Mapping Documents

Generate _MAP.md files providing hierarchical document structure with semantic annotations. Maps show section summaries, typed claims (result/definition/method/caveat/open-question), symbol definitions, and cross-section dependencies — all anchored to page numbers.

The structural analog to tree-sitting: tree-sitter parses code via grammar, docmap parses documents via font analysis + LLM extraction.

Installation

pip install pdfplumber anthropic --break-system-packages -q

Generate Maps

# Full run (structure + semantic extraction via Claude API)
python /mnt/skills/user/mapping-documents/scripts/docmap.py paper.pdf \
  --out docs/ --genre paper --workers 4

# Structure only (no API calls, no cost)
python /mnt/skills/user/mapping-documents/scripts/docmap.py paper.pdf \
  --out docs/ --structure-only

API key resolution: --api-key flag > ANTHROPIC_API_KEY env > API_KEY env.

Output Artifacts

Four files, forming a three-layer progressive-disclosure stack:

CLAUDE.md / project instructions     ← curated invariants (you write this)
    ↕ (_USAGE.md bridges the gap)
_MAP.md + JSON indexes               ← navigable document map (docmap generates)
    ↕
raw PDF                              ← the source document

File	Purpose	When to read
{stem}_USAGE.md	Snippet for pasting into CLAUDE.md / AGENTS.md / project knowledge. Describes the reading order and JSON query patterns.	Once, at setup
{stem}_MAP.md	Section map: TOC with summaries, typed claims, defined symbols, dependencies. All page-anchored.	Any question about what the document says
{stem}.symbols.json	Flat symbol index: where defined, where used, what it means.	"Where is X defined?"
{stem}.anchors.json	Every claim: section ID, type, text, page number.	"What caveats exist?" / "What does §3 claim?"

After Generating: Wire It Up

Generating the map is step 1. Step 2 is telling the agent the map exists.

For a code repo (CLAUDE.md / AGENTS.md):

# Paste the generated usage snippet into your agent instructions
cat docs/paper_USAGE.md >> CLAUDE.md

For Claude.ai project knowledge: Upload _MAP.md as a project knowledge file, or paste the _USAGE.md content into project instructions.

The _USAGE.md snippet includes copy-pasteable query commands for the JSON indexes. Replace QUERY and SECTION_ID placeholders with actual values.

Navigate Via Maps

After generating and wiring up, use the map for navigation — read _MAP.md, not the raw PDF.

Workflow:

1. Read _USAGE.md block in CLAUDE.md for orientation
2. Read top-level TOC in _MAP.md for structure and section summaries
3. Drill into relevant sections for typed claims and symbol definitions
4. Query .symbols.json for "where is X defined?" lookups
5. Query .anchors.json for claim filtering by type or section
6. Read the raw PDF only when exact wording or figures are needed

Querying the JSON indexes:

# Symbol lookup
python3 -c "import json; [print(f'§{s[\"defined_in\"]} p.{s[\"defined_at_page\"]}') \
  for s in json.load(open('docs/paper.symbols.json')) if 'edl' in s['symbol']]"

# All caveats in the document
python3 -c "import json; [print(f'p.{c[\"page\"]} {c[\"text\"]}') \
  for c in json.load(open('docs/paper.anchors.json')) if c['type'] == 'caveat']"

# All claims in a section
python3 -c "import json; [print(f'[{c[\"type\"]}] {c[\"text\"]}') \
  for c in json.load(open('docs/paper.anchors.json')) if c['section'] == '4.3']"

Genre Support

Genre controls the claim taxonomy used in semantic extraction.

Genre	Claim types	Best for
paper (default)	definition, result, method, claim, caveat, open-question	Academic papers, arXiv preprints
spec	requirement, definition, constraint, example, note	RFCs, API specs, technical standards
legal	definition, obligation, right, exception, condition, reference	Contracts, policy documents, regulations

Limitations (v0.1.x)

• PDF-only. No DOCX, HTML, or plain text input yet.
• Single-column layout assumed. Two-column papers may mis-order text within sections.
• No caching. Re-running re-extracts everything.
• No citation cross-referencing.
• Genre must be specified manually.
• Semantic extraction can hallucinate. Every claim is page-anchored, but the page number comes from the LLM. Verify critical claims against the source.

CLI Reference

python docmap.py paper.pdf [options]

Options:
  --genre {paper,spec,legal}   Claim taxonomy (default: paper)
  --structure-only             Skip LLM pass (free, fast)
  --out DIR                    Output directory (default: .)
  --api-key KEY                Anthropic API key
  --model MODEL                Model (default: claude-sonnet-5-5)
  --workers N                  Parallel workers (default: 4)
  --no-usage-snippet           Skip _USAGE.md generation
  -v                           Verbose structural parsing