Issues found running the system end-to-end on the NIST CFReDS Hacking Case
disk image (SCHARDT.001, Mr. Evil). Four interconnected fixes:
1. HypothesisAgent boundary leak (two layers)
B.1 Tool set: BaseAgent._register_graph_tools was registering
add_phenomenon / add_lead / link_to_entity for every agent. With
an empty graph in Phase 2, HypothesisAgent "compensated" by
inventing phenomena, dispatching leads, and linking entities.
B.2 Prompt leak: BaseAgent's shared system prompt hard-coded "Call
investigation tools (list_directory, parse_registry_key, etc.)".
HypothesisAgent hallucinated list_directory and wasted 2 LLM
rounds on 'unknown tool' errors before backing off.
Fix:
- Split _register_graph_tools into _register_graph_read_tools +
_register_graph_write_tools.
- HypothesisAgent, ReportAgent, TimelineAgent override
_register_graph_tools to skip write tools.
- HypothesisAgent and TimelineAgent override _build_system_prompt
with focused, role-specific workflows (no Phase A-D investigation
boilerplate).
2. JSON parse failures in Phase 3 lead generation (5/6 hypotheses lost)
DeepSeek emits JSON with stray backslashes (Windows path references)
and occasional minor syntax slips. Old single-stage sanitize couldn't
recover; per-hypothesis fallback silently swallowed each failure.
Fix:
- _safe_json_loads: progressive — stage 0 as-is, stage 1 escape stray
\X (anything not in valid JSON escape set), log raw input on final
failure for diagnosis.
- New _call_llm_for_json helper: on parse failure, append the error
to the prompt and re-call LLM (self-correcting retry, up to 2).
- All 4 LLM-JSON callsites in orchestrator refactored to use it.
3. Phase 1 sometimes skipped add_phenomenon (LLM treated <answer> as deliverable)
Strengthen BaseAgent's RECORDING REQUIREMENT — explicit "your <answer>
is DISCARDED; only graph mutations propagate" plus a new rule:
negative findings (searched X, found nothing) MUST also be recorded
as phenomena, since they constrain the hypothesis space.
4. Phase 4 Timeline was a no-op
TimelineAgent inherited BaseAgent's Phase A-D prompt and never called
add_temporal_edge — produced 0 temporal edges. Override the prompt
with concrete workflow (build_filesystem_timeline ->
get_timestamped_phenomena -> 15-40 add_temporal_edge calls) and
restrict tool set to read-only + its 3 temporal tools.
Verified end-to-end: HypothesisAgent now 8 tools (no writes), ReportAgent
13 (no graph writes), TimelineAgent 10 (read + temporal + timeline).
All 60 unit tests pass.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
