AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
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Sync local skills repository with upstream changes from obra/superpowers-skills
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See how to installReview the instructions the agent will receive before you install.
Pull and merge upstream changes from obra/superpowers-skills into your local skills repository while preserving your personal modifications.
Announce at start: "I'm using the Updating Skills skill to sync with upstream."
Your skills repo must have a tracking branch configured. The plugin sets this up automatically (either as a fork with origin remote, or with an upstream remote).
Run:
cd ~/.config/superpowers/skills
git status
If working directory is dirty: Proceed to Step 2 (stash changes) If clean: Skip to Step 3
Run:
git stash push -m "Temporary stash before upstream update"
Record: Whether changes were stashed (you'll need to unstash later)
First, detect which remote to use:
TRACKING_REMOTE=$(git rev-parse --abbrev-ref --symbolic-full-name @{u} 2>/dev/null | cut -d'/' -f1 || echo "")
Then fetch from the appropriate remote:
if [ -n "$TRACKING_REMOTE" ]; then
git fetch "$TRACKING_REMOTE" 2>/dev/null || true
else
git fetch upstream 2>/dev/null || git fetch origin 2>/dev/null || true
fi
Expected: Fetches latest commits from the tracking remote (or falls back to upstream/origin)
Run:
git log HEAD..@{u} --oneline
Show user: List of new commits being pulled
Note: @{u} refers to the upstream tracking branch for your current branch
First, try a fast-forward merge (cleanest option):
git merge --ff-only @{u}
If fast-forward succeeds: Skip to Step 7 (no conflicts possible with fast-forward) If fast-forward fails: Your branch has diverged. Try regular merge:
git merge @{u}
If merge succeeds cleanly: Proceed to Step 7 If conflicts occur: Proceed to conflict resolution
If conflicts:
git status to see conflicted filesgit add <resolved-file> for eachgit commit to complete mergeIf you stashed changes:
git stash pop
If conflicts with unstashed changes: Help user resolve them
Run:
../using-skills/find-skills
Expected: Skills list displays correctly
Tell user:
"Already up to date": Your local repo is current, no action needed
"fatal: no upstream configured": Your branch isn't tracking a remote branch. Check git remote -v to see available remotes, then set tracking with git branch --set-upstream-to=<remote>/<branch>
Detached HEAD: You're not on a branch. Ask user if they want to create a branch or check out main.
Fast-forward fails, diverged branches: Your local branch has commits that aren't in the remote. Regular merge will be needed, which may cause conflicts.
This skill is written to stay usable across GitHub Copilot, Claude Code, and Codex.
$CODEX_HOME/skills/pulling-updates-from-skills-repository and restart Codex after major changes.Preferred MCP Server: None required
pulling-updates-from-skills-repository outside its documented task boundary.Before claiming the pulling-updates-from-skills-repository workflow succeeded:
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AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
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Improve the clarity and voice of AI-assisted academic writing (papers, theses, rebuttals) and
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12-agent academic paper writing pipeline. 11 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure/rebuttal-audit). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX-via-Pandoc/PDF output. Style Calibration + Writing Quality Check + Anti-Patterns with IRON RULE markers. Triggers: write paper, academic paper, guide my paper, parse reviews, audit my rebuttal, check my response draft, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見, 評估回覆, 논문 작성, 초록 작성, 논문 수정, 논문 계획을 도와줘, 심사 의견 반영, 답변서 점검, AI 사용 고지.
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Systematic writing framework for philosophy and interdisciplinary academic papers from optimized outline to submission-ready manuscript. Use when users want to: (1) write a paper from a detailed outline, (2) ensure quality control during writing, (3) maintain consistency across chapters, (4) prepare a submission-ready manuscript, or (5) systematically execute a planned paper. Triggered by phrases like 'write the paper from this outline,' 'compose the full manuscript,' 'execute the outline,' or when users have completed strategic planning (academic-paper-strategist skill) and are ready to write. Takes optimized outline as input; outputs complete manuscript with iterative quality checks.
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Multi-perspective academic paper review with dynamic reviewer personas. Runs a 5-seat, role-separated review panel (Journal-Fit Reviewer + 3 peer-review roles + Devil's Advocate) with field-specific expertise; role separation is not a claim of independent error processes. Supports full review, re-review (verification), quick assessment, methodology focus, Socratic guided, and calibration modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy, 審查論文, 論文審查, 模擬審查, 同儕審查, 幫我審這篇, 以審查人角度評估, 審查者校準, 논문 심사, 동료 심사, 모의 심사, 심사자 관점에서 평가, 심사자 보정.
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Systematic strategic planning framework for philosophy and interdisciplinary academic papers targeting preprint platforms (PhilArchive, arXiv, PhilSci-Archive). Use when users want to: (1) plan a paper on a specific topic, (2) identify research gaps and assess originality, (3) develop optimized paper outlines, (4) prepare for preprint submission, or (5) understand platform requirements and writing standards. Triggered by phrases like 'plan a paper on,' 'help me design a paper about,' 'identify research gaps in,' 'is this idea original,' or when users need structured research planning. The skill guides through three phases: Platform Analysis (identifying target venue and studying sample papers), Theoretical Framework (AI-driven literature search and gap identification), and Outline Optimization (structured design with reviewer-perspective self-assessment). Each phase includes quality evaluation standards and validation checkpoints.
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