scholaraio

Agent Reference

This document is the deeper reference for agents and maintainers. The root entry docs such as AGENTS.md, CLAUDE.md, and .qwen/QWEN.md are intentionally kept lighter and should stay focused on durable project facts, hard constraints, and navigation. For the full repository knowledge map, start at docs/DESIGN.md.

Instruction Layering

Use the instruction stack in this order:

1. Root wrapper for your host tool
   • CLAUDE.md
   • AGENTS.md
   • .qwen/QWEN.md
   • .cursor/rules/scholaraio.mdc
   • .clinerules
   • .windsurfrules
   • .github/copilot-instructions.md
2. Matching project skill under .claude/skills/<name>/SKILL.md
3. Focused reference docs such as CLI, setup, writing, or migration specs
4. Source code and tests

Practical rule:

• if the content is a durable fact or invariant, keep it in the entry doc
• if the content is a reusable multi-step workflow, make it a skill
• if the content is long-form reference, keep it in docs or skill supporting files

Repository Knowledge System

ScholarAIO treats repository-local Markdown as the system of record for agent context. AGENTS.md is the map injected early in agent sessions; it should not become the encyclopedia.

Key indexes:

• docs/DESIGN.md: repository knowledge map and directory roles
• docs/design-docs/index.md: architecture and runtime design authorities
• docs/generated/index.md: generated reference rules
• docs/product-specs/index.md: product behavior spec rules

Internal plans, validation records, and audits are intentionally excluded from the published documentation site.

How Skills Are Organized

The canonical project skill source is:

• .claude/skills/<skill-name>/SKILL.md

Cross-agent discovery wrappers expose the same skill set through:

• .agents/skills/
• .qwen/skills/
• skills/

For reuse from another project, prefer the automated registration command:

scholaraio setup agent
scholaraio setup agent --apply
scholaraio setup agent check

It previews and applies shell runtime wiring, Codex/OpenClaw global skill discovery, project-local wrappers for supported hosts, and Claude Code plugin instructions where automation is not possible.

Project-local wrappers are local machine integration blocks. They may contain absolute paths to the active ScholarAIO checkout and config, so review them before committing target-project files.

Project guidance for maintaining skills:

• keep SKILL.md focused on entry instructions and decision rules
• move large examples, templates, or helper scripts into sibling files inside the same skill directory
• if a skill grows into long reference material, split the detail into supporting files and link them from SKILL.md
• if a repo-wide instruction file starts turning into a checklist or operating procedure, move that procedure into a skill instead

Representative skills:

• Core research: search, show, ingest, workspace, audit, translate
• Writing: academic-writing, nature-workflow, literature-review, paper-guided-reading, paper-writing, citation-check, writing-polish, review-response, research-gap, poster, technical-report
• Outputs and tooling: draw, document, publish, scientific-runtime, scientific-tool-onboarding

Repo And Module Map

ScholarAIO’s canonical implementation namespaces are:

• scholaraio/core/
• scholaraio/providers/
• scholaraio/stores/
• scholaraio/projects/
• scholaraio/services/
• scholaraio/interfaces/cli/

High-signal mental model:

• core/: config, logging, runtime foundations
• providers/: external APIs, parsing backends, transport adapters
• stores/: persistent storage helpers and durable library roots
• projects/: workspace and project-level structures
• services/: business logic and orchestration
• interfaces/cli/: parser, startup, and user-facing command handlers

The breaking cleanup generation removed legacy public facades such as scholaraio.index, scholaraio.workspace, scholaraio.translate, and scholaraio.ingest.pipeline.

Current import rules:

• implementation code must import canonical namespaces directly
• scholaraio.cli is only the published entrypoint
• internal CLI patch/wiring surfaces live in scholaraio.interfaces.cli.compat

Current Runtime Layout

Fresh-layout runtime:

• durable libraries under data/libraries/
• inbox and pending queues under data/spool/
• stateful indexes and rebuildable state under data/state/
• user project outputs under workspace/
• final audited deliverable archives under git-ignored published/

Breaking cleanup behavior:

• legacy roots such as data/papers/, data/explore/, data/proceedings/, and data/inbox* are no longer opened implicitly
• root/public facade imports are no longer supported
• supported old-layout roots should be upgraded with scholaraio migrate upgrade --migration-id <id> --confirm

Workspace rules:

• workspace/<name>/ is a free-form user project tree, not a rigid scaffold
• paper references live in refs/papers.json
• workspace.yaml is additive metadata only
• system-owned outputs should converge under workspace/_system/

Migration rules:

• runtime-layout migration control lives under .scholaraio-control/
• use scholaraio migrate upgrade --migration-id <id> --confirm for the normal one-command upgrade path
• use scholaraio migrate plan|verify|run|cleanup|finalize only when inspecting or repairing individual migration steps
• current covered move stores are citation_styles, toolref, explore, proceedings, spool, and papers
• migrate finalize --confirm is the hardened one-click post-migration cleanup flow for real user roots

Agent Operating Model

ScholarAIO is meant to be used through an agent, not only through direct shell scripting.

Agents should:

• prefer real CLI execution over only explaining intended steps
• load information progressively from lightweight metadata toward heavier full text
• treat paper conclusions as claims and compare evidence across sources
• keep user-facing outputs inside workspace/
• avoid direct edits to runtime data when tested helpers or CLI flows already exist

Notes And Cross-Session Analysis

When analysis should persist across sessions, use paper-level notes.md.

Conventions:

• location: <papers_dir>/<Author-Year-Title>/notes.md
• append sections in the form ## YYYY-MM-DD | <source> | <analysis type>
• keep long-lived findings, cross-paper links, and notable limitations there
• scholaraio show "<paper-id>" --append-notes "..." is the user-facing append path

Useful mental model:

• T1: final answer for the current conversation
• T2: durable notes worth keeping in notes.md
• T3: ephemeral search or reasoning details that should not be persisted

Deep Links

Use the smallest doc that answers the question:

• Product overview: docs/index.md
• Repository knowledge map: docs/DESIGN.md
• Agent setup: docs/getting-started/agent-setup.md
• Installation: docs/getting-started/installation.md
• Configuration: docs/getting-started/configuration.md
• CLI reference: docs/guide/cli-reference.md
• Writing workflows: docs/guide/writing.md
• Runtime layout authority: docs/design-docs/directory-structure-spec.md
• Migration execution order: docs/design-docs/directory-migration-sequence.md
• Migration control-plane contract: docs/design-docs/migration-mechanism-spec.md

The maintenance rule for this repo is simple:

• keep entry docs slim
• keep procedures in skills
• keep heavy reference material in dedicated docs

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