Java Refactoring Extract Method
github/awesome-copilot
Refactoring using Extract Methods in Java Language. An agent skill from github/awesome-copilot.
Extract and compare data-collection methods across a set of empirical papers.
MITAuto-check passed
Install Method Audit
$ npx skills add flonat/flonat-research --skill method-audit -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install flonat/flonat-research method-audit --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/flonat/flonat-research.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/method-audit .claude/skills/method-audit && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "method-audit" agent skill from https://github.com/flonat/flonat-research/tree/main/skills/method-audit into .claude/skills/method-audit/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "method-audit", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/flonat/flonat-research/tree/main/skills/method-auditType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add flonat/flonat-research --skill method-audit -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install flonat/flonat-research method-audit --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/flonat/flonat-research.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/method-audit .agents/skills/method-audit && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "method-audit" agent skill from https://github.com/flonat/flonat-research/tree/main/skills/method-audit into .agents/skills/method-audit/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "method-audit", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add flonat/flonat-research --skill method-audit -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install flonat/flonat-research method-audit --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/flonat/flonat-research.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/method-audit .cursor/skills/method-audit && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "method-audit" agent skill from https://github.com/flonat/flonat-research/tree/main/skills/method-audit into .cursor/skills/method-audit/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "method-audit", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/flonat/flonat-research.git --path skills/method-audit--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add flonat/flonat-research --skill method-audit -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install flonat/flonat-research method-audit --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/flonat/flonat-research.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/method-audit .gemini/skills/method-audit && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "method-audit" agent skill from https://github.com/flonat/flonat-research/tree/main/skills/method-audit into .gemini/skills/method-audit/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "method-audit", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install flonat/flonat-research method-auditInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add flonat/flonat-research --skill method-audit -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/flonat/flonat-research.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/method-audit .github/skills/method-audit && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "method-audit" agent skill from https://github.com/flonat/flonat-research/tree/main/skills/method-audit into .github/skills/method-audit/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "method-audit", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add flonat/flonat-research --skill method-audit -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install flonat/flonat-research method-audit --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/flonat/flonat-research.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/method-audit .opencode/skills/method-audit && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "method-audit" agent skill from https://github.com/flonat/flonat-research/tree/main/skills/method-audit into .opencode/skills/method-audit/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "method-audit", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
method-audit- GitHub stars
- 145
- Token cost
- ~1.7k tokens
- SKILL.md length
- 598 words
- Files
- 1
- Skills in repo
- 83
- Repo updated
- First seen
- Licence
- MIT
At a glance
Extract and compare data-collection methods across a set of empirical papers.
- Works in 4 steps: Corpus Assembly → Method Extraction → Comparative Analysis → …
- The user needs a cross-paper methods matrix
- SKILL.md covers Output Path, When to Use, When NOT to Use and Input, plus 3 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Method Audit is an agent skill from flonat/flonat-research. Extract and compare data-collection methods across a set of empirical papers. Use when the user needs a cross-paper methods matrix or wants to assess how a literature gathers evidence.
Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
The repository describes itself as: Shareable Claude Code + Codex infrastructure for PhD researchers — skills, agents, hooks, and rules for academic workflows. The licence is MIT.
When your agent uses it
- The user needs a cross-paper methods matrix
- Wants to assess how a literature gathers evidence
Example prompts
- “/method-audit”
Requirements
- Pre-approved tools (allowed-tools): Read, Write, Edit, Glob, Grep, Bash(uv*), Bash(uv:*), Task, WebSearch, WebFetch, Bash(paperpile*)
Workflow steps
4 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit da27600. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves these tools, so the agent can use them without asking each time:
ReadWriteEditGlobGrepBash(uv*)Bash(uv:*)TaskWebSearchWebFetch
…and 1 more on the same allowed-tools line.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are markdown).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Method Audit loads about 1.7k tokens when it runs. Until then it costs about 49 tokens; SKILL.md has 598 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from flonat/flonat-research at commit da27600, republished under its MIT licence (© flonat). 598 words, ~1,669 tokens.
Download SKILL.mdSave it as
.claude/skills/method-audit/SKILL.md (or your agent's skills folder).- name
- method-audit
- description
- Extract and compare data-collection methods across a set of empirical papers. Use when the user needs a cross-paper methods matrix or wants to assess how a literature gathers evidence.
- allowed-tools
- Read, Write, Edit, Glob, Grep, Bash(uv*), Bash(uv:*), Task, WebSearch, WebFetch, Bash(paperpile*)
- argument-hint
- [topic, .bib file, or paper directory]
- skill-dependencies
- causal-design, split-pdf
Method Audit
Reverse-engineer the data collection and empirical methods across a corpus of papers. Produce a critical comparison table that surfaces methodological blind spots.
Output Path
Per rules/review-artefact-routing.md (auto-loads in research projects (path-scoped to paper-*/ and paper/)):
- Source slug:
method-audit - Write reports to:
reviews/_project/method-audit/<YYYY-MM-DD-HHMM>.mdinside the project. Path is relative to the research project root, not the Task-Management repo. - Never at project root (
./CRITIC-REPORT.md-style filenames are forbidden — pre-rule layout). - Idempotency: timestamps include hour+minute (HHMM) to disambiguate same-day runs; never overwrite an earlier run's report.
- Index update: if
reviews/INDEX.mdexists, write a one-line entry under "Latest per source" pointing at the new file. Otherwisereview-recapwill rebuild the index next time it runs. - Infrastructure repos (Task-Management, atlas-workspace, etc.): this section does not apply — the path-scoped rule won't load there.
When to Use
- Writing a methodology section — need to justify your approach relative to the literature
- Reviewing empirical papers — need to compare data quality across studies
- Identifying methodological gaps — what approach has nobody tried yet?
- Preparing a replication or extension — need to understand exactly how prior work was done
When NOT to Use
- Theoretical papers — use an installed theoretical-comparison workflow instead
- Single-paper deep read — use
split-pdf - Your own research design — use
causal-designorexperiment-design - Code review — use the
code-reviewagent
Input
A .bib file, PDF directory, topic description, or list of papers. If ambiguous, ask.
Workflow
Phase 1: Corpus Assembly
Assemble 10-20 empirical papers from the supplied bibliography or directory, or through configured scholarly-search tools. Prioritise papers with empirical content and filter out pure theory, editorials, and commentaries.
Phase 2: Method Extraction
For each paper, read using split-pdf methodology. Extract:
- Research design — experimental, quasi-experimental, observational, survey, qualitative, mixed
- Data source — where the data comes from (name the dataset, survey instrument, or archive)
- Sample
- Population and sampling frame
- Sample size (N)
- Unit of observation
- Time period
- Response rate (if survey)
- Attrition (if longitudinal)
- Variables
- Dependent variable(s) and how measured
- Key independent variable(s) and how measured
- Controls included
- Estimation strategy
- Statistical method (OLS, IV, DiD, RCT, qualitative coding, etc.)
- Identification strategy (what makes the estimate causal, if claimed)
- Robustness checks reported
- Biases acknowledged — what limitations the authors discuss
- Biases NOT acknowledged — what you can spot that they don't mention
Show full SKILL.md (226 more words)Show less
Phase 3: Comparative Analysis
3.1 Methods Comparison Table
| Paper | Design | Data Source | N | Period | Method | ID Strategy | Response Rate |
|---|
Sort by sample size (largest first).
3.2 Technique Distribution
Count how many papers use each:
- Design type (experimental, observational, etc.)
- Estimation method (OLS, IV, DiD, etc.)
- Data type (survey, admin, experimental, scraped, etc.)
Flag any technique that is dominant (>60% of papers) — this signals a methodological monoculture.
3.3 Bias Audit
For each paper, classify biases:
| Paper | Biases Acknowledged | Biases Missed | Severity |
|---|
Common missed biases to check for:
- Selection bias — non-random sampling without correction
- Measurement error — self-reported outcomes, proxy variables
- External validity — single-country, single-firm, WEIRD samples
- Survivorship bias — studying only firms/people that survived
- Publication bias — significant results overrepresented
- Endogeneity — causal claims without credible identification
- Multiple testing — many outcomes tested without correction
3.4 Methodological Gaps
- Designs nobody has tried (e.g., no RCT in a field of observational studies)
- Data sources nobody has used (e.g., admin data when everyone uses surveys)
- Robustness checks nobody runs (e.g., no placebo tests, no sensitivity analysis)
- Populations understudied (e.g., only US data in a global phenomenon)
Phase 4: Output
Write to METHOD-AUDIT.md in the project directory.
Output Format
# Method Audit: [Topic]
**Date:** YYYY-MM-DD
**Corpus:** [N] empirical papers
**Dominant design:** [Most common research design]
**Dominant method:** [Most common estimation method]
## Comparison Table
| Paper | Design | Data | N | Period | Method | ID Strategy | Biases Noted |
|-------|--------|------|---|--------|--------|-------------|-------------|
## Technique Distribution
| Category | Count | Papers |
|----------|-------|--------|
## Bias Audit
### Commonly Acknowledged
- [Bias type] — mentioned by [N] papers
### Commonly Missed
- [Bias type] — present in [N] papers but acknowledged by [M]
- **Why it matters:** [Impact on findings]
- **Papers affected:** [List]
## Methodological Gaps
1. **No [design/method] studies** — [Why this matters]
2. **Understudied population:** [Who is missing]
3. **Missing robustness check:** [What should be tested]
## Implications for Your Research
- **Opportunity:** [What methodological gap you could fill]
- **Risk:** [What bias to watch for in your own design]
- **Benchmark:** [What sample size / design quality is expected in this field]Cross-References
| Skill | When to use instead/alongside |
|---|---|
| Installed theoretical-comparison workflow | For theoretical rather than methodological comparison |
causal-design | To design your own identification strategy |
experiment-design | To design experiments or surveys |
replication-audit | To check which findings have been replicated |
© flonat, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/method-audit of flonat/flonat-research.
Open the folder on GitHubat commit da27600
Compare with similar skills
Method Audit next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Method Audit this skillflonat/flonat-research | 145 | — | ~1.7k | Automated safety check: Pass | MIT | |
| Java Refactoring Extract Methodgithub/awesome-copilot | 40k | 1 repos | ~873 | Automated safety check: Pass | MIT | |
| Extractalirezarezvani/claude-skills | 28k | — | ~1.4k | Automated safety check: Pass | MIT | |
| Brand Extractnexu-io/open-design | 100k | — | ~3.1k | Automated safety check: Pass | Apache-2.0 | |
| Design Extractnexu-io/open-design | 100k | — | ~549 | Automated safety check: Pass | Apache-2.0 | |
| Refactor Method Complexity Reducegithub/awesome-copilot | 40k | 1 repos | ~1.1k | Automated safety check: Pass | MIT |
Similar skills
- Official
Extract
alirezarezvani/claude-skills
Turn a proven pattern or debugging solution into a standalone reusable skill with SKILL.md, reference docs, and examples.
Brand Extract
nexu-io/open-design
Extract a complete Brand Kit from a live website by driving the in-app browser.
Design Extract
nexu-io/open-design
Extract design tokens (color / typography / spacing) from imported source code, screenshots, or Figma exports into the canonical token bag token-map consumes.
- Official
Refactor Method Complexity Reduce
github/awesome-copilot
Refactor given method ${input:methodName} to reduce its cognitive complexity to ${input:complexityThreshold} or below, by extracting helper methods.
Kg Extract
ruvnet/ruflo
Extract entities and relations from source files to build a knowledge graph
More from flonat/flonat-research
All 83 skills in this repoLatex Posters
flonat/flonat-research
Create a large-format academic poster in LaTeX using beamerposter, tikzposter, or baposter.
Skill Creator
flonat/flonat-research
Create, revise, and evaluate reusable AI workflow skills, including trigger-quality tests.
DOCX
flonat/flonat-research
Create, read, edit, or convert Microsoft Word documents while preserving professional document structure.
PDF
flonat/flonat-research
Read, create, combine, split, rotate, OCR, watermark, secure, or extract content from PDF files.
Init Project Orchestration
flonat/flonat-research
Create or migrate project-level agents, repeatable project workflows, and planning state from one client-neutral contract, then render repository-scoped adapters for both Claude Code and Codex.
Pre Commit Audit
flonat/flonat-research
Deliver a fast pre-commit safety scan: file size, anonymity (author / affiliation strings in tex/bib), hardcoded secrets, and invisible-Unicode carriers.
Questions about Method Audit
What does Method Audit do?
Extract and compare data-collection methods across a set of empirical papers. Method Audit is an agent skill from flonat/flonat-research. Extract and compare data-collection methods across a set of empirical papers.
When should I use Method Audit?
Method Audit fits situations like: the user needs a cross-paper methods matrix; wants to assess how a literature gathers evidence.
How do I install Method Audit in Claude Code?
Run `npx skills add flonat/flonat-research --skill method-audit -a claude-code`. Or copy the skill folder (skills/method-audit in flonat/flonat-research) into .claude/skills/method-audit in your project. Claude Code loads it when a task matches its description.
How do I install Method Audit in Codex?
Run `npx skills add flonat/flonat-research --skill method-audit -a codex`. Or copy the skill folder (skills/method-audit in flonat/flonat-research) into .agents/skills/method-audit in your project. Codex loads it when a task matches its description.
Can I use Method Audit in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add flonat/flonat-research --skill method-audit -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/method-audit, .gemini/skills/method-audit, .github/skills/method-audit and .opencode/skills/method-audit in your project.
What does Method Audit need to run?
SKILL.md names no scripts, command-line tools or credentials: Method Audit is instructions for the agent only. Its frontmatter pre-approves these tools: Read, Write, Edit, Glob, Grep, Bash(uv*), Bash(uv:*), Task, WebSearch, WebFetch, Bash(paperpile*).
Does Method Audit access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Method Audit safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Method Audit use?
Method Audit is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Method Audit use?
About 1.7k tokens (SKILL.md is roughly 6.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Method Audit?
Skills that share tags, products or a category with Method Audit: Java Refactoring Extract Method (github/awesome-copilot, 40k stars), Extract (alirezarezvani/claude-skills, 28k stars), Brand Extract (nexu-io/open-design, 100k stars) and Design Extract (nexu-io/open-design, 100k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Method Audit?
flonat (a GitHub user) maintains it in flonat/flonat-research, which has 145 GitHub stars. The repository holds 83 skills in this directory. The repository was last updated on September 29, 2026.
Source: flonat/flonat-research on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.