fix(tests): resolve 4 pre-existing test failures + 2 env issues

.env.example

@@ -28,3 +28,51 @@ NEO4J_AUTH=neo4j/neo4jpassword
 # ------------------------------
 NEO4J_HEAP_INIT=1G
 NEO4J_HEAP_MAX=2G
+
+# ------------------------------
+# GraphRAG / ChatSEEK Integration
+# ------------------------------
+# Enable GraphRAG features (set to 1 to enable)
+# REQUIRES: pip install -r requirements-graphrag.txt
+#           (installs PyTorch + CUDA stack, 4-8GB download)
+# Lightweight install: pip install -r requirements.txt (chat disabled)
+SCIDK_GRAPHRAG_ENABLED=0
+
+# LLM provider: "local_ollama" (default), "openai", or "azure_openai"
+SCIDK_GRAPHRAG_LLM_PROVIDER=local_ollama
+
+# Ollama model name (default: llama3:8b)
+SCIDK_GRAPHRAG_MODEL=llama3:8b
+
+# Schema cache TTL in seconds (default: 300)
+SCIDK_GRAPHRAG_SCHEMA_CACHE_TTL_SEC=300
+
+# Verbose mode: include extracted entities and Cypher in responses (0 or 1)
+SCIDK_GRAPHRAG_VERBOSE=0
+
+# Query library path for curated Cypher examples (Sprint 1)
+SCIDK_QUERY_LIBRARY_PATH=query_library/scidk_queries.yaml
+
+# Privacy filters (comma-separated, optional)
+SCIDK_GRAPHRAG_ALLOW_LABELS=
+SCIDK_GRAPHRAG_DENY_LABELS=
+SCIDK_GRAPHRAG_EXCLUDE_PROPERTIES=
+
+# ------------------------------
+# Chat Provider Settings (for reasoning path)
+# ------------------------------
+# Chat LLM provider: "ollama" (default), "anthropic", "openai"
+SCIDK_CHAT_LLM_PROVIDER=ollama
+
+# Ollama settings
+SCIDK_CHAT_OLLAMA_ENDPOINT=http://localhost:11434
+SCIDK_CHAT_OLLAMA_MODEL=llama3.1:8b
+
+# Claude settings (optional, for reasoning path)
+SCIDK_CHAT_CLAUDE_API_KEY=
+
+# OpenAI settings (optional, for reasoning path)
+SCIDK_CHAT_OPENAI_API_KEY=
+
+# Anthropic key for entity extraction (optional, falls back to pattern matching)
+SCIDK_ANTHROPIC_API_KEY=

.gitignore

@@ -70,3 +70,8 @@ dev/code-imports/nc3rsEDA/
 
 # Backups are for local work, not the repository
 backups/
+
+# Documentation cleanup - archived and temporary docs
+dev/test-runs/tmp/
+dev/code-imports/
+docs/archive/