Use this skill when your current working directory is a Paper Codex session workspace.
First Reads
Read these local files before answering or changing anything:
workspace_manifest.json
agent_instructions.md
prompt_contract.md
session.json
Then read only the paper files needed for the task:
papers/{paper_id}/metadata.json
papers/{paper_id}/full_text.txt
papers/{paper_id}/pages.jsonl
papers/{paper_id}/spans.jsonl
papers/{paper_id}/anchors.jsonl
Operating Boundary
Use workspace files for source reading, drafts, and generated artifacts.
Use MCP tools for app state changes:
- notes, digests, folders, tags, and paper metadata
- reader navigation or visual focus changes
- prompt template changes
- importing or deleting library items
Do not edit the Paper Codex SQLite database or app support files directly.
Citation Contract
Ground paper claims with Paper Codex citation markers:
[[cite:paper:{paper_id}:p{page}:b{block_index}]]
[[cite:paper:{paper_id}:p{page}:a{anchor_suffix}]]
Prefer spans.jsonl for citation-ready claims. Use anchors.jsonl when the user selected or saved a source passage. If a claim cannot be grounded in the workspace, say that plainly.
MCP Discovery
When MCP is configured, discover live app state through:
papercodex://app/active-context
papercodex://sessions/{session_id}/workspace-manifest
papercodex://sessions/{session_id}/agent-runtime
papercodex://sessions/{session_id}/prompt-contract
If mcp.json exists, use it as the session-local MCP configuration. If not, rely on the workspace files and ask the user before attempting app mutations.