Waypoint File Formats (+2)

Waypoint File Formats

JSON Waypoints (Steps 0, 1):

• Structured data for programmatic access
• Small file sizes (1-15KB)
• Easy to parse and reference

Markdown Waypoints (Steps 2, 3, 4):

• Step 2: 02_protocol_foundation.md (Sections 1-6)
• Step 3: 03_protocol_intervention.md (Sections 7-8)
• Step 4: 04_protocol_operations.md (Sections 9-12)
• Step 4: 02_protocol_draft.md (concatenated complete protocol)
• Human-readable protocol documents
• Can be directly edited by users
• Individual section files preserved for easier regeneration

Data Minimization Strategy

Each step implements aggressive summarization:

• Keep: Top-N results (5-10 max)
• Keep: Key facts and IDs (NCT numbers, endpoint types)
• Keep: Concise rationale (2-3 sentences)
• Discard: Raw MCP query results (not needed after analysis)
• Discard: Full FDA guidance text (only excerpts/citations kept)
• Discard: Lower-ranked search results

Step Independence

Each subskill is designed to:

• Read only from waypoint files (not conversation history)
• Produce complete output in single execution
• Not depend on conversation context from previous steps
• Be runnable standalone