Adds think, checkpoint, and flag tools for agent reasoning visibility:
- think: records observation/hypothesis/next_action before investigation
- checkpoint: summarizes learned/unknown/next_phase after file clusters
- flag: marks notable findings to flags.jsonl with severity levels
Additional changes:
- Step numbering in investigation system prompt
- Text blocks from agent now printed to stderr (step labels visible)
- flag tool available in both investigation and synthesis passes
- analyze_directory() returns (brief, detailed, flags) three-tuple
- format_flags() in report.py renders flags sorted by severity
- Per-directory max_turns increased from 10 to 14
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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