Agent skill

Manage Project

A skill your agent uses when managing a manuscript project over time.

Install Manage Project

skills CLI

$ npx skills add Aperivue/medsci-skills --skill manage-project -a claude-code

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

GitHub CLI

$ gh skill install Aperivue/medsci-skills manage-project --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/Aperivue/medsci-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/manage-project .claude/skills/manage-project && 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/

Paste into Claude Code

Install the "manage-project" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/manage-project into .claude/skills/manage-project/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "manage-project", 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

$skill-installer install https://github.com/Aperivue/medsci-skills/tree/main/skills/manage-project

Type 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.

skills CLI

$ npx skills add Aperivue/medsci-skills --skill manage-project -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install Aperivue/medsci-skills manage-project --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/manage-project .agents/skills/manage-project && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "manage-project" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/manage-project into .agents/skills/manage-project/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "manage-project", 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.

skills CLI

$ npx skills add Aperivue/medsci-skills --skill manage-project -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install Aperivue/medsci-skills manage-project --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/manage-project .cursor/skills/manage-project && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "manage-project" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/manage-project into .cursor/skills/manage-project/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "manage-project", 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

$ gemini skills install https://github.com/Aperivue/medsci-skills.git --path skills/manage-project

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add Aperivue/medsci-skills --skill manage-project -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install Aperivue/medsci-skills manage-project --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/manage-project .gemini/skills/manage-project && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "manage-project" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/manage-project into .gemini/skills/manage-project/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "manage-project", 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.

GitHub CLI

$ gh skill install Aperivue/medsci-skills manage-project

Installs 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).

skills CLI

$ npx skills add Aperivue/medsci-skills --skill manage-project -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/manage-project .github/skills/manage-project && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "manage-project" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/manage-project into .github/skills/manage-project/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "manage-project", 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.

skills CLI

$ npx skills add Aperivue/medsci-skills --skill manage-project -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install Aperivue/medsci-skills manage-project --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/manage-project .opencode/skills/manage-project && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "manage-project" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/manage-project into .opencode/skills/manage-project/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "manage-project", 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: manage-project
GitHub stars: 331
Token cost: ~1.6k tokens
SKILL.md length: 608 words
Files: 13 (incl. scripts, references)
Skills in repo: 54
Repo updated: Oct 5, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

A skill your agent uses when managing a manuscript project over time.

Managing a manuscript project over time
SKILL.md covers Commands and Project State Conventions
Runs Python and Shell scripts from its folder; calls python3; needs ZOTERO_API_KEY
Tasks that involve Project scaffolding

What it does

Manage Project is an agent skill from Aperivue/medsci-skills. Use when managing a manuscript project over time. Scaffolds the project structure, tracks writing progress across phases, maintains project memory files, and generates submission checklists and backwards timelines (commands init, status, sync-memory, checklist, timeline).

Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 16 other files, including scripts and reference files (for example `references/init_scaffold.md`, `references/pre_submission_checklist.md` and `references/project_state_template.json`).

It sits in Research & Science, covering Project scaffolding, Agent memory and Citation management. It works with Zotero. The repository describes itself as: Agent Skills for medical research — literature search, reporting-guideline & citation checks, statistics, publication figures, submission. Works with Claude Code, Codex, Cursor &… The licence is MIT.

When your agent uses it

Managing a manuscript project over time
Tasks that involve Project scaffolding
Tasks that involve Agent memory

Example prompts

“/manage-project”

Requirements

Python 3
A Bash shell
A credential in ZOTERO_API_KEY

What it can do on your machine

Read from SKILL.md and the folder at commit 3b14ae2. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 3 files in scripts/ (Python and Shell), which the agent can run.
Shell commands in SKILL.md call:
- python3
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 these keys or tokens, usually read from environment variables:
- ZOTERO_API_KEY
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Manage Project loads about 1.6k tokens when it runs, and up to ~3.8k if it reads all its reference files. Until then it costs about 72 tokens; SKILL.md has 608 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~72
When it runs · the whole SKILL.md, loaded when a task matches: ~1.6k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~3.8k

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); the scripts in this folder are not scanned.

SKILL.md

The full file from Aperivue/medsci-skills at commit 3b14ae2, republished under its MIT licence (© Aperivue). 608 words, ~1,590 tokens.

Download SKILL.mdSave it as .claude/skills/manage-project/SKILL.md (or your agent's skills folder). This skill also uses 12 other files; get the full folder from GitHub.

name: manage-project
description: Use when managing a manuscript project over time. Scaffolds the project structure, tracks writing progress across phases, maintains project memory files, and generates submission checklists and backwards timelines (commands init, status, sync-memory, checklist, timeline).
metadata.triggers: manage project, project init, project status, submission checklist, project scaffold, create project, new paper project

Manage-Project Skill -- Research Project Management

Commands

`/manage-project init {name} --type {type} --journal {journal} [--ssot] [--zotero-collection NAME]`

Parameters:

{name} -- Project identifier (e.g., nnunet-skull-fracture, rfa-meta-analysis)
--type -- Paper type: original | meta | case | animal | technical | ai_validation | letter
--journal -- Target journal: RYAI | AJR | Radiology | European_Radiology | KJR | INSI | AJNR | generic
--ssot -- Emit SSOT.yaml (schema v1) from templates/SSOT.yaml.template instead of legacy project.yaml. Required, but not sufficient, for Phase 1C auto-enforce (the PostToolUse verify-refs hook blocks instead of warns): enforce also needs qc/migration_complete, which init does not write. After init, run migrate_project_to_ssot.py --project-root {target_dir} --mark-complete to validate the SSOT.yaml and write the marker. New projects should pass --ssot; legacy in-flight projects stay on project.yaml until /manage-project migrate-ssot is run.
--zotero-collection NAME -- Optional. Create a Zotero collection via pyzotero and populate library_id + collection_key in the contract. Requires ZOTERO_API_KEY + ZOTERO_LIBRARY_ID (optionally ZOTERO_LIBRARY_TYPE, default user). With pyzotero or the credentials missing, the contract is scaffolded with library_id: null / collection_key: null and a WARN is printed.

SSOT template substitutions: {{PROJECT_ID}} → {name}; {{PROJECT_TYPE}} → the SSOT project_type enum mapped from --type (original → original_research, meta → meta_analysis, case → case_report, ai_validation → ai_validation, else other). Without --zotero-collection, library_id / collection_key stay null until the owner links an existing collection.

Run scripts/init_project.py:

bash

python3 "${CLAUDE_SKILL_DIR}/scripts/init_project.py" \
    --name {name} --type {type} --journal {journal} [--ssot] \
    --project-root {target_dir}

It writes the contract file (SSOT.yaml with --ssot, else legacy project.yaml), the directory scaffold, the minimal stubs scripts/validate_project_contract.py requires (manuscript/index.qmd, artifact_manifest.json, qc/status.json), the memory-file stubs, and project_state.json. qc/migration_complete is NOT written by init — that marker belongs to the migrate script. For an --ssot project, run it with --mark-complete (no project.yaml needed): it validates the existing SSOT.yaml and writes the marker only on PASS. Until then the reference hook stays in warn mode.

Do not hand-build the scaffold. The script is the source of truth for the tree and for project_state.json; a hand-built one drifts from what the contract validator expects. Read ${CLAUDE_SKILL_DIR}/references/init_scaffold.md only when you need to know where a scaffolded file lands or what a project_state.json field means.

After the script, copy the matching reporting-guideline checklist from ${CLAUDE_SKILL_DIR}/../check-reporting/references/checklists/ into references/checklist_{GUIDELINE}.md.

Show full SKILL.md (285 more words)Show less

`/manage-project migrate-ssot [--no-mark-complete]`

Converts a legacy project.yaml project into SSOT.yaml form and, by default, touches qc/migration_complete so Phase 1C auto mode switches from warn to enforce. On an SSOT-native project (SSOT.yaml present, no project.yaml — e.g. init --ssot) there is nothing to convert: --mark-complete validates the existing SSOT.yaml and writes the marker on PASS; SSOT.yaml is not rewritten.

bash

python3 "${CLAUDE_SKILL_DIR}/scripts/migrate_project_to_ssot.py" \
    --project-root . --write --mark-complete

--no-mark-complete: run with --write only. Use it when the project still has open QC failures — enforcement is deferred until the migration is validated.
The migrate script refuses to touch qc/migration_complete unless the generated SSOT.yaml passes validate_project_contract.py AND contract_mode=ssot. Do not touch qc/migration_complete manually.

Re-run after resolving failures; the script is idempotent.

`/manage-project status`

Report current progress: read project_state.json, scan the existing files, and check whether the project memory files are present and aligned. Take word-count limits from the target journal's profile, ${CLAUDE_SKILL_DIR}/../write-paper/references/journal_profiles/{JOURNAL}.md, not from memory. Lay the report out as in ${CLAUDE_SKILL_DIR}/references/status_output_format.md.

`/manage-project sync-memory`

Audit and refresh the project memory files:

check for PROJECT.md, STATUS.md, CLAIMS.md, DATA_DICTIONARY.md, ANALYSIS_PLAN.md, REVIEW_LOG.md
identify stale or contradictory project metadata
propose the minimum files to create or update; create them from ${CLAUDE_SKILL_DIR}/references/scaffold_templates.md
align project_state.json with the current manuscript phase

`/manage-project checklist`

Read the pre-submission checklist from ${CLAUDE_SKILL_DIR}/references/pre_submission_checklist.md and write it to submission/pre_submission_checklist.md. Then recommend /self-review (manuscript quality gate), /verify-refs (citation verification) and AI pattern removal (/write-paper Phase 7).

`/manage-project timeline {submission_date}`

Generate a backwards timeline from the submission date, in the layout of ${CLAUDE_SKILL_DIR}/references/timeline_example.md.

Project State Conventions

Phase numbers:

0 = Init (scaffold created)
1 = Outline approved
2 = Table/Figure shells approved
3 = Methods (critic >= 85)
4 = Results (critic >= 85)
5 = Discussion (critic >= 85)
6 = Introduction + Abstract (critic >= 85)
7 = Polish complete (AI pattern removal + checklist + self-review >= 80)

Phase status values: pending | in_progress | complete | blocked

Files

SKILL.md and 12 other files (scripts, references) in skills/manage-project of Aperivue/medsci-skills.

SKILL.md
references/init_scaffold.md
references/pre_submission_checklist.md
references/project_state_template.json
references/scaffold_templates.md
references/status_output_format.md
references/timeline_example.md
scripts/init_project.py
scripts/migrate_project_to_ssot.py
scripts/validate_project_contract.py
skill.yml
templates/SSOT.yaml.template
tests/test_ssot_mark_complete.sh

Open the folder on GitHubat commit 3b14ae2

Compare with similar skills

Manage Project 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.

Manage Project compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Manage Project this skillAperivue/medsci-skills	331	—	~1.6k	Automated safety check: Pass	MIT	4 days ago
Systematic Review ScreenerImbad0202/academic-research-skills	51k	—	~8.4k	Automated safety check: Pass	Custom licence	yesterday
Citation Verification GuideGalaxy-Dawn/claude-scholar	5.7k	2 repos	~1.9k	Automated safety check: Pass	MIT	16 days ago
Cnki Exportcookjohn/cnki-skills	983	2 repos	~1.7k	Automated safety check: Pass	None	7 mo ago
Annotate Paper54yyyu/zotero-mcp	5.3k	—	~1.5k	Automated safety check: Pass	MIT	2 days ago
Zotero CLI54yyyu/zotero-mcp	5.3k	—	~2.3k	Automated safety check: Pass	MIT	2 days ago

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Questions about Manage Project

What does Manage Project do?

A skill your agent uses when managing a manuscript project over time. Manage Project is an agent skill from Aperivue/medsci-skills. Use when managing a manuscript project over time.

When should I use Manage Project?

Manage Project fits situations like: managing a manuscript project over time; tasks that involve Project scaffolding; tasks that involve Agent memory.

How do I install Manage Project in Claude Code?

Run `npx skills add Aperivue/medsci-skills --skill manage-project -a claude-code`. Or copy the skill folder (skills/manage-project in Aperivue/medsci-skills) into .claude/skills/manage-project in your project. Claude Code loads it when a task matches its description.

How do I install Manage Project in Codex?

Run `npx skills add Aperivue/medsci-skills --skill manage-project -a codex`. Or copy the skill folder (skills/manage-project in Aperivue/medsci-skills) into .agents/skills/manage-project in your project. Codex loads it when a task matches its description.

Can I use Manage Project 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 Aperivue/medsci-skills --skill manage-project -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/manage-project, .gemini/skills/manage-project, .github/skills/manage-project and .opencode/skills/manage-project in your project.

What does Manage Project need to run?

Going by SKILL.md and its folder, Manage Project needs Python and a shell for the scripts in its folder, the command-line tools its instructions call (python3) and credentials named ZOTERO_API_KEY. Our summary lists: Python 3; A Bash shell; A credential in ZOTERO_API_KEY.

Does Manage Project 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 Manage Project 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Manage Project use?

Manage Project 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 Manage Project use?

About 1.6k tokens (SKILL.md is roughly 6.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 2.2k tokens, read only when the agent opens those files.

What are the alternatives to Manage Project?

Skills that share tags, products or a category with Manage Project: Systematic Review Screener (Imbad0202/academic-research-skills, 51k stars), Citation Verification Guide (Galaxy-Dawn/claude-scholar, 5.7k stars), Cnki Export (cookjohn/cnki-skills, 983 stars) and Annotate Paper (54yyyu/zotero-mcp, 5.3k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Manage Project?

Aperivue (a GitHub organization) maintains it in Aperivue/medsci-skills, which has 331 GitHub stars. The repository holds 54 skills in this directory. The repository was last updated on October 5, 2026.

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

Install Manage Project

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Manage-Project Skill -- Research Project Management

Commands

/manage-project init {name} --type {type} --journal {journal} [--ssot] [--zotero-collection NAME]

/manage-project migrate-ssot [--no-mark-complete]

/manage-project status

/manage-project sync-memory

/manage-project checklist

/manage-project timeline {submission_date}

Project State Conventions

Files

Compare with similar skills

Similar skills

More from Aperivue/medsci-skills

Related

Questions about Manage Project

`/manage-project init {name} --type {type} --journal {journal} [--ssot] [--zotero-collection NAME]`

`/manage-project migrate-ssot [--no-mark-complete]`

`/manage-project status`

`/manage-project sync-memory`

`/manage-project checklist`

`/manage-project timeline {submission_date}`