🔄 Automated Skill Updates Available#28
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Updated Skills
Submodule skills/scientific-agent-skills 9881fe4..e6cabc2:
Updated Skills
-Submodule skills/humanizer a2ace14..9600f2b:
Updated Skills
--Submodule skills/humanizer 8b3a178..a2ace14:
-- > Add em/en dash cut, gap-filling tell, and diff-anchored pattern (v2.7.0)
-- > Cleanup pass: cut bloat and fix the aggressiveness contradiction (v2.6.0)
-- > Replace WARP.md with tool-neutral AGENTS.md
-- > Merge pull request #84 from mvanhorn/fix/78-content-preservation
-- > Merge pull request #113 from philippdubach/detection-guidance
-- > Merge pull request #121 from Longman006/fix/section-26-attributive-vs-predicate-hyphens
-- > Merge pull request #119 from MackDing/mack/pr-20260519-1107-humanizer
--Submodule skills/scientific-agent-skills 5bd00bf..9312485:
-- > chore: update security scan report [skip ci]
-- > Update scvi-tools
-- > Update scikit-bio
-- > Update Modal skill
-- > Add bulk-rnaseq workflow skill
-- > Add pathway-enrichment skill
-- > Bump version
-- > Add support for Nextflow
-- > Bump version
-- > docs: update dependencies and skills documentation for dask, pymoo, and scanpy
-- > docs: update skills documentation for scientific-critical-thinking and stable-baselines3
-- > docs: update scikit-learn skill documentation and references
-- > docs: update research grants skill documentation and templates
-- > docs: update skills documentation for histolab and astropy
-- > docs: enhance README with new star encouragement section
-- > docs: update README to include Star History and refine skills usage descriptions
-- > Update directory for compatibility
-- > Update directory
-- > docs: update SKILL.md for bgpt-paper-search compatibility and usage instructions
-- > docs: update SKILL.md for Adaptyv API enhancements
-- > docs: update SKILL.md and related references for Benchling integration
-- > docs: update README and SKILL.md files for versioning and new features
-- > docs: update README to include Google Antigravity support and enhance follow-up information
-- > chore: keep agent guidance local
-- > docs: enhance README with contribution guidelines and citation practices
-- > chore: update metadata for scientific skills
-- > chore: update documentation and descriptions for scientific skills
-- > chore: update PyTorch Lightning documentation and installation instructions
-- > chore: update scientific-agent-skills version to 2.42.0
-- > Add suppor for LiteParse from LlamaIndex
-- > chore: bump scientific-agent-skills version to 2.41.0
-- > refactor: enhance medchem and esm documentation and functionality
-- > chore: update Biopython and Datamol documentation
-- > chore: update .gitignore and bump scientific-agent-skills version to 2.40.0
-- > Bump version
--diff --git a/update_summary.md b/update_summary.md
--index 7f6f6a1..98b6e19 100644
----- a/update_summary.md
--+++ b/update_summary.md
--@@ -1,4076 +1,2 @@
-- ## Updated Skills
---Submodule skills/scientific-agent-skills 63de55a..5bd00bf:
--- > chore: update security scan report [skip ci]
--- > Merge pull request #156 from Beifang/feature/pacsomatic
--- > Merge pull request #90 from StevenDillmann/feat/simbad-database-skill
--- > Update README.md for improved link formatting and table of contents consistency
--- > Bump version and added community contributions
---diff --git a/update_summary.md b/update_summary.md
---index e08889b..98b6e19 100644
------ a/update_summary.md
---+++ b/update_summary.md
---@@ -1,4063 +1,2 @@
--- ## Updated Skills
----Submodule skills/scientific-agent-skills cbcae7b..63de55a:
---- > chore: update security scan report [skip ci]
---- > Merge pull request #116 from robotlearning123/fix/neuropixels-broken-links
---- > Merge pull request #94 from jiaodu1307/fix/rdkit-skill-gzip-import-clean
---- > Merge pull request #125 from yarikoptic/enh-bids
---- > Merge pull request #147 from xiaolai/fix/nlpm-scanpy-license-typo
---- > Merge pull request #164 from mvanhorn/fix/159-research-lookup-yaml-frontmatter
---- > Merge pull request #165 from Travisma2233/venue-templates/add-elsarticle
----diff --git a/update_summary.md b/update_summary.md
----index d98bc33..98b6e19 100644
------- a/update_summary.md
----+++ b/update_summary.md
----@@ -1,4048 +1,2 @@
---- ## Updated Skills
-----Submodule skills/scientific-agent-skills 37a148b..cbcae7b:
----- > chore: update security scan report [skip ci]
----- > Merge pull request #143 from tgonzalezc5/feat/exa-search-skill
-----diff --git a/skills/superpowers/executing-plans/SKILL.md b/skills/superpowers/executing-plans/SKILL.md
-----index e67f94c..a591862 100644
-------- a/skills/superpowers/executing-plans/SKILL.md
-----+++ b/skills/superpowers/executing-plans/SKILL.md
-----@@ -65,6 +65,6 @@ After all tasks complete and verified:
----- ## Integration
----- Required workflow skills:
------- superpowers:using-git-worktrees - REQUIRED: Set up isolated workspace before starting
-----+- superpowers:using-git-worktrees - Ensures isolated workspace (creates one or verifies existing)
----- - superpowers:writing-plans - Creates the plan this skill executes
----- - superpowers:finishing-a-development-branch - Complete development after all tasks
-----diff --git a/skills/superpowers/finishing-a-development-branch/SKILL.md b/skills/superpowers/finishing-a-development-branch/SKILL.md
-----index c308b43..43da0ae 100644
-------- a/skills/superpowers/finishing-a-development-branch/SKILL.md
-----+++ b/skills/superpowers/finishing-a-development-branch/SKILL.md
-----@@ -9,7 +9,7 @@ description: Use when implementation is complete, all tests pass, and you need t
----- Guide completion of development work by presenting clear options and handling chosen workflow.
------Core principle: Verify tests → Present options → Execute choice → Clean up.
-----+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."
-----@@ -37,7 +37,24 @@ Stop. Don't proceed to Step 2.
----- If tests pass: Continue to Step 2.
------### Step 2: Determine Base Branch
-----+### Step 2: Detect Environment
-----+
-----+Determine workspace state before presenting options:
-----+
-----+
bash -----+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) -----+-----+
-----+This determines which menu to show and how cleanup works:
-----+
-----+| State | Menu | Cleanup |
-----+|-------|------|---------|
-----+|
GIT_DIR == GIT_COMMON(normal repo) | Standard 4 options | No worktree to clean up |-----+|
GIT_DIR != GIT_COMMON, named branch | Standard 4 options | Provenance-based (see Step 6) |-----+|
GIT_DIR != GIT_COMMON, detached HEAD | Reduced 3 options (no merge) | No cleanup (externally managed) |-----+
-----+### Step 3: Determine Base Branch
----- ```bash
----- # Try common base branches
-----@@ -46,9 +63,9 @@ git merge-base HEAD main 2>/dev/null || git merge-base HEAD master 2>/dev/null
----- Or ask: "This branch split from main - is that correct?"
------### Step 3: Present Options
-----+### Step 4: Present Options
------Present exactly these 4 options:
-----+Normal repo and named-branch worktree — present exactly these 4 options:
-----
----- Implementation complete. What would you like to do? -----@@ -61,30 +78,45 @@ Implementation complete. What would you like to do? ----- Which option? ----------+Detached HEAD — present exactly these 3 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) -----+3. Discard this work -----+ -----+Which option? -----+-----+
----- Don't add explanation - keep options concise.
------### Step 4: Execute Choice
-----+### Step 5: Execute Choice
----- #### Option 1: Merge Locally
----- ```bash
------# Switch to base branch
------git checkout
-----+# Get main repo root for CWD safety
-----+MAIN_ROOT=$(git -C "$(git rev-parse --git-common-dir)/.." rev-parse --show-toplevel)
-----+cd "$MAIN_ROOT"
------# Pull latest
-----+# Merge first — verify success before removing anything
-----+git checkout
----- git pull
------# Merge feature branch
----- git merge
----- # Verify tests on merged result
-----
------# If tests pass
------git branch -d
-----+# Only after merge succeeds: cleanup worktree (Step 6), then delete branch
----- ```
------Then: Cleanup worktree (Step 5)
-----+Then: Cleanup worktree (Step 6), then delete branch:
-----+
-----+
bash -----+git branch -d <feature-branch> -----+----- #### Option 2: Push and Create PR
-----@@ -103,7 +135,7 @@ EOF
----- )"
----- ```
------Then: Cleanup worktree (Step 5)
-----+Do NOT clean up worktree — user needs it alive to iterate on PR feedback.
----- #### Option 3: Keep As-Is
-----@@ -127,36 +159,46 @@ Wait for exact confirmation.
----- If confirmed:
-----
bash ------git checkout <base-branch> ------git branch -D <feature-branch> -----+MAIN_ROOT=$(git -C "$(git rev-parse --git-common-dir)/.." rev-parse --show-toplevel) -----+cd "$MAIN_ROOT" -----------Then: Cleanup worktree (Step 5)
-----+Then: Cleanup worktree (Step 6), then force-delete branch:
-----+
bash -----+git branch -D <feature-branch> -----+------### Step 5: Cleanup Worktree
-----+### Step 6: Cleanup Workspace
------For Options 1, 2, 4:
-----+Only runs for Options 1 and 4. Options 2 and 3 always preserve the worktree.
------Check if in worktree:
-----
bash ------git worktree list | grep $(git branch --show-current) -----+GIT_DIR=$(cd "$(git rev-parse --git-dir)" 2>/dev/null && pwd -P) -----+GIT_COMMON=$(cd "$(git rev-parse --git-common-dir)" 2>/dev/null && pwd -P) -----+WORKTREE_PATH=$(git rev-parse --show-toplevel) -----------If yes:
-----+If
GIT_DIR == GIT_COMMON: Normal repo, no worktree to clean up. Done.-----+
-----+If worktree path is under
.worktrees/,worktrees/, or~/.config/superpowers/worktrees/: Superpowers created this worktree — we own cleanup.-----+
-----
bash ------git worktree remove <worktree-path> -----+MAIN_ROOT=$(git -C "$(git rev-parse --git-common-dir)/.." rev-parse --show-toplevel) -----+cd "$MAIN_ROOT" -----+git worktree remove "$WORKTREE_PATH" -----+git worktree prune # Self-healing: clean up any stale registrations -----------For Option 3: Keep worktree.
-----+Otherwise: The host environment (harness) owns this workspace. Do NOT remove it. If your platform provides a workspace-exit tool, use it. Otherwise, leave the workspace in place.
----- ## Quick Reference
----- ## Common Mistakes
-----@@ -165,13 +207,25 @@ git worktree remove
----- - Fix: Always verify tests before offering options
----- Open-ended questions
------- Problem: "What should I do next?" → ambiguous
------- Fix: Present exactly 4 structured options
-----+- Problem: "What should I do next?" is ambiguous
-----+- Fix: Present exactly 4 structured options (or 3 for detached HEAD)
------Automatic worktree cleanup
------- Problem: Remove worktree when might need it (Option 2, 3)
-----+Cleaning up worktree for Option 2
-----+- Problem: Remove worktree user needs for PR iteration
----- - Fix: Only cleanup for Options 1 and 4
-----+Deleting branch before removing worktree
-----+- Problem:
git branch -dfails because worktree still references the branch-----+- Fix: Merge first, remove worktree, then delete branch
-----+
-----+Running git worktree remove from inside the worktree
-----+- Problem: Command fails silently when CWD is inside the worktree being removed
-----+- Fix: Always
cdto main repo root beforegit worktree remove-----+
-----+Cleaning up harness-owned worktrees
-----+- Problem: Removing a worktree the harness created causes phantom state
-----+- Fix: Only clean up worktrees under
.worktrees/,worktrees/, or~/.config/superpowers/worktrees/-----+
----- No confirmation for discard
----- - Problem: Accidentally delete work
----- - Fix: Require typed "discard" confirmation
-----@@ -183,18 +237,15 @@ git worktree remove
----- - Merge without verifying tests on result
----- - Delete work without confirmation
----- - Force-push without explicit request
-----+- Remove a worktree before confirming merge success
-----+- Clean up worktrees you didn't create (provenance check)
-----+- Run
git worktree removefrom inside the worktree----- Always:
----- - Verify tests before offering options
------- Present exactly 4 options
-----+- Detect environment before presenting menu
-----+- Present exactly 4 options (or 3 for detached HEAD)
----- - Get typed confirmation for Option 4
----- - Clean up worktree for Options 1 & 4 only
------## Integration
------Called by:
------- subagent-driven-development (Step 7) - After all tasks complete
------- executing-plans (Step 5) - After all batches complete
------Pairs with:
------- using-git-worktrees - Cleans up worktree created by that skill
-----+-
cdto main repo root before worktree removal-----+- Run
git worktree pruneafter removal-----diff --git a/skills/superpowers/requesting-code-review/SKILL.md b/skills/superpowers/requesting-code-review/SKILL.md
-----index fe7c8d9..34b8340 100644
-------- a/skills/superpowers/requesting-code-review/SKILL.md
-----+++ b/skills/superpowers/requesting-code-review/SKILL.md
-----@@ -5,7 +5,7 @@ description: Use when completing tasks, implementing major features, or before m
----- # Requesting Code Review
------Dispatch superpowers:code-reviewer subagent to catch issues before they cascade. The reviewer gets precisely crafted context for evaluation — never your session's history. This keeps the reviewer focused on the work product, not your thought process, and preserves your own context for continued work.
-----+Dispatch a code reviewer subagent to catch issues before they cascade. The reviewer gets precisely crafted context for evaluation — never your session's history. This keeps the reviewer focused on the work product, not your thought process, and preserves your own context for continued work.
----- Core principle: Review early, review often.
-----@@ -29,16 +29,15 @@ BASE_SHA=$(git rev-parse HEAD~1) # or origin/main
----- HEAD_SHA=$(git rev-parse HEAD)
----- ```
------2. Dispatch code-reviewer subagent:
-----+2. Dispatch code reviewer subagent:
------Use Task tool with superpowers:code-reviewer type, fill template at
code-reviewer.md-----+Use Task tool with
general-purposetype, fill template atcode-reviewer.md----- Placeholders:
-------
{WHAT_WAS_IMPLEMENTED}- What you just built-----+-
{DESCRIPTION}- Brief summary of what you built----- -
{PLAN_OR_REQUIREMENTS}- What it should do----- -
{BASE_SHA}- Starting commit----- -
{HEAD_SHA}- Ending commit-------
{DESCRIPTION}- Brief summary----- 3. Act on feedback:
----- - Fix Critical issues immediately
-----@@ -56,12 +55,11 @@ You: Let me request code review before proceeding.
----- BASE_SHA=$(git log --oneline | grep "Task 1" | head -1 | awk '{print $1}')
----- HEAD_SHA=$(git rev-parse HEAD)
------[Dispatch superpowers:code-reviewer subagent]
------ WHAT_WAS_IMPLEMENTED: Verification and repair functions for conversation index
-----+[Dispatch code reviewer subagent]
-----+ DESCRIPTION: Added verifyIndex() and repairIndex() with 4 issue types
----- PLAN_OR_REQUIREMENTS: Task 2 from docs/superpowers/plans/deployment-plan.md
----- BASE_SHA: a7981ec
----- HEAD_SHA: 3df7661
------ DESCRIPTION: Added verifyIndex() and repairIndex() with 4 issue types
----- [Subagent returns]:
----- Strengths: Clean architecture, real tests
-----@@ -82,7 +80,7 @@ You: [Fix progress indicators]
----- - Fix before moving to next task
----- Executing Plans:
------- Review after each batch (3 tasks)
-----+- Review after each task or at natural checkpoints
----- - Get feedback, apply, continue
----- Ad-Hoc Development:
-----diff --git a/skills/superpowers/requesting-code-review/code-reviewer.md b/skills/superpowers/requesting-code-review/code-reviewer.md
-----index 3c427c9..525e4b4 100644
-------- a/skills/superpowers/requesting-code-review/code-reviewer.md
-----+++ b/skills/superpowers/requesting-code-review/code-reviewer.md
-----@@ -1,111 +1,133 @@
------# Code Review Agent
-----+# Code Reviewer Prompt Template
------You are reviewing code changes for production readiness.
-----+Use this template when dispatching a code reviewer subagent.
------Your task:
------1. Review {WHAT_WAS_IMPLEMENTED}
------2. Compare against {PLAN_OR_REQUIREMENTS}
------3. Check code quality, architecture, testing
------4. Categorize issues by severity
------5. Assess production readiness
-----+Purpose: Review completed work against requirements and code quality standards before it cascades into more work.
------## What Was Implemented
-----+```
-----+Task tool (general-purpose):
-----+ description: "Review code changes"
-----+ prompt: |
-----+ You are a Senior Code Reviewer with expertise in software architecture,
-----+ design patterns, and best practices. Your job is to review completed work
-----+ against its plan or requirements and identify issues before they cascade.
------{DESCRIPTION}
-----+ ## What Was Implemented
------## Requirements/Plan
-----+ {DESCRIPTION}
------{PLAN_REFERENCE}
-----+ ## Requirements / Plan
------## Git Range to Review
-----+ {PLAN_OR_REQUIREMENTS}
------Base: {BASE_SHA}
------Head: {HEAD_SHA}
-----+ ## Git Range to Review
------
bash ------git diff --stat {BASE_SHA}..{HEAD_SHA} ------git diff {BASE_SHA}..{HEAD_SHA} -----------+ Base: {BASE_SHA}
-----+ Head: {HEAD_SHA}
------## Review Checklist
------Code Quality:
------- Clean separation of concerns?
------- Proper error handling?
------- Type safety (if applicable)?
------- DRY principle followed?
------- Edge cases handled?
------Architecture:
------- Sound design decisions?
------- Scalability considerations?
------- Performance implications?
------- Security concerns?
------Testing:
------- Tests actually test logic (not mocks)?
------- Edge cases covered?
------- Integration tests where needed?
------- All tests passing?
------Requirements:
------- All plan requirements met?
------- Implementation matches spec?
------- No scope creep?
------- Breaking changes documented?
------Production Readiness:
------- Migration strategy (if schema changes)?
------- Backward compatibility considered?
------- Documentation complete?
------- No obvious bugs?
------## Output Format
-----+
bash -----+ git diff --stat {BASE_SHA}..{HEAD_SHA} -----+ git diff {BASE_SHA}..{HEAD_SHA} -----+------### Strengths
------[What's well done? Be specific.]
-----+ ## What to Check
------### Issues
-----+ Plan alignment:
-----+ - Does the implementation match the plan / requirements?
-----+ - Are deviations justified improvements, or problematic departures?
-----+ - Is all planned functionality present?
------#### Critical (Must Fix)
------[Bugs, security issues, data loss risks, broken functionality]
-----+ Code quality:
-----+ - Clean separation of concerns?
-----+ - Proper error handling?
-----+ - Type safety where applicable?
-----+ - DRY without premature abstraction?
-----+ - Edge cases handled?
------#### Important (Should Fix)
------[Architecture problems, missing features, poor error handling, test gaps]
-----+ Architecture:
-----+ - Sound design decisions?
-----+ - Reasonable scalability and performance?
-----+ - Security concerns?
-----+ - Integrates cleanly with surrounding code?
------#### Minor (Nice to Have)
------[Code style, optimization opportunities, documentation improvements]
-----+ Testing:
-----+ - Tests verify real behavior, not mocks?
-----+ - Edge cases covered?
-----+ - Integration tests where they matter?
-----+ - All tests passing?
------For each issue:
------- File:line reference
------- What's wrong
------- Why it matters
------- How to fix (if not obvious)
-----+ Production readiness:
-----+ - Migration strategy if schema changed?
-----+ - Backward compatibility considered?
-----+ - Documentation complete?
-----+ - No obvious bugs?
------### Recommendations
------[Improvements for code quality, architecture, or process]
-----+ ## Calibration
------### Assessment
-----+ Categorize issues by actual severity. Not everything is Critical.
-----+ Acknowledge what was done well before listing issues — accurate praise
-----+ helps the implementer trust the rest of the feedback.
-----+
-----+ If you find significant deviations from the plan, flag them specifically
-----+ so the implementer can confirm whether the deviation was intentional.
-----+ If you find issues with the plan itself rather than the implementation,
-----+ say so.
-----+
-----+ ## Output Format
-----+
-----+ ### Strengths
-----+ [What's well done? Be specific.]
-----+
-----+ ### Issues
------Ready to merge? [Yes/No/With fixes]
-----+ #### Critical (Must Fix)
-----+ [Bugs, security issues, data loss risks, broken functionality]
------Reasoning: [Technical assessment in 1-2 sentences]
-----+ #### Important (Should Fix)
-----+ [Architecture problems, missing features, poor error handling, test gaps]
------## Critical Rules
-----+ #### Minor (Nice to Have)
-----+ [Code style, optimization opportunities, documentation polish]
-----+
-----+ For each issue:
-----+ - File:line reference
-----+ - What's wrong
-----+ - Why it matters
-----+ - How to fix (if not obvious)
-----+
-----+ ### Recommendations
-----+ [Improvements for code quality, architecture, or process]
-----+
-----+ ### Assessment
-----+
-----+ Ready to merge? [Yes | No | With fixes]
-----+
-----+ Reasoning: [1-2 sentence technical assessment]
-----+
-----+ ## Critical Rules
-----+
-----+ DO:
-----+ - Categorize by actual severity
-----+ - Be specific (file:line, not vague)
-----+ - Explain WHY each issue matters
-----+ - Acknowledge strengths
-----+ - Give a clear verdict
-----+
-----+ DON'T:
-----+ - Say "looks good" without checking
-----+ - Mark nitpicks as Critical
-----+ - Give feedback on code you didn't actually read
-----+ - Be vague ("improve error handling")
-----+ - Avoid giving a clear verdict
-----+```
------DO:
------- Categorize by actual severity (not everything is Critical)
------- Be specific (file:line, not vague)
------- Explain WHY issues matter
------- Acknowledge strengths
------- Give clear verdict
-----+Placeholders:
-----+-
{DESCRIPTION}— brief summary of what was built-----+-
{PLAN_OR_REQUIREMENTS}— what it should do (plan file path, task text, or requirements)-----+-
{BASE_SHA}— starting commit-----+-
{HEAD_SHA}— ending commit------DON'T:
------- Say "looks good" without checking
------- Mark nitpicks as Critical
------- Give feedback on code you didn't review
------- Be vague ("improve error handling")
------- Avoid giving a clear verdict
-----+Reviewer returns: Strengths, Issues (Critical / Important / Minor), Recommendations, Assessment
----- ## Example Output
-----diff --git a/skills/superpowers/subagent-driven-development/SKILL.md b/skills/superpowers/subagent-driven-development/SKILL.md
-----index 5150b18..ea7ac8f 100644
-------- a/skills/superpowers/subagent-driven-development/SKILL.md
-----+++ b/skills/superpowers/subagent-driven-development/SKILL.md
-----@@ -11,6 +11,8 @@ Execute plan by dispatching fresh subagent per task, with two-stage review after
----- Core principle: Fresh subagent per task + two-stage review (spec then quality) = high quality, fast iteration
-----+Continuous execution: Do not pause to check in with your human partner between tasks. Execute all tasks from the plan without stopping. The only reasons to stop are: BLOCKED status you cannot resolve, ambiguity that genuinely prevents progress, or all tasks complete. "Should I continue?" prompts and progress summaries waste their time — they asked you to execute the plan, so execute it.
-----+
----- ## When to Use
----- ```dot
-----@@ -265,7 +267,7 @@ Done!
----- ## Integration
----- Required workflow skills:
------- superpowers:using-git-worktrees - REQUIRED: Set up isolated workspace before starting
-----+- superpowers:using-git-worktrees - Ensures isolated workspace (creates one or verifies existing)
----- - superpowers:writing-plans - Creates the plan this skill executes
----- - superpowers:requesting-code-review - Code review template for reviewer subagents
----- - superpowers:finishing-a-development-branch - Complete development after all tasks
-----diff --git a/skills/superpowers/subagent-driven-development/code-quality-reviewer-prompt.md b/skills/superpowers/subagent-driven-development/code-quality-reviewer-prompt.md
-----index a04201a..51f901a 100644
-------- a/skills/superpowers/subagent-driven-development/code-quality-reviewer-prompt.md
-----+++ b/skills/superpowers/subagent-driven-development/code-quality-reviewer-prompt.md
-----@@ -7,14 +7,13 @@ Use this template when dispatching a code quality reviewer subagent.
----- Only dispatch after spec compliance review passes.
----- ```
------Task tool (superpowers:code-reviewer):
-----+Task tool (general-purpose):
----- Use template at requesting-code-review/code-reviewer.md
------ WHAT_WAS_IMPLEMENTED: [from implementer's report]
-----+ DESCRIPTION: [task summary, from implementer's report]
----- PLAN_OR_REQUIREMENTS: Task N from [plan-file]
----- BASE_SHA: [commit before task]
----- HEAD_SHA: [current commit]
------ DESCRIPTION: [task summary]
----- ```
----- In addition to standard code quality concerns, the reviewer should check:
-----diff --git a/skills/superpowers/systematic-debugging/CREATION-LOG.md b/skills/superpowers/systematic-debugging/CREATION-LOG.md
-----index 024d00a..9aa0309 100644
-------- a/skills/superpowers/systematic-debugging/CREATION-LOG.md
-----+++ b/skills/superpowers/systematic-debugging/CREATION-LOG.md
-----@@ -4,7 +4,7 @@ Reference example of extracting, structuring, and bulletproofing a critical skil
----- ## Source Material
------Extracted debugging framework from
/Users/jesse/.claude/CLAUDE.md:-----+Extracted debugging framework from
~/.claude/CLAUDE.md:----- - 4-phase systematic process (Investigation → Pattern Analysis → Hypothesis → Implementation)
----- - Core mandate: ALWAYS find root cause, NEVER fix symptoms
----- - Rules designed to resist time pressure and rationalization
-----diff --git a/skills/superpowers/systematic-debugging/root-cause-tracing.md b/skills/superpowers/systematic-debugging/root-cause-tracing.md
-----index 9484774..12ef522 100644
-------- a/skills/superpowers/systematic-debugging/root-cause-tracing.md
-----+++ b/skills/superpowers/systematic-debugging/root-cause-tracing.md
-----@@ -33,7 +33,7 @@ digraph when_to_use {
----- ### 1. Observe the Symptom
-----
------Error: git init failed in /Users/jesse/project/packages/core -----+Error: git init failed in ~/project/packages/core ---------- ### 2. Find Immediate Cause
-----diff --git a/skills/superpowers/using-git-worktrees/SKILL.md b/skills/superpowers/using-git-worktrees/SKILL.md
-----index e153843..134d371 100644
-------- a/skills/superpowers/using-git-worktrees/SKILL.md
-----+++ b/skills/superpowers/using-git-worktrees/SKILL.md
-----@@ -1,104 +1,117 @@
----- name: using-git-worktrees
------description: Use when starting feature work that needs isolation from current workspace or before executing implementation plans - creates isolated git worktrees with smart directory selection and safety verification
-----+description: Use when starting feature work that needs isolation from current workspace or before executing implementation plans - ensures an isolated workspace exists via native tools or git worktree fallback
----- # Using Git Worktrees
----- ## Overview
------Git worktrees create isolated workspaces sharing the same repository, allowing work on multiple branches simultaneously without switching.
-----+Ensure work happens in an isolated workspace. Prefer your platform's native worktree tools. Fall back to manual git worktrees only when no native tool is available.
------Core principle: Systematic directory selection + safety verification = reliable isolation.
-----+Core principle: Detect existing isolation first. Then use native tools. Then fall back to git. Never fight the harness.
----- Announce at start: "I'm using the using-git-worktrees skill to set up an isolated workspace."
------## Directory Selection Process
-----+## Step 0: Detect Existing Isolation
------Follow this priority order:
------### 1. Check Existing Directories
-----+Before creating anything, check if you are already in an isolated workspace.
-----
bash ------# Check in priority order ------ls -d .worktrees 2>/dev/null # Preferred (hidden) ------ls -d worktrees 2>/dev/null # Alternative -----+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) -----+BRANCH=$(git branch --show-current) -----------If found: Use that directory. If both exist,
.worktreeswins.------### 2. Check CLAUDE.md
-----+Submodule guard:
GIT_DIR != GIT_COMMONis also true inside git submodules. Before concluding "already in a worktree," verify you are not in a submodule:-----
bash ------grep -i "worktree.*director" CLAUDE.md 2>/dev/null -----+# If this returns a path, you're in a submodule, not a worktree — treat as normal repo -----+git rev-parse --show-superproject-working-tree 2>/dev/null -----------If preference specified: Use it without asking.
-----+If
GIT_DIR != GIT_COMMON(and not a submodule): You are already in a linked worktree. Skip to Step 3 (Project Setup). Do NOT create another worktree.------### 3. Ask User
-----+Report with branch state:
-----+- On a branch: "Already in isolated workspace at
<path>on branch<name>."-----+- Detached HEAD: "Already in isolated workspace at
<path>(detached HEAD, externally managed). Branch creation needed at finish time."------If no directory exists and no CLAUDE.md preference:
-----+If
GIT_DIR == GIT_COMMON(or in a submodule): You are in a normal repo checkout.------```
------No worktree directory found. Where should I create worktrees?
-----+Has the user already indicated their worktree preference in your instructions? If not, ask for consent before creating a worktree:
------1. .worktrees/ (project-local, hidden)
------2. ~/.config/superpowers/worktrees// (global location)
-----+> "Would you like me to set up an isolated worktree? It protects your current branch from changes."
------Which would you prefer?
------```
-----+Honor any existing declared preference without asking. If the user declines consent, work in place and skip to Step 3.
-----+
-----+## Step 1: Create Isolated Workspace
-----+
-----+You have two mechanisms. Try them in this order.
-----+
-----+### 1a. Native Worktree Tools (preferred)
-----+
-----+The user has asked for an isolated workspace (Step 0 consent). Do you already have a way to create a worktree? It might be a tool with a name like
EnterWorktree, `WorktreeCreate`, a `/worktree` command, or a `--worktree` flag. If you do, use it and skip to Step 3.-----+
-----+Native tools handle directory placement, branch creation, and cleanup automatically. Using `git worktree add` when you have a native tool creates phantom state your harness can't see or manage.
-----+
-----+Only proceed to Step 1b if you have no native worktree tool available.
------## Safety Verification
-----+### 1b. Git Worktree Fallback
------### For Project-Local Directories (.worktrees or worktrees)
-----+Only use this if Step 1a does not apply — you have no native worktree tool available. Create a worktree manually using git.
-----+
-----+#### Directory Selection
-----+
-----+Follow this priority order. Explicit user preference always beats observed filesystem state.
-----+
-----+1. Check your instructions for a declared worktree directory preference. If the user has already specified one, use it without asking.
-----+
-----+2. Check for an existing project-local worktree directory:
-----+
bash -----+ ls -d .worktrees 2>/dev/null # Preferred (hidden) -----+ ls -d worktrees 2>/dev/null # Alternative -----+-----+ If found, use it. If both exist,
.worktreeswins.-----+
-----+3. Check for an existing global directory:
-----+
bash -----+ project=$(basename "$(git rev-parse --show-toplevel)") -----+ ls -d ~/.config/superpowers/worktrees/$project 2>/dev/null -----+-----+ If found, use it (backward compatibility with legacy global path).
-----+
-----+4. If there is no other guidance available, default to
.worktrees/at the project root.-----+
-----+#### Safety Verification (project-local directories only)
----- MUST verify directory is ignored before creating worktree:
-----
bash ------# Check if directory is ignored (respects local, global, and system gitignore) ----- git check-ignore -q .worktrees 2>/dev/null || git check-ignore -q worktrees 2>/dev/null -----------If NOT ignored:
------Per Jesse's rule "Fix broken things immediately":
------1. Add appropriate line to .gitignore
------2. Commit the change
------3. Proceed with worktree creation
-----+If NOT ignored: Add to .gitignore, commit the change, then proceed.
----- Why critical: Prevents accidentally committing worktree contents to repository.
------### For Global Directory (~/.config/superpowers/worktrees)
------No .gitignore verification needed - outside project entirely.
-----+Global directories (
~/.config/superpowers/worktrees/) need no verification.------## Creation Steps
------### 1. Detect Project Name
-----+#### Create the Worktree
-----
bash ----- project=$(basename "$(git rev-parse --show-toplevel)") ------------### 2. Create Worktree
-----+# Determine path based on chosen location
-----+# For project-local: path="$LOCATION/$BRANCH_NAME"
-----+# For global: path="~/.config/superpowers/worktrees/$project/$BRANCH_NAME"
------```bash
------# Determine full path
------case $LOCATION in
------ .worktrees|worktrees)
------ path="$LOCATION/$BRANCH_NAME"
------ ;;
------
/.config/superpowers/worktrees/*)/.config/superpowers/worktrees/$project/$BRANCH_NAME"------ path="
------ ;;
------esac
------# Create worktree with new branch
----- git worktree add "$path" -b "$BRANCH_NAME"
----- cd "$path"
----- ```
------### 3. Run Project Setup
-----+Sandbox fallback: If
git worktree addfails with a permission error (sandbox denial), tell the user the sandbox blocked worktree creation and you're working in the current directory instead. Then run setup and baseline tests in place.-----+
-----+## Step 3: Project Setup
----- Auto-detect and run appropriate setup:
-----@@ -117,23 +130,20 @@ if [ -f pyproject.toml ]; then poetry install; fi
----- if [ -f go.mod ]; then go mod download; fi
----- ```
------### 4. Verify Clean Baseline
-----+## Step 4: Verify Clean Baseline
------Run tests to ensure worktree starts clean:
-----+Run tests to ensure workspace starts clean:
-----
bash ------# Examples - use project-appropriate command ------npm test ------cargo test ------pytest ------go test ./... -----+# Use project-appropriate command -----+npm test / cargo test / pytest / go test ./... ---------- If tests fail: Report failures, ask whether to proceed or investigate.
----- If tests pass: Report ready.
------### 5. Report Location
-----+### Report
----- ```
----- Worktree ready at
-----@@ -145,16 +155,32 @@ Ready to implement
.worktrees/existsworktrees/exists.worktrees/.worktrees/----- ## Common Mistakes
-----+### Fighting the harness
-----+
-----+- Problem: Using
git worktree addwhen the platform already provides isolation-----+- Fix: Step 0 detects existing isolation. Step 1a defers to native tools.
-----+
-----+### Skipping detection
-----+
-----+- Problem: Creating a nested worktree inside an existing one
-----+- Fix: Always run Step 0 before creating anything
-----+
----- ### Skipping ignore verification
----- - Problem: Worktree contents get tracked, pollute git status
-----@@ -163,56 +189,27 @@ Ready to implement
----- ### Assuming directory location
----- - Problem: Creates inconsistency, violates project conventions
------- Fix: Follow priority: existing > CLAUDE.md > ask
-----+- Fix: Follow priority: existing > global legacy > instruction file > default
----- ### Proceeding with failing tests
----- - Problem: Can't distinguish new bugs from pre-existing issues
----- - Fix: Report failures, get explicit permission to proceed
------### Hardcoding setup commands
------- Problem: Breaks on projects using different tools
------- Fix: Auto-detect from project files (package.json, etc.)
------## Example Workflow
------```
------You: I'm using the using-git-worktrees skill to set up an isolated workspace.
------[Check .worktrees/ - exists]
------[Verify ignored - git check-ignore confirms .worktrees/ is ignored]
------[Create worktree: git worktree add .worktrees/auth -b feature/auth]
------[Run npm install]
------[Run npm test - 47 passing]
------Worktree ready at /Users/jesse/myproject/.worktrees/auth
------Tests passing (47 tests, 0 failures)
------Ready to implement auth feature
------```
----- ## Red Flags
----- Never:
-----+- Create a worktree when Step 0 detects existing isolation
-----+- Use
git worktree addwhen you have a native worktree tool (e.g.,EnterWorktree). This is the #1 mistake — if you have it, use it.-----+- Skip Step 1a by jumping straight to Step 1b's git commands
----- - Create worktree without verifying it's ignored (project-local)
----- - Skip baseline test verification
----- - Proceed with failing tests without asking
------- Assume directory location when ambiguous
------- Skip CLAUDE.md check
----- Always:
------- Follow directory priority: existing > CLAUDE.md > ask
-----+- Run Step 0 detection first
-----+- Prefer native tools over git fallback
-----+- Follow directory priority: existing > global legacy > instruction file > default
----- - Verify directory is ignored for project-local
----- - Auto-detect and run project setup
----- - Verify clean test baseline
------## Integration
------Called by:
------- brainstorming (Phase 4) - REQUIRED when design is approved and implementation follows
------- subagent-driven-development - REQUIRED before executing any tasks
------- executing-plans - REQUIRED before executing any tasks
------- Any skill needing isolated workspace
------Pairs with:
------- finishing-a-development-branch - REQUIRED for cleanup after work complete
-----diff --git a/skills/superpowers/using-superpowers/references/codex-tools.md b/skills/superpowers/using-superpowers/references/codex-tools.md
-----index 539b2b1..f50d40d 100644
-------- a/skills/superpowers/using-superpowers/references/codex-tools.md
-----+++ b/skills/superpowers/using-superpowers/references/codex-tools.md
-----@@ -4,9 +4,9 @@ Skills use Claude Code tool names. When you encounter these in a skill, use your
Tasktool (dispatch subagent)spawn_agent(see Named agent dispatch)Tasktool (dispatch subagent)spawn_agent(see Subagent dispatch requires multi-agent support)Taskcalls (parallel)spawn_agentcallswaitwait_agentclose_agentto free slotTodoWrite(task tracking)update_planSkilltool (invoke a skill)~/.codex/config.toml):------This enables
spawn_agent,wait, andclose_agentfor skills likedispatching-parallel-agentsandsubagent-driven-development.-----+This enables
spawn_agent,wait_agent, andclose_agentfor skills likedispatching-parallel-agentsandsubagent-driven-development.------## Named agent dispatch
------Claude Code skills reference named agent types like
superpowers:code-reviewer.------Codex does not have a named agent registry —
spawn_agentcreates generic agents------from built-in roles (
default,explorer,worker).------When a skill says to dispatch a named agent type:
------1. Find the agent's prompt file (e.g.,
agents/code-reviewer.mdor the skill's------ local prompt template like
code-quality-reviewer-prompt.md)------2. Read the prompt content
------3. Fill any template placeholders (
{BASE_SHA},{WHAT_WAS_IMPLEMENTED}, etc.)------4. Spawn a
workeragent with the filled content as themessageTask tool (superpowers:code-reviewer)spawn_agent(agent_type="worker", message=...)withcode-reviewer.mdcontentTask tool (general-purpose)with inline promptspawn_agent(message=...)with the same prompt------### Message framing
------The
messageparameter is user-level input, not a system prompt. Structure it------for maximum instruction adherence:
------```
------Your task is to perform the following. Follow the instructions below exactly.
------
------[filled prompt content from the agent's .md file]
------
------Execute this now. Output ONLY the structured response following the format
------specified in the instructions above.
------```
------- Use task-delegation framing ("Your task is...") rather than persona framing ("You are...")
------- Wrap instructions in XML tags — the model treats tagged blocks as authoritative
------- End with an explicit execution directive to prevent summarization of the instructions
------### When this workaround can be removed
------This approach compensates for Codex's plugin system not yet supporting an
agents------field in
plugin.json. WhenRawPluginManifestgains anagentsfield, the------plugin can symlink to
agents/(mirroring the existingskills/symlink) and------skills can dispatch named agent types directly.
-----+Legacy note: Codex builds before
rust-v0.115.0exposed spawned-agent-----+waiting as
wait. Current Codex useswait_agentfor spawned agents. The-----+
waitname now belongs to code-modeexec/wait, which resumes a yielded exec-----+cell by
cell_id; it is not the spawned-agent result tool.----- ## Environment Detection
-----diff --git a/skills/superpowers/using-superpowers/references/copilot-tools.md b/skills/superpowers/using-superpowers/references/copilot-tools.md
-----index 4316cdb..ae3cf5a 100644
-------- a/skills/superpowers/using-superpowers/references/copilot-tools.md
-----+++ b/skills/superpowers/using-superpowers/references/copilot-tools.md
-----@@ -12,23 +12,13 @@ Skills use Claude Code tool names. When you encounter these in a skill, use your
----- |
Glob(search files by name) |glob|----- |
Skilltool (invoke a skill) |skill|----- |
WebFetch|web_fetch|------|
Tasktool (dispatch subagent) |task(see Agent types) |-----+|
Tasktool (dispatch subagent) |taskwithagent_type: "general-purpose"or"explore"|----- | Multiple
Taskcalls (parallel) | Multipletaskcalls |----- | Task status/output |
read_agent,list_agents|----- |
TodoWrite(task tracking) |sqlwith built-intodostable |----- |
WebSearch| No equivalent — useweb_fetchwith a search engine URL |----- |
EnterPlanMode/ExitPlanMode| No equivalent — stay in the main session |------## Agent types
------Copilot CLI's
tasktool accepts anagent_typeparameter:general-purpose"general-purpose"Explore"explore"superpowers:code-reviewer)----- ## Async shell sessions
----- Copilot CLI supports persistent async shell sessions, which have no direct Claude Code equivalent:
-----diff --git a/skills/superpowers/using-superpowers/references/gemini-tools.md b/skills/superpowers/using-superpowers/references/gemini-tools.md
-----index f869803..91ef404 100644
-------- a/skills/superpowers/using-superpowers/references/gemini-tools.md
-----+++ b/skills/superpowers/using-superpowers/references/gemini-tools.md
-----@@ -14,11 +14,29 @@ Skills use Claude Code tool names. When you encounter these in a skill, use your
----- |
Skilltool (invoke a skill) |activate_skill|----- |
WebSearch|google_web_search|----- |
WebFetch|web_fetch|------|
Tasktool (dispatch subagent) | No equivalent — Gemini CLI does not support subagents |-----+|
Tasktool (dispatch subagent) |@agent-name(see Subagent support) |------## No subagent support
-----+## Subagent support
------Gemini CLI has no equivalent to Claude Code's
Tasktool. Skills that rely on subagent dispatch (subagent-driven-development,dispatching-parallel-agents) will fall back to single-session execution viaexecuting-plans.-----+Gemini CLI supports subagents natively via the
@syntax. Use the built-in@generalistagent to dispatch any task — it has access to all tools and follows the prompt you provide.-----+
-----+When a skill says to dispatch a named agent type, use
@generalistwith the full prompt from the skill's prompt template:-----+
-----+| Skill instruction | Gemini CLI equivalent |
-----+|-------------------|----------------------|
-----+|
Task tool (superpowers:implementer)|@generalistwith the filledimplementer-prompt.mdtemplate |-----+|
Task tool (superpowers:spec-reviewer)|@generalistwith the filledspec-reviewer-prompt.mdtemplate |-----+|
Task tool (superpowers:code-reviewer)|@code-reviewer(bundled agent) or@generalistwith the filled review prompt |-----+|
Task tool (superpowers:code-quality-reviewer)|@generalistwith the filledcode-quality-reviewer-prompt.mdtemplate |-----+|
Task tool (general-purpose)with inline prompt |@generalistwith your inline prompt |-----+
-----+### Prompt filling
-----+
-----+Skills provide prompt templates with placeholders like
{WHAT_WAS_IMPLEMENTED}or[FULL TEXT of task]. Fill all placeholders and pass the complete prompt as the message to@generalist. The prompt template itself contains the agent's role, review criteria, and expected output format —@generalistwill follow it.-----+
-----+### Parallel dispatch
-----+
-----+Gemini CLI supports parallel subagent dispatch. When a skill asks you to dispatch multiple independent subagent tasks in parallel, request all of those
@generalistor named subagent tasks together in the same prompt. Keep dependent tasks sequential, but do not serialize independent subagent tasks just to preserve a simpler history.----- ## Additional Gemini CLI tools
-----diff --git a/skills/superpowers/writing-plans/SKILL.md b/skills/superpowers/writing-plans/SKILL.md
-----index 0d9c00b..847412e 100644
-------- a/skills/superpowers/writing-plans/SKILL.md
-----+++ b/skills/superpowers/writing-plans/SKILL.md
-----@@ -13,7 +13,7 @@ Assume they are a skilled developer, but know almost nothing about our toolset o
----- Announce at start: "I'm using the writing-plans skill to create the implementation plan."
------Context: This should be run in a dedicated worktree (created by brainstorming skill).
-----+Context: If working in an isolated worktree, it should have been created via the
superpowers:using-git-worktreesskill at execution time.----- Save plans to:
docs/superpowers/plans/YYYY-MM-DD-<feature-name>.md----- - (User preferences for plan location override this default)
-----diff --git a/update_summary.md b/update_summary.md
-----index adc2819..2ff7b8d 100644
-------- a/update_summary.md
-----+++ b/update_summary.md
-----@@ -1,1955 +1,1036 @@
----- ## Updated Skills
------Submodule skills/AI-research-SKILLs 9aff750..28f2d29:
------ > feat: add Agent-Native Research Artifact (ARA) category — 23rd, 3 skills
------Submodule skills/scientific-agent-skills 33b69c5..37a148b:
-----+Submodule skills/scientific-agent-skills 37a148b..cbcae7b:
----- > chore: update security scan report [skip ci]
------ > Merge pull request #141 from renato-umeton/feature/autoskill
------ > Merge pull request #145 from xiaolai/fix/nlpm-uv-uv-pip-install
------ > Merge pull request #146 from xiaolai/fix/nlpm-latchbio-uv-install
------ > Add support of Hugging Science
------ > Add author
------ > Bump version
------ > Update Pyhealth
------ > docs: remove community section from README
------ > fix: disclose data transmission to api.parallel.ai and openrouter.ai in research-lookup (#149)
------ > feat: enhance infographic generation with context image support
------ > fix: upgrade infographic review to Gemini 3.1 Pro and harden review failure handling (#153)
------diff --git a/update_summary.md b/update_summary.md
------index 67c512f..98b6e19 100644
--------- a/update_summary.md
------+++ b/update_summary.md
------@@ -1,1933 +1,2 @@
------ ## Updated Skills
-------Submodule skills/scientific-agent-skills aaf95ee..33b69c5:
------- > chore: update security scan report [skip ci]
------- > chore: update security scan report [skip ci]
-------diff --git a/update_summary.md b/update_summary.md
-------index 23c8fb5..98b6e19 100644
---------- a/update_summary.md
-------+++ b/update_summary.md
-------@@ -1,1923 +1,2 @@
------- ## Updated Skills
--------Submodule skills/AI-research-SKILLs 05f1958..9aff750:
-------- > fix: correct welcome screen defaults and sync package-lock.json
-------- > Merge pull request #51 from RUFFY-369/feat/hermes-agent-support
--------Submodule skills/scientific-agent-skills eb20fb0..aaf95ee:
-------- > chore: update version of scientific-agent-skills to 2.37.1
-------- > docs: enhance README with installation options for Scientific Agent Skills
-------- > chore: update security scan report [skip ci]
-------- > enhance: integrate parallel-web skill for literature reviews and research lookups
-------- > refactor: update output file formats in parallel-web references to JSON
-------- > chore: update security scan report [skip ci]
--------diff --git a/update_summary.md b/update_summary.md
--------index 0ed368e..98b6e19 100644
----------- a/update_summary.md
--------+++ b/update_summary.md
--------@@ -1,1906 +1,2 @@
-------- ## Updated Skills
---------Submodule skills/AI-research-SKILLs 22bca4d..05f1958:
--------- > Merge pull request #47 from Gitsamshi/main
--------- > Refactor ml-paper-writing: extract systems-paper-writing skill, bump to v1.5.2
--------- > Merge pull request #48 from tianhao909/tianhao909-add-mlsys-260408
---------diff --git a/update_summary.md b/update_summary.md
---------index cf32912..98b6e19 100644
------------ a/update_summary.md
---------+++ b/update_summary.md
---------@@ -1,1895 +1,2 @@
--------- ## Updated Skills
----------Submodule skills/AI-research-SKILLs a728954..22bca4d:
---------- > Merge pull request #31 from dailycafi/add-ml-training-recipes
---------- > docs: add citation guidance for researchers using the library
----------Submodule skills/claude-scientific-skills contains modified content
----------Submodule skills/claude-scientific-skills 71add64..899a51b:
---------- > Simplify installation
---------- > Remove skill that LLMs already know well and some old skills. Also updated Rowan skill.
---------- > Merge pull request #120 from corinwagen/main
---------- > Add optimize-for-gpu skill
---------- > Update Adaptyv Bio skill to use new API
---------- > Update README, examples and kills list
---------- > Add paper-lookup skill
---------- > Remove old literature databases
---------- > Add combined database-lookup skill
---------- > Update torch-geometric skill
---------- > Remove all individual skill databases which are now part of database-lookup
----------Submodule skills/humanizer 12881ab..8b3a178:
---------- > Add passive voice rule to humanizer (#80)
---------- > Integrate remaining prompt updates coherently (#79)
---------- > feat: add OpenCode support (#47)
---------- > Merge pull request #77 from spiritualhost/less-actually
---------- > Merge pull request #74 from marcoenricovd-lang/fix/warp-pattern-count
---------- > Merge pull request #64 from mvanhorn/feat/voice-calibration
----------diff --git a/skills/superpowers/using-superpowers/SKILL.md b/skills/superpowers/using-superpowers/SKILL.md
----------index d813535..c8a8570 100644
------------- a/skills/superpowers/using-superpowers/SKILL.md
----------+++ b/skills/superpowers/using-superpowers/SKILL.md
----------@@ -29,13 +29,15 @@ If CLAUDE.md, GEMINI.md, or AGENTS.md says "don't use TDD" and a skill says "alw
---------- In Claude Code: Use the
Skilltool. When you invoke a skill, its content is loaded and presented to you—follow it directly. Never use the Read tool on skill files.----------+In Copilot CLI: Use the
skilltool. Skills are auto-discovered from installed plugins. Theskilltool works the same as Claude Code'sSkilltool.----------+
---------- In Gemini CLI: Skills activate via the
activate_skilltool. Gemini loads skill metadata at session start and activates the full content on demand.---------- In other environments: Check your platform's documentation for how skills are loaded.
---------- ## Platform Adaptation
-----------Skills use Claude Code tool names. Non-CC platforms: see
references/codex-tools.md(Codex) for tool equivalents. Gemini CLI users get the tool mapping loaded automatically via GEMINI.md.----------+Skills use Claude Code tool names. Non-CC platforms: see
references/copilot-tools.md(Copilot CLI),references/codex-tools.md(Codex) for tool equivalents. Gemini CLI users get the tool mapping loaded automatically via GEMINI.md.---------- # Using Skills
----------diff --git a/update_summary.md b/update_summary.md
----------index 4db0e51..98b6e19 100644
------------- a/update_summary.md
----------+++ b/update_summary.md
----------@@ -1,1844 +1,2 @@
---------- ## Updated Skills
-----------Submodule skills/AI-research-SKILLs 085c480..a728954:
----------- > fix: update marketplace.json to include academic-plotting skill
----------- > refactor: restructure ml-paper-writing skill into nested directory
----------- > Merge pull request #41 from Orchestra-Research/add-academic-plotting-skill
----------- > docs: add concrete OpenClaw cron.add instructions to autoresearch skill
----------- > chore: Gitignore marketing drafts and image in autoresearch skill
----------- > docs: add contributors widget and clean up contributing section
----------- > Merge pull request #39 from tang-vu/contribai/fix/security/critical-prompt-injection-in-claude-code
-----------Submodule skills/claude-scientific-skills contains modified content
-----------Submodule skills/claude-scientific-skills 1346c01..71add64:
----------- > Remove planning with files skill becasue it is specific to Claude Code
----------- > Make writing skills more explicit
----------- > Add Security Disclaimer section to README
----------- > Bump version
----------- > Improve token discovery for Modal
----------- > Update Modal skill
----------- > Add planning with files skill from @OthmanAdi
----------- > Add K-Dense BYOK AI co-scientist to README with features and links
----------- > Add writing skills
-----------Submodule skills/humanizer d8085c7..12881ab:
----------- > Merge pull request #56 from mvanhorn/osc/42-add-hyphenation-pattern
----------- > Merge pull request #57 from mvanhorn/osc/35-remove-separator-rules
----------- > Merge pull request #58 from mvanhorn/osc/7-add-license-file
-----------Submodule skills/paper-polish-workflow-skill 7e430bd..bb72126:
----------- > fix: track assets/logo.jpg so README logo displays on GitHub
----------- > fix: correct SKILL.md path in CI validation workflow
----------- > fix: remove package.json to prevent recursive npm nesting
----------- > fix: remove duplicate files to fix ENAMETOOLONG on plugin install
----------- > fix: add explicit skills path in plugin.json
----------- > fix: update plugin.json version to 2.3.0
----------- > fix: remove .planning/ from git tracking (136 files)
----------- > fix: use HTTPS git URL instead of GitHub SSH source
----------- > fix: switch marketplace source from npm to GitHub repo
----------- > fix: add explicit npmjs.com registry to marketplace.json
----------- > feat: migrate to official Claude Code plugin marketplace, bump v2.3.0
----------- > feat: add Claude Code plugin format with auto-install postinstall script
----------- > feat: add get-paper skill, bump to v2.2.0
-----------diff --git a/skills/superpowers/brainstorming/SKILL.md b/skills/superpowers/brainstorming/SKILL.md
-----------index edbc2b5..06cd0a2 100644
-------------- a/skills/superpowers/brainstorming/SKILL.md
-----------+++ b/skills/superpowers/brainstorming/SKILL.md
-----------@@ -27,7 +27,7 @@ You MUST create a task for each of these items and complete them in order:
----------- 4. Propose 2-3 approaches — with trade-offs and your recommendation
----------- 5. Present design — in sections scaled to their complexity, get user approval after each section
----------- 6. Write design doc — save to
docs/superpowers/specs/YYYY-MM-DD-<topic>-design.mdand commit------------7. Spec review loop — dispatch spec-document-reviewer subagent with precisely crafted review context (never your session history); fix issues and re-dispatch until approved (max 3 iterations, then surface to human)
-----------+7. Spec self-review — quick inline check for placeholders, contradictions, ambiguity, scope (see below)
----------- 8. User reviews written spec — ask user to review the spec file before proceeding
----------- 9. Transition to implementation — invoke writing-plans skill to create implementation plan
-----------@@ -43,8 +43,7 @@ digraph brainstorming {
----------- "Present design sections" [shape=box];
----------- "User approves design?" [shape=diamond];
----------- "Write design doc" [shape=box];
------------ "Spec review loop" [shape=box];
------------ "Spec review passed?" [shape=diamond];
-----------+ "Spec self-review\n(fix inline)" [shape=box];
----------- "User reviews spec?" [shape=diamond];
----------- "Invoke writing-plans skill" [shape=doublecircle];
-----------@@ -57,10 +56,8 @@ digraph brainstorming {
----------- "Present design sections" -> "User approves design?";
----------- "User