Workspace Operations SOP

Architecture

The workspace is a local Git repository, auto-initialized on first use. Every workspace_save creates a Git commit (debounced 5s for rapid batches). Files over 10 MB are auto-added to .gitignore. The repo is local-only — it never pushes to any remote.

The dashboard shows file tree, recent commits, and file previews. It does NOT expose rollback — you are the user's interface for rollback and diff.

Directory Conventions

sources/
  papers/        ← imported PDFs, full-text downloads
  data/          ← datasets, raw data files
  references/    ← BibTeX, RIS, supplementary materials
outputs/
  drafts/        ← manuscript drafts, notes
  figures/       ← generated plots, diagrams
  exports/       ← PDF/DOCX exports, slide decks
  reports/       ← analysis reports, summaries
.ResearchClaw/   ← system files (hidden from dashboard)

sources/ = user inputs. outputs/ = agent-generated files.

Commit Message Prefixes

Prefix	Usage
Add:	New file created
Update:	Existing file modified
Upload:	User-uploaded file saved
Restore:	File restored from history
Delete:	File removed
Export:	Binary format converted from text source

Tool Chain (11 tools)

Tool	Purpose
workspace_save	Write text file + auto-commit → emits file_card
workspace_read	Read file contents
workspace_list	List files (glob filter + git status)
workspace_diff	Show changes (no range = uncommitted vs HEAD)
workspace_history	List commits for a file or path
workspace_restore	Checkout historical version + commit as Restore:
workspace_move	Rename/move file + commit
workspace_export	Convert text → binary format (md→docx/pdf, csv→xlsx)
workspace_delete	Delete a file + auto-commit (requires confirm=true) → recoverable via workspace_restore
workspace_append	Append content to an existing file (or create) → emits file_card
workspace_download	Download URL → save binary to workspace (PDFs, images) → emits file_card

Version Control Operations

• Undo / rollback: workspace_history → present commits → user selects → workspace_restore → report with file_card.
• Diff: workspace_diff (default: uncommitted vs HEAD).
• Proactive: Mention git history after overwrites. Note workspace_restore on delete.
• Delete: workspace_delete (requires confirm=true). Always mention workspace_restore as recovery option.

Write Discipline

• Pre-check mandatory: Before any workspace_save (overwrite), you MUST call workspace_read or workspace_list to verify existence and content to prevent accidental data loss.
• Append vs. Overwrite: When the intent is to "add to" a file, read the existing content first and concatenate. Never overwrite a multi-section file with only the new snippet.
• Prefer append: When adding content to an existing file, use workspace_append instead of read + concatenate + save. It prevents accidental overwrites and uses fewer tokens.
• Root-only Scope: All workspace_* tools operate strictly on relative paths within the workspace root.
• Out-of-bound (OOB) Rule: For paths outside the workspace, workspace_save will fail or lose versioning. Do NOT attempt to use workspace tools for system-level files; use standard CLI (with approval_card) if necessary, but note these have no Git/History support.

Binary Format Exports

workspace_save writes UTF-8 text only. For Word/Excel/PDF output:

1. Save content as Markdown/CSV: workspace_save("outputs/drafts/paper.md", content)
2. Convert: workspace_export({ source: "outputs/drafts/paper.md", format: "docx" })

Source	→ Target	Engine
.md .txt	.docx	pandoc
.md .txt	.pdf	pandoc + xelatex (CJK supported)
.csv .json	.xlsx	Python pandas + openpyxl

Output defaults to outputs/exports/{name}.{format}. Override with output param.

NEVER call workspace_save with a binary extension (.docx, .xlsx, .pdf, .pptx, etc.) — the tool will reject the write and guide you to workspace_export.

Native Install Dependencies

Docker images ship with all dependencies pre-installed. For native (non-Docker) installs, workspace_export requires external tools. If conversion fails with ENOENT or command not found, guide the user through installation:

macOS (Homebrew):

# Install Homebrew first if missing:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Then install conversion dependencies:
brew install pandoc            # md → docx
brew install --cask basictex   # md → pdf (xelatex engine)
pip3 install openpyxl          # csv → xlsx (pandas is usually present)

Windows: Download pandoc installer from https://pandoc.org/installing.html, install MiKTeX for PDF support.

Note: .pptx generation is NOT supported by workspace_export. PPT creation goes through the dedicated PPT extension (ExtensionsPanel → PPT Master).

Download & Import

Use workspace_download to save PDFs, images, and other binary files from URLs:

workspace_download({ url: "https://arxiv.org/pdf/2301.00001", path: "sources/papers/paper.pdf" })

After downloading a PDF to sources/papers/, offer library_add_paper to index it.

CLI Execution Safety

Safe without approval (no approval_card needed):

wc, du, grep, find, pandoc, pdftotext, python3, xelatex, jq

Requires approval_card:

pip install, brew install, curl, wget, any operation outside workspace.

Cross-Module Triggers

• PDF saved/downloaded to sources/papers/ → offer library_add_paper
• Paper added to library → suggest workspace_save BibTeX to sources/references/refs.bib via workspace_append
• Code file created → suggest task_create to track the work
• Analysis output generated → emit file_card + task_complete if linked

Related Research-Plugins Skills

• tools/document/ — PDF parsing, GROBID, format conversion, markdown workflows
• tools/diagram/ — Mermaid, PlantUML, scientific illustrations for workspace outputs