Organizing Research over Years

STORY

A STAR takes the STAGE to tell a STORY

The master's and doctoral thesis companion to STAR and STAGE — it shapes graduate research, applicable publications, and fingerprinted evidence into one defensible, deposit-ready thesis: every number traces to an evidence file or is visibly marked as missing, reused publications keep their attribution, and committee comments and degree requirements stay on file.

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16Workflow Skills
7AI Agents Supported
2Languages · EN 中文
MITOpen Source

The STAR family

One research life cycle.
Three focused toolchains.

Each works independently. Connect them when you want upstream work to flow downstream as fingerprinted, read-only evidence.

01 · RESEARCH

STAR

Systematic Toolchain for AI Research

Runs one research project from idea through reproducible experiments to paper-ready evidence.

Website ↗ GitHub ↗
02 · PAPER

STAGE

Systematic Toolchain for Authoring, Guiding, and Editing

Turns one contribution into a traceable paper, review cycle, and submission package.

Website ↗ GitHub ↗
03 · THESIS Current

STORY

Systematic Toolchain for Organizing Research over Years

Shapes graduate research into a defensible master's thesis or doctoral dissertation, defense, and deposit.

Website ↗ GitHub ↗

Why STORY

Years of graduate research.
One defensible thesis.

A thesis rots when evidence lives in old repositories, numbers live in chat history, and attribution lives in someone's head. STORY moves the whole chain of custody — evidence, claims, publications, milestones — into the repository itself.

One repository, one degree thesis

Front matter, chapters, appendices, figures, tables, and bibliography each have one predictable home under manus/ — and the template compiles out of the box, in English or 简体中文.

A read-only evidence layer

STAR research artifacts, STAGE paper materials, or hand-registered drops are snapshotted into mates/ with a fingerprint per file. Evidence flows one way — never edited in place.

Thesis-level coherence, on file

notes/story.md owns the central argument, contributions.md maps each contribution to its evidence and chapters, outline.md holds the chapter architecture, and claims.md joins them as the ledger.

The fabrication boundary

Every quantitative claim in manus/ either traces to a fingerprinted mates/ entry or is written as \todo{...} — no third state. Institutional rules and degree_level: master|doctoral enter degree/ only as author-confirmed facts; a published paper is evidence, never automatically the thesis's final wording. A visible \todo is a state; a plausible invented number is a defect.

Attribution beside traceability

notes/publications.md records which chapters reuse published material, who contributed what, and which permissions and overlaps apply. Evidence traceability never replaces authorship boundaries — STORY requires both, so collaborative work is never presented as solo work.

Milestones as data

Each proposal, review, pre-defense, defense, correction, or deposit stage that the confirmed degree program requires lives in milestones/<slug>/ — received feedback preserved verbatim, point-by-point responses, and a frozen outcome record. A deposit package cannot be declared ready while a required check or an open promise remains unresolved.

AI-agent native, STAR-and-STAGE paired

Sixteen skills ship for Codex, Claude Code, Cursor, DeepSeek Harness, Kimi Code, Pi, and Qwen Code — in English and Chinese, from one shared skill source. Import evidence from any paired STAR or STAGE repository with one command, or work standalone with hand-registered drops.

Project structure

Nine directories.
One research arc.

The abbreviated names follow the STAR family convention: short to type, unambiguous to search, and identical across every STORY repository.

tree ~/my-thesis
STORY/ ├── manus/ # the thesis │ ├── main.tex # entry — always compiles │ ├── main-zh.tex # buildable 中文 starter │ ├── fronts/ # abstract, acknowledgements, declarations │ ├── chaps/ # chapters: <n>_<slug>.tex │ ├── backs/ # appendices & back matter │ ├── figs/ # rendered figures, with sources │ ├── tabs/ # evidence-backed tables │ ├── bibs/ # reference.bib │ └── stys/ # story.cls · story.sty · story.bst ├── mates/ # fingerprinted evidence — read-only │ └── MANIFEST.md # the fingerprint ledger ├── degree/ # profile, requirements, committee ├── notes/ # story, claims, outline, publications │ └── refs/ # reading notes per paper ├── milestones/ # proposal → defense → deposit ├── tasks/ # durable open work & promises ├── wkdrs/ # builds & reports (gitignored) ├── execs/ │ ├── run.sh # ← the single build entrypoint │ ├── update.sh # sync skills; --adopt installs the skeleton │ └── scpts/ # import.sh · lint.sh · fmt.sh ├── .env # machine-local config (never committed) └── AGENTS.md # shared human + agent instructions
manus/Manuscripts — the thesis's LaTeX sources
mates/Materials — fingerprinted evidence snapshots, read-only
degree/Degree facts — author-confirmed institutional record
notes/Writing metadata — story, outline, and the claim ledger
milestones/Milestones — one directory per examination event
tasks/Tasks — durable open work and feedback promises
wkdrs/Work directories — builds and ephemeral reports, never committed
scpts/Scripts — evidence import and deterministic checks

Degree-aware thesis workflow

Sixteen skills.
One audit trail.

From imported evidence to a frozen deposit — each skill writes its state into project files, so the whole thesis is auditable and resumable at any point.

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Set upWire the repo and bring in fingerprinted evidence.

$story-proj-adopt

Adopt an existing master's or doctoral thesis without disturbing it — survey, record, and keep every institutional fact author-confirmed.

$story-evid-curator

Import from STAR or STAGE repositories, register manual drops, refresh fingerprints, and integrity-check mates/.

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PlanShape the thesis argument and the chapter architecture.

$story-syns-coach

Establish the research arc and degree contributions at the confirmed master's or doctoral level.

$story-outl-planner

Turn the arc into a coherent chapter architecture, each chapter serving the thesis-wide argument.

$story-refs-curator

Verified bibliography records and reading notes behind every literature assertion.

✦

WriteDraft from evidence, never from memory.

$story-chap-drafter

One chapter per run, from its confirmed brief, the thesis story, and mapped evidence — missing numbers become \todo{}.

$story-tabs-builder

Tables from mates/ evidence only — one % src: fingerprint anchor per data row.

$story-figs-designer

Each figure end to end: purpose, editable source, rendered PDF, evidence-mapped caption.

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Polish & auditHarmonize the prose. Trace every number.

$story-copy-editor

Clarity, voice, terminology, and cross-chapter flow — facts, numbers, and claim scope untouchable.

$story-clms-auditor

Every number and comparison traced to a fingerprint: matched / mismatched / unsourced.

$story-cite-auditor

Every \cite resolves; every literature assertion checkable against a reading note.

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ExaminationReview, respond, defend, deposit.

$story-exam-reviewer

A level-appropriate examiner pass over the built thesis — contribution scope, coherence, evidence, defense readiness.

$story-revs-resolver

Track and resolve committee feedback point by point — received comments are never edited in place.

$story-defn-builder

Prepare and check an applicable defense deck against the thesis it presents.

$story-depo-packer

Preflight the deposit package against degree/ requirements and freeze the final record.

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Read acrossReport the whole flow, name the next action.

$story-flow-status

Read-only map of chapters, claims, evidence, and milestone gates — and the single next action with its exact command. Never writes.

Every skill ships for Codex, Claude Code, Cursor, DeepSeek Harness, Kimi Code, Pi, and Qwen Code — in English and Chinese — from one shared source under .agents/skills/.

STORY master's and doctoral thesis workflow: fingerprinted evidence flows through synthesis and chapter writing to applicable examination, defense, and deposit stages
The full arc — evidence in, degree out, and where every stage writes its state.

Quick start

Six steps to a compiling thesis.

Start fresh from the template — the generic class compiles immediately, and institutional templates and degree rules enter degree/ only as facts you have confirmed.

zsh — my-thesis
# 1 · Start a thesis repo from the STORY template — one degree thesis, one repo ❯ git clone https://github.com/wanghao9610/STORY my-thesis && cd my-thesis ❯ rm -rf .git && git init # drop STORY's history # 2 · Confirm master or doctoral in the durable degree profile ❯ $EDITOR degree/profile.tex # degree_level: master | doctoral # 3 · Configure the local runtime ❯ cp .env.example .env && $EDITOR .env # RESEARCH_HOME (optional) · STORY_MAIN · LATEX_ENGINE · STORY_LANG # 4 · Import evidence from a paired STAR or STAGE repo — or drop files into mates/manual/ ❯ bash execs/scpts/import.sh --source ../my-stage-paper --slug paper-a # 5 · Build & lint — a fresh checkout compiles out of the box ❯ bash execs/run.sh ❯ bash execs/scpts/lint.sh # 6 · Pick up the workflow — it names the single next action for you ❯ $story-flow-status ❯

Get started

Give your graduate research a
thesis worth defending.

STORY is free, MIT-licensed, and agent-agnostic. Use it as a GitHub template, or adopt it into the master's or doctoral thesis you already have.

✦ Use the Template Read the Docs Pair it with STAR Pair it with STAGE