Case Study 04: CodeExplorer vs Graphify.

# CodeExplorer (ce v1.75.0) OpenCypher Queries:
# C1 (Endpoints):
MATCH (e:Endpoint)-[:EXPOSED_BY]->(f:Function) RETURN f.file_path, f.start_line, f.name, e.http_method, e.route_template
# C2 (Outbound HTTP):
MATCH (ext:ExternalService)-[r:CALLED_BY]->(f:Function) WHERE COALESCE(ext.protocol, 'http') <> 'graphql' RETURN f.file_path, COALESCE(r.line, f.start_line), f.name, COALESCE(ext.url, ext.name)
# C3 & C8 (Queues / Topics):
MATCH (t:Topic)-[:PUBLISHED_BY]->(f:Function) RETURN f.file_path, f.start_line, f.name, t.name;
MATCH (t:Topic)-[:SUBSCRIBED_BY]->(m:Function) RETURN m.file_path, m.start_line, m.name, t.name
# C4 & C10 (ORM Tables & Schema):
MATCH (t:Table) OPTIONAL MATCH (t)-[:IMPLEMENTED_BY]->(ent:Type) RETURN COALESCE(ent.file_path, t.path), ent.start_line, COALESCE(ent.name, t.name), t.name
# C5 (Read/Write Lineage):
MATCH (q:Query)-[r:WRITES_TO|READS_FROM]->(t:Table) OPTIONAL MATCH (q)-[:ACCESSED_BY]->(f:Function) RETURN COALESCE(f.file_path, q.file_path), q.start_line, COALESCE(f.name, q.name), type(r), t.name
# C6 (Call Graph & DI Callers):
MATCH (caller:Function)-[:CALLS]->(callee:Function) WHERE callee.name IN [<target_methods>] OPTIONAL MATCH (enclosing:Function)-[:DECLARES]->(caller) RETURN caller.file_path, COALESCE(enclosing.start_line, caller.start_line), COALESCE(enclosing.name, caller.name), callee.name
# C7 (Inheritance & implements):
MATCH (c:Type)-[r:INHERITS_FROM|IMPLEMENTS]->(p) RETURN c.file_path, c.start_line, c.name, type(r), p.name

# ------------------------------------------------------------------------------
# Graphify (v0.9.104) graph.json Node & Link Extraction (eval_ce_vs_graphify.py):
# - Cold indexing command: `graphify index <repo_path> --code-only`
# - C6 (Call Graph): Links in `graph.json["links"]` where `relation == "calls"`, matching source function `(source_file, source_line, label)` and target method `.label.split(".")[-1]`.
# - C7 (Inheritance & implements): Links in `graph.json["links"]` where `relation in ("inherits", "implements")`, matching child class `(source_file, source_line, label)` and parent class/interface label.

# 1. Graph Schema / Stats
# CodeExplorer (`ce mcp --root <repo>`):
{"name": "get_taxonomy", "arguments": {}}
# Graphify (`python -m graphify.serve graphify-out/graph.json`):
{"name": "graph_stats", "arguments": {}}

# 2. Multi-Token Semantic / BFS Search
# CodeExplorer:
{"name": "search_identifiers", "arguments": {"query": "authentication token validate", "limit": 15}}
# Graphify:
{"name": "query_graph", "arguments": {"question": "authentication token validate", "depth": 2}}

# 3. Direct Symbol Lookup
# CodeExplorer:
{"name": "find_symbol", "arguments": {"name": "AuthService"}}
# Graphify:
{"name": "get_node", "arguments": {"label": "AuthService"}}

# 4. Inbound Callers by Method Name
# CodeExplorer:
{"name": "get_callers", "arguments": {"target": "validate"}}
# Graphify:
{"name": "get_neighbors", "arguments": {"label": "validate", "relation_filter": "calls"}}

# 5. Call Chain / Shortest Path + OpenCypher Query
# CodeExplorer:
{"name": "get_call_chain", "arguments": {"startFunction": "login", "endFunction": "validate"}}
{"name": "execute_custom_read_cypher", "arguments": {"query": "MATCH (n:Function) RETURN n.name LIMIT 10"}}
# Graphify:
{"name": "shortest_path", "arguments": {"source": "<login_node_id>", "target": "<validate_node_id>", "undirected": true}}

Identical 371 ground-truth items (`seed = 42`) used in Case Study 03 across `twentyhq/twenty` (`12e8fae471865e9dab60c0b0fd59f318505c804e`) and `immich-app/immich` (`2153d22f34349de690cd98890ee4c635808da638`):
- Group A (130 Basic Code Items across L1 to L3): C1 Incoming Endpoints (40), C2 Outbound HTTP Calls (18), C6 Call Graph & DI Callers (32), C7 Class Inheritance & Interface Implementation (40).
- Group B (241 Architectural Items across L4 to L5): C3 Queue Producers & Consumers (70), C4 ORM Tables (40), C5 Code-to-Table Read/Write Lineage (40), C8 Topic Resolution (37), C9 Services & Topology Edges (14), C10 Table Columns & Relations (28), C11 End-to-End Architectural Queries (12).