexec dependency, or resetting the atuin database.

Nushell (nu) pitfalls, parse-time constraints, and koopa activation architecture. Use when writing or debugging .nu files, editing lang/nushell/include/header.nu or any activate-*.nu, sourcing prompt tools (starship, zoxide), or porting shell logic from bash/zsh/fish to nushell.

Elvish shell programming pitfalls, namespace semantics, and koopa activation architecture. Use when writing or debugging .elv files, editing lang/elvish/include/header.elv or any activate-*.elv, or porting shell logic from bash/zsh to elvish.