Where Files Go

Use this page when you are unsure where to save something.

Canonical Workspace Map

/workspace/
  PROJECT_CHARTER.md       project purpose and scope
  TEAM_BRIEF.md            summary for the working group
  QUESTIONS_FOR_USER.md    batched questions for the PI Liaison
  DECISIONS.md             decision log
  ASSUMPTIONS.md           assumption register
  MEMORY.md                durable working memory
  documents/               shared scientific documents
  projects/                project routing maps for imports, repos, and external data
  literature/              citation notes and evidence inventories
  data/                    local data manifests and small examples
  analysis/                analysis notes and scripts
  figures/                 figures generated by analysis
  outputs/                 reports, tables, maps, logs, artifacts
  agent_reports/           role-specific reports
  daily_notes/             session notes
  runtime/                 runtime notes and generated state
  cache/                   disposable cache

Safe To Edit

• PROJECT_CHARTER.md
• TEAM_BRIEF.md
• QUESTIONS_FOR_USER.md
• DECISIONS.md
• ASSUMPTIONS.md
• documents/
• daily_notes/

Generated Or Disposable

• cache/
• some runtime/ files,
• temporary logs,
• rebuilt output indexes.

Do Not Commit

• .env,
• tokens,
• private credentials,
• restricted data,
• large raw data,
• unreviewed sensitive files.

Large data should live in external storage with a manifest that records source, license, access method, citation, and checksum when available.

Use projects/<project-slug>/ when a project connects several sources: imported snapshots, GitHub repositories, mounted drives, STAC catalogs, object stores, or remote institutional storage. The project folder should stay small and point to data rather than contain everything.