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Agent skill

Research Phase

by alchemiststudiosDOTai in alchemiststudiosDOTai/harness-engineering

This skill should be used when mapping or researching a codebase to understand its structure, patterns, and architecture.

MITAuto-check: notes

Install Research Phase

skills CLI
$ npx skills add alchemiststudiosDOTai/harness-engineering --skill research-phase -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install alchemiststudiosDOTai/harness-engineering research-phase --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/alchemiststudiosDOTai/harness-engineering.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/research-phase .claude/skills/research-phase && rm -rf skills-src

Use ~/.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/

Facts

Skill name
research-phase
GitHub stars
105
Token cost
~1.4k tokens
SKILL.md length
373 words
Files
5 (incl. scripts)
Skills in repo
8
Repo updated
First seen
Licence
MIT

At a glance

This skill should be used when mapping or researching a codebase to understand its structure, patterns, and architecture.

  • Works in 4 steps: Deploy 3 Research Tasks in Parallel → Run Scripts for Structural Analysis → Wait and Synthesize → …
  • The user asks to map the codebase
  • SKILL.md covers Core Principle, Available Scripts, Research Workflow and When to Use Each Script, plus 2 more sections
  • Runs Shell scripts from its folder

What it does

Research Phase is an agent skill from alchemiststudiosDOTai/harness-engineering. This skill should be used when mapping or researching a codebase to understand its structure, patterns, and architecture. Use when the user asks to "map the codebase", "research how X works", "find all Y patterns", or needs to understand code organization. Produces factual structural maps in .artifacts/research/—no suggestions, no recommendations, just what exists. Uses ast-grep for structural pattern matching.

Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts (for example `scripts/ast-scan.sh`, `scripts/dependency-graph.sh` and `scripts/structure-map.sh`).

The repository describes itself as: harness-engineering discussion of shortcuts, automation, hacks and overall productivity with code agents like claude code, codex, and other harness. The licence is MIT.

When your agent uses it

  • The user asks to map the codebase
  • Research how X works
  • Find all Y patterns
  • Needs to understand code organization

Example prompts

  • “map the codebase”
  • “research how X works”
  • “find all Y patterns”
  • “/research-phase”

Requirements

  • A Bash shell
  • Pre-approved tools (allowed-tools): Bash, Read, Write, Edit, Glob, Grep, Agent

Workflow steps

4 steps, taken from the step headings in SKILL.md.

  1. Deploy 3 Research Tasks in Parallel
  2. Run Scripts for Structural Analysis
  3. Wait and Synthesize
  4. Document Findings

What it can do on your machine

Read from SKILL.md and the folder at commit 7a9fa15. 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:

    • Bash
    • Read
    • Write
    • Edit
    • Glob
    • Grep
    • Agent

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 4 files in scripts/ (Shell), which the agent can run.

    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

Research Phase loads about 1.4k tokens when it runs. Until then it costs about 107 tokens; SKILL.md has 373 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~107
When it runs · the whole SKILL.md, loaded when a task matches
~1.4k

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: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
    allowed-tools: Bash, Read, Write, Edit, Glob, Grep, Agent

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); the scripts in this folder are not scanned.

SKILL.md

The full file from alchemiststudiosDOTai/harness-engineering at commit 7a9fa15, republished under its MIT licence (© alchemiststudiosDOTai). 373 words, ~1,407 tokens.

Download SKILL.mdSave it as .claude/skills/research-phase/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.
name
research-phase
description
This skill should be used when mapping or researching a codebase to understand its structure, patterns, and architecture. Use when the user asks to "map the codebase", "research how X works", "find all Y patterns", or needs to understand code organization. Produces factual structural maps in .artifacts/research/—no suggestions, no recommendations, just what exists. Uses ast-grep for structural pattern matching.
allowed-tools
Bash, Read, Write, Edit, Glob, Grep, Agent
writes-to
.artifacts/research/
hard-guards
Facts only - no recommendations or implementation advice, Store research output in .artifacts/research/, Include exact file paths and line numbers where…

Research Phase

Map and document codebase structure using structural analysis. This skill produces factual maps only—no suggestions, no recommendations, no opinions. Document what exists, where it lives, and how it connects.

Core Principle

Map, don't suggest. The output is a structural map that another developer (or Claude instance) can use to navigate the codebase. Include:

  • File paths with line numbers
  • Pattern locations
  • Dependency relationships
  • Symbol definitions

Exclude:

  • Improvement suggestions
  • Refactoring recommendations
  • "Should" or "could" statements
  • Opinions about code quality

Available Scripts

scripts/ast-scan.sh - Structural Pattern Scanner

Find code patterns using ast-grep.

bash
# Scan for all function definitions
scripts/ast-scan.sh functions src/

# Find all class definitions
scripts/ast-scan.sh classes

# Find all exports
scripts/ast-scan.sh exports lib/

# Find API routes
scripts/ast-scan.sh routes

# Available patterns: functions, classes, exports, imports, types, components, routes, handlers, all
scripts/structure-map.sh - Directory Tree

Generate filtered directory structure.

bash
# Basic tree (auto-filters node_modules, .git, etc.)
scripts/structure-map.sh ./

# Limit depth
scripts/structure-map.sh ./ --depth 3

# Code files only
scripts/structure-map.sh src/ --code-only

# Include file counts
scripts/structure-map.sh ./ --with-stats
scripts/symbol-index.sh - Public Symbol Index

Extract all exported/public symbols.

bash
# Index all exports
scripts/symbol-index.sh src/

# Shows: exported functions, classes, types, interfaces, constants
scripts/dependency-graph.sh - Import Tracer

Map dependency relationships.

bash
# Show all imports
scripts/dependency-graph.sh src/

# Trace specific file's dependencies
scripts/dependency-graph.sh ./ --file src/core/auth.ts

# Shows: what it imports + what imports it

Research Workflow

Step 1: Deploy 3 Research Tasks in Parallel

If subagents are available: Spawn exactly 3 Task research tasks in parallel for comprehensive coverage.

Deploy these tasks simultaneously in a single message:

  1. codebase-locator - Find WHERE files and components live

    • Prompt: "Locate all files related to [topic]. Find directory structure, entry points, and related modules."

  2. codebase-analyzer - Understand HOW specific code works

    • Prompt: "Analyze the implementation of [component]. Map function signatures, class hierarchies, and data flow."

  3. context-synthesis - Connect findings across components

    • Prompt: "Find connections between [area A] and [area B]. Trace dependencies and shared patterns."
YOU MUST DEPLOY ALL 3 TASKS IN A SINGLE MESSAGE
DO NOT DEPLOY SEQUENTIALLY - USE PARALLEL TASK CALLS

If subagents are NOT available: Execute the workflow in order — locator first, then analyzer, then synthesis.

Show full SKILL.md (149 more words)Show less
Step 2: Run Scripts for Structural Analysis

While waiting for agents, run ast-grep scripts:

bash
scripts/structure-map.sh ./ --with-stats
scripts/ast-scan.sh all src/
scripts/symbol-index.sh src/
Step 3: Wait and Synthesize

Wait for ALL research tasks to complete, then compile findings:

  • Merge agent results with script output
  • Cross-reference file paths
  • Identify patterns across different findings
Step 4: Document Findings

Create .artifacts/research/YYYY-MM-DD_HH-MM-SS_<topic>.md using format:

markdown
---
title: "<topic> research findings"
link: "<topic>-research"
type: research
ontological_relations:
  - relates_to: [[<related-doc>]]
tags: [research, <topic>]
uuid: "<uuid>"
created_at: "<ISO-8601 timestamp>"
---

## Structure
- Directory layout with purposes

## Key Files
- `path/file.ts:L123` → what it defines

## Patterns Found
- Pattern name: locations where it appears

## Dependencies
- Module A → imports → Module B

## Symbol Index
- Exported symbols with locations

When to Use Each Script

NeedScript
"What's the file structure?"structure-map.sh
"Where are the functions?"ast-scan.sh functions
"What does this module export?"symbol-index.sh
"What depends on this file?"dependency-graph.sh --file
"Where are the API routes?"ast-scan.sh routes
"Find all React components"ast-scan.sh components

Output Requirements

All research output must:

  • Include exact file paths
  • Include line numbers where applicable
  • State only what was found (no interpretation)
  • Group related findings together
  • Be reproducible (another scan would find the same things)

Handoff

After writing the research document to .artifacts/research/, proceed to plan-phase if the next step is the Plan phase.

© alchemiststudiosDOTai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 4 other files (scripts) in skills/research-phase of alchemiststudiosDOTai/harness-engineering.

  • SKILL.md
  • scripts/ast-scan.sh
  • scripts/dependency-graph.sh
  • scripts/structure-map.sh
  • scripts/symbol-index.sh

Open the folder on GitHubat commit 7a9fa15

Compare with similar skills

Research Phase 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.

Research Phase compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Research Phase this skillalchemiststudiosDOTai/harness-engineering105—~1.4kAutomated safety check: NotesMIT
UX Researcher Designeralirezarezvani/claude-skills28k1 repos~3kAutomated safety check: PassMIT
Researchalirezarezvani/claude-skills28k—~4.3kAutomated safety check: PassMIT
Research Ops Skillsalirezarezvani/claude-skills28k—~2.8kAutomated safety check: PassMIT
Deep Researchruvnet/ruflo74k1 repos~1.3kAutomated safety check: NotesMIT
Researchcodewhale-hq/Codewhale41k—~138Automated safety check: PassMIT

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More from alchemiststudiosDOTai/harness-engineering

All 8 skills in this repo

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  • Execute Phase

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    Execute implementation plans from .artifacts/plan/. An agent skill from alchemiststudiosDOTai/harness-engineering.

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  • Harness Map

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  • Agents Md Mapper

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    This skill should be used when creating, refreshing, or validating a repository AGENTS.md so it stays concise, current, and grounded in repository evidence.

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  • Differential Session Runner

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  • Plan Phase

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    Generate execution-ready implementation plans from research docs - planning ONLY, no fixing or verifying.

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Questions about Research Phase

What does Research Phase do?

This skill should be used when mapping or researching a codebase to understand its structure, patterns, and architecture. Research Phase is an agent skill from alchemiststudiosDOTai/harness-engineering. This skill should be used when mapping or researching a codebase to understand its structure, patterns, and architecture.

When should I use Research Phase?

Research Phase fits situations like: the user asks to map the codebase; research how X works; find all Y patterns; needs to understand code organization.

How do I install Research Phase in Claude Code?

Run `npx skills add alchemiststudiosDOTai/harness-engineering --skill research-phase -a claude-code`. Or copy the skill folder (skills/research-phase in alchemiststudiosDOTai/harness-engineering) into .claude/skills/research-phase in your project. Claude Code loads it when a task matches its description.

How do I install Research Phase in Codex?

Run `npx skills add alchemiststudiosDOTai/harness-engineering --skill research-phase -a codex`. Or copy the skill folder (skills/research-phase in alchemiststudiosDOTai/harness-engineering) into .agents/skills/research-phase in your project. Codex loads it when a task matches its description.

Can I use Research Phase 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 alchemiststudiosDOTai/harness-engineering --skill research-phase -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/research-phase, .gemini/skills/research-phase, .github/skills/research-phase and .opencode/skills/research-phase in your project.

What does Research Phase need to run?

Going by SKILL.md and its folder, Research Phase needs a shell for the scripts in its folder. Our summary lists: A Bash shell. Its frontmatter pre-approves these tools: Bash, Read, Write, Edit, Glob, Grep, Agent.

Does Research Phase 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 Research Phase safe to install?

Our automated static check of SKILL.md found notes only (pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Research Phase use?

Research Phase 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 Research Phase use?

About 1.4k tokens (SKILL.md is roughly 5.6k 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 Research Phase?

Skills that share tags, products or a category with Research Phase: UX Researcher Designer (alirezarezvani/claude-skills, 28k stars), Research (alirezarezvani/claude-skills, 28k stars), Research Ops Skills (alirezarezvani/claude-skills, 28k stars) and Deep Research (ruvnet/ruflo, 74k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Research Phase?

alchemiststudiosDOTai (a GitHub organization) maintains it in alchemiststudiosDOTai/harness-engineering, which has 105 GitHub stars. The repository holds 8 skills in this directory. The repository was last updated on March 17, 2026.

Source: alchemiststudiosDOTai/harness-engineering on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.