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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.
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Based on SOC occupation classification
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.
| name | koopa-dotfiles |
| description | 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. |
opt/dotfiles/ is a standalone git clone of github.com/acidgenomics/dotfiles,
not a submodule of koopa. It is cloned by koopa install dotfiles and pinned at a
specific commit (blobless partial clone with partialclonefilter = blob:none).
The chezmoi source tree lives inside it at opt/dotfiles/chezmoi/. See skill
koopa-chezmoi-dotfiles for editing dotfiles via chezmoi.
koopa install pins the clone at a specific commit, leaving it in detached HEAD
state. Any git commit from a detached HEAD lands on no branch and will be
unreachable after a git checkout.
Before committing any change inside opt/dotfiles/, always check:
cd opt/dotfiles
git status # "(HEAD detached at <sha>)" means detached
git checkout main # re-attach to main before committing
Then commit normally and push to origin (github.com/acidgenomics/dotfiles).
The repo carries a single top-level LICENSE file (no extension). There are no
per-file SPDX headers or package-metadata license fields.
In June 2026 the license was switched from AGPL-3.0 to Apache-2.0, matching koopa. The Apache-2.0 text is the verbatim stock text (APPENDIX placeholders left unfilled); the README carries the attribution line:
Apache-2.0 — Copyright 2016 Acid Genomics LLC — see [LICENSE](LICENSE).
To verify no AGPL traces remain: grep -i "affero\|agpl" opt/dotfiles/LICENSE
should return nothing.