BITE: Instructions file for Codex

Agent Guide

Public agent-facing usage starts from README.md and .claude/skills/README.md. Internal deployment notes stay under _private/.

BITE is a local-first research workflow for structured paper analysis. Its goal is to turn academic PDFs into machine-actionable evidence notes, retrieval indexes, and downstream idea or review artifacts. PaperBite acts as the upstream public evidence layer: it provides reusable structured paper assets, while BITE focuses on local analysis, retrieval, comparison, idea generation, and research decision support.

Working Surface

• obsidian-vault/paperPDFs/ stores source PDFs.
• obsidian-vault/analysis/ stores structured local analysis notes.
• obsidian-vault/index/ stores generated indexes and Obsidian navigation.
• obsidian-vault/ideas/ stores local idea, focus, and review notes.

Local Pipeline

collect candidate papers / import local PDFs
  -> download when needed
  -> integrated analysis chain
     (MinerU parse/reuse -> structured analysis -> vault export)
  -> optional index refresh
  -> query / ideate / focus / review / export

Branch Sync Policy

This branch is the canonical place for changes that should later appear in the public main worktree. Make shared README, public docs, public assets, and public workflow updates here first, then sync them to main after review.

Keep branch-specific and local-development material out of main:

• _private/ local notes, archives, deployment notes, and operation history
• Obsidian workspace/runtime state
• provider-specific defaults or private model choices
• internal branch/worktree coordination notes

AGENTS.md itself is branch-specific. Do not blindly sync this file to main; the public main copy should contain only project background and public agent-facing guidance.

Rules

1. Treat the local vault paths above as the current working surface.
2. Write only through the skill that owns the target output path.
3. Analysis language defaults to zh unless the request overrides it.
4. Pipeline steps are idempotent; already-completed steps should be skipped.
5. Planned analysis batches must declare goal, source, selection rule, budget, and output target before agents run.
6. Agents must preserve source anchors in notes, logs, and generated outputs.
7. Reports and profiles must be generated from available evidence, not new unsupported claims.
8. When prose needs to mention Markdown or Obsidian reserved characters such as *, [, ], |, or #, escape them with backslashes or wrap them in inline code so reading view does not reinterpret the text.
9. In Markdown tables, aliased Obsidian wikilinks are allowed only when the alias separator is escaped as [[full/path\|abbr]]; an unescaped | splits table columns. Outside tables, normal [[full/path|abbr]] links are fine.
10. Generated exports, snapshots, backups, local storage, and symlinks stay out of Git.