Claude Code Task: ECC Research Atlas System Build Continuation

You are Claude Code working as an implementation agent. Hermes is the orchestrator and verifier. Do not ask the user questions. Work inside this project only:

/Users/bylee/Documents/Research_Knowledge/ECC_Research_Atlas/

Goal

Continue building the ECC Research Atlas system until the next coherent checkpoint. The project is a Markdown-based research atlas anchored in Victor C. Li's 2019 Springer book Engineered Cementitious Composites (ECC): Bendable Concrete for Sustainable and Resilient Infrastructure.

Constraints

1. Preserve all original PDFs and extracted text.
2. Do not fabricate facts beyond the provided extracted text and existing project files.
3. Keep professor/lab-specific integration deferred. Do not edit 06_lab_position/ except to read it if needed.
4. Do not delete existing files.
5. Prefer additive files or careful targeted edits.
6. Any claim requiring exact page/table/figure should be marked as needs verification unless directly present in project files.

Current state

Existing files include:

• index.md, README.md, PROJECT_RULES.md
• Victor Li source materials under 00_sources/victor_li_book/
• concept nodes under 02_concepts/
• material/application nodes under 04_material_systems/
• experiment nodes under 05_experiments/
• visualization files under 07_visualization/

Recent orchestration files:

• 07_visualization/node_inventory.md
• 07_visualization/concept_graph_expanded.json
• 07_visualization/concept_graph_expanded.md
• 07_visualization/edge_list_expanded.csv
• 07_visualization/edge_list_expanded.jsonl
• 07_visualization/graph_validation_report.md
• 07_visualization/backlink_insertion_plan.md
• 07_visualization/missing_and_reinforcement_report.md
• 07_visualization/node_evidence_status.md

Your task for this run

Perform the next implementation checkpoint:

A. Generate full graph plan and expanded node-edge data

1. Read graph_validation_report.md, node_inventory.md, cross_link_map.md, and concept_graph_expanded.json.
2. Create 07_visualization/full_graph_expansion_plan.md explaining how to move from the 36-node high-level graph to a fuller graph that includes currently omitted Markdown nodes.
3. Create 07_visualization/full_graph_candidate_edges.csv with candidate edges for omitted nodes. - columns: source,target,relation,source_file,target_file,status,notes - status should be candidate unless the relation is already in concept_graph_expanded.json.

B. Create evidence-upgrade plan

Create 07_visualization/evidence_upgrade_plan.md with:

• Priority 1: Chapter 2 equations/criteria and Chapter 4 direct tension/crack width
• Priority 2: Chapter 7 durability data and Chapter 8 LCA assumptions
• Priority 3: Chapter 10 self-healing/self-sensing
• For each priority: files to upgrade, source files to inspect, and exact output artifacts to create.

C. Apply limited backlinks to high-value nodes only

Add or normalize ## Linked nodes sections in these files:

• 02_concepts/micromechanics_based_design.md
• 02_concepts/strain_hardening_criteria.md
• 02_concepts/fiber_bridging_law.md
• 02_concepts/durability.md
• 02_concepts/resilience.md
• 02_concepts/sustainability.md

Do not rewrite the whole file unnecessarily. Preserve existing content.

D. Handoff report

Create 09_ai_workflows/claude_handoff_report.md containing:

• files created
• files modified
• assumptions
• unresolved blockers
• recommended next task for Claude

Verification

After editing, verify that created files exist and that the six modified concept files still contain ## Linked nodes sections.

Return a concise summary only after completing all tasks.