doc-to-everything

name	doc-to-everything
description	Use when you need to fully process a PDF into Markdown, chunks, and table exports in one workflow

Doc to Everything

Orchestrate a complete document extraction pipeline. Converts PDF to Markdown, chunks the output, extracts tables, applies OCR if needed, and produces a manifest summarizing the entire workflow.

When to use

• Converting a complex PDF document into a complete structured workspace
• Need full extraction: text, chunks, tables, and metadata in one step
• Setting up a reusable document archive

Inputs to gather

• PDF file path (required)
• OCR flag: --ocr to force OCR on all documents (optional)
• Workspace directory: --workspace (optional; defaults to the directory containing the PDF)

Procedure

1. Create the output workspace directory at <workspace>/<stem>/, where <stem> is the PDF filename without extension. If --workspace is not specified, use the directory containing the PDF.
2. Copy the source PDF into the workspace as source.pdf.
3. Check for text layer in the PDF. If missing or sparse and --ocr was not passed, ask the user; if --ocr is passed or confirmed, run ocr-scanned-pdf on the PDF and work from the OCR'd version.
4. Run pdf-to-markdown on the (possibly OCR'd) PDF. Save output as <workspace>/<stem>/full.md.
5. Run chunk-markdown on full.md. Output chunks go to <workspace>/<stem>/chunks/.
6. Run extract-tables on the (possibly OCR'd) PDF. Output tables go to <workspace>/<stem>/tables/.
7. After all steps, create <workspace>/<stem>/manifest.toon with fields:
   • source: relative path to source.pdf
   • extractor: which extractor was used for PDF-to-markdown (marker, docling, etc.)
   • ocr_applied: boolean, true if OCR was run
   • chunk_count: number of chunks created
   • table_count: number of tables extracted
   • generated_at: ISO 8601 timestamp
   • tool_versions: dict with versions of key tools (ocrmypdf, marker, etc.)
8. Print summary to console showing workspace path, file counts, and manifest location.

Output / side effects

• Workspace directory structure created at <workspace>/<stem>/
• source.pdf copied into workspace
• full.md with complete document text
• chunks/ directory with chunked Markdown and index
• tables/ directory with extracted CSVs and index
• manifest.toon with extraction metadata
• If OCR was applied, the OCR'd PDF is also in the workspace (optional; can be kept or deleted)

Safety / constraints

• Failures in individual steps (e.g., table extraction) should not abort the pipeline; report the failure and continue with other steps
• Workspace directory must be writable; fail clearly if it is not
• Do not overwrite existing workspaces without asking the user
• Original source PDF is never modified; only copied