AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
日本語の概要は準備中です。原文の説明を表示しています。
Complete feature development with structured options for merge, PR, or cleanup
インストールする前に、エージェントに与えられる指示の中身を確認できます。
Core principle: Verify tests → Detect environment → Present options → Execute choice → Clean up.
Announce at start: "I'm using the finishing-a-development-branch skill to complete this work."
Run the project's full test suite (npm test / cargo test / pytest / go test ./...).
If tests fail, report the failures and stop — the menu comes after a green suite:
Tests failing (<N> failures). Must fix before completing:
[Show failures]
If tests pass: continue to Step 2.
GIT_DIR=$(cd "$(git rev-parse --git-dir)" 2>/dev/null && pwd -P)
GIT_COMMON=$(cd "$(git rev-parse --git-common-dir)" 2>/dev/null && pwd -P)
# Capture now, while still inside the workspace — Step 5 changes directory
# before cleanup (Step 6) needs this value
WORKTREE_PATH=$(git rev-parse --show-toplevel)
This determines which menu to show and how cleanup works:
| State | Menu | Cleanup |
|---|---|---|
GIT_DIR == GIT_COMMON (normal repo) | Standard 3 options | No worktree to clean up |
GIT_DIR != GIT_COMMON, named branch | Standard 3 options | Provenance-based (see Step 6) |
GIT_DIR != GIT_COMMON, detached HEAD | Reduced 2 options (no merge) | Externally managed — leave in place |
The base branch is whatever this work forked from — usually named in the plan, the conversation, or the branch's upstream. If it is not already known, ask: "This branch split from <your best guess> - is that correct?" Confirm before merging: merging into the wrong base is expensive to undo.
Normal repo and named-branch worktree — present exactly these 3 options:
Implementation complete. What would you like to do?
1. Merge back to <base-branch> locally
2. Push and create a Pull Request
3. Keep the branch as-is (I'll handle it later)
Which option?
Detached HEAD — present exactly these 2 options:
Implementation complete. You're on a detached HEAD (externally managed workspace).
1. Push as new branch and create a Pull Request
2. Keep as-is (I'll handle it later)
Which option?
Present the menu exactly as written — concise, with every option coming from the list above. Discarding the work happens only in response to your human partner explicitly asking for it (see "If your human partner asks to discard the work" below). Wait for their answer; the integration decision is theirs.
# Get main repo root for CWD safety
MAIN_ROOT=$(git -C "$(git rev-parse --git-common-dir)/.." rev-parse --show-toplevel)
cd "$MAIN_ROOT"
# Merge first — verify success before removing anything
git checkout <base-branch>
git pull
git merge <feature-branch>
# Verify tests on merged result
<test command>
If tests fail on the merged result: stop, leave the worktree and branch in place, and investigate — nothing has been pushed, so the merge is local and recoverable.
Once the merged result is green: clean up the worktree (Step 6), then delete the branch:
git branch -d <feature-branch>
git push -u origin <feature-branch>
# From a detached HEAD, name the new branch on the remote:
# git push origin HEAD:refs/heads/<new-branch>
Then create the pull/merge request against <base-branch> with the forge's tooling — its CLI if one is available, or the creation URL most forges print when you push — following the repo's PR template and conventions if present, and report the URL to your human partner.
Keep the worktree — your human partner iterates on PR feedback there.
Report: "Keeping branch <name>. Worktree preserved at <path>."
This path exists only as a response to an explicit request to throw the work away. Confirm first:
This will permanently delete:
- Branch <name>
- All commits: <commit-list>
- Worktree at <path>
Type 'discard' to confirm.
Wait for that exact confirmation. When it arrives:
MAIN_ROOT=$(git -C "$(git rev-parse --git-common-dir)/.." rev-parse --show-toplevel)
cd "$MAIN_ROOT"
Then clean up the worktree (Step 6) and force-delete the branch:
git branch -D <feature-branch>
Runs for Option 1 and confirmed discards. Options 2 and 3 always
preserve the worktree. Both callers have already changed directory to the
main repo root — worktree removal must run from outside the worktree —
and use the GIT_DIR/GIT_COMMON/WORKTREE_PATH values captured in
Step 2, from before that directory change.
If GIT_DIR == GIT_COMMON: Normal repo, no worktree to clean up. Done.
If WORKTREE_PATH is under .worktrees/ or worktrees/: Superpowers
created this worktree — we own cleanup:
git worktree remove "$WORKTREE_PATH"
git worktree prune # Self-healing: clean up any stale registrations
If removal is refused (contains modified or untracked files): the
worktree holds files that exist nowhere else — uncommitted plans, notes,
or scratch work. Never --force on your own initiative. Show your human
partner what is at stake and ask:
git -C "$WORKTREE_PATH" status --porcelain -uall
Worktree removal refused — these files were never committed:
<file list>
1. Commit them to <branch> before cleanup
2. Move them into <main repo root>
3. Delete them (unrecoverable)
Which?
Carry out the choice, then remove the worktree.
Otherwise: The host environment owns this workspace — leave it in place. If your platform provides a workspace-exit tool, use it.
| Option | Merge | Push | Keep Worktree | Cleanup Branch |
|---|---|---|---|---|
| 1. Merge locally | yes | - | - | yes |
| 2. Create PR | - | yes | yes | - |
| 3. Keep as-is | - | - | yes | - |
| Discard (explicit request only) | - | - | - | yes (force) |
| Excuse | Reality |
|---|---|
| "Tests passed earlier this session" | Run the suite on the tree you are about to integrate. A green run only proves the tree it ran on. |
| "They obviously want it merged" | Integration is your human partner's decision. Present the menu and wait. |
| "They seem done with this feature — I'll offer to discard it" | The menu is complete as written. Discard happens only when your human partner asks for it in so many words. |
| "'Yeah, get rid of it' counts as confirmation" | Only the typed word discard authorizes deletion. |
| "The PR is up, so the worktree is clutter now" | PR feedback gets fixed in that worktree. It stays until the work lands. |
| "This other worktree looks stale — I'll clean it too" | Clean up only worktrees under .worktrees/ or worktrees/. Everything else belongs to the host. |
"Removal refused — --force is just finishing the cleanup" | The refusal means files exist only in that worktree. --force destroys them permanently. Show your human partner and ask. |
| "The merged-result failure is probably flaky" | A failing merged result stops everything. Branch and worktree stay put while you investigate. |
| "The base branch is obviously main" | Confirm the fork point or ask. Merging into the wrong base is expensive to undo. |
| "The push was rejected — force-push will fix it" | A rejected push means the remote moved. Investigate; force-push only on your human partner's explicit request. |
This skill is written to stay usable across GitHub Copilot, Claude Code, and Codex.
$CODEX_HOME/skills/finishing-a-development-branch and restart Codex after major changes.Preferred MCP Server: None required
finishing-a-development-branch outside its documented task boundary.Before claiming the finishing-a-development-branch workflow succeeded:
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概要と使いどころ
AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
日本語の概要は準備中です。原文の説明を表示しています。
Improve the clarity and voice of AI-assisted academic writing (papers, theses, rebuttals) and
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。