fix: analysis package

Author: pedronauck

README.md

@@ -184,59 +184,27 @@ gograph analyze . \
 
 ### 3. Essential Graph Visualization Queries
 
-Once connected, try these queries to explore your codebase:
+Once connected to Neo4j Browser, you can explore your codebase using Cypher queries.
 
-#### **Complete Project Overview**
+**📚 For a comprehensive collection of queries, see [docs/QUERIES.md](docs/QUERIES.md)**
+
+Here are a few essential queries to get you started:
 
 ```cypher
 // View the entire project structure
 MATCH (n)
 WHERE n.project_id = 'my-awesome-project'
 RETURN n
 LIMIT 500
-```
-
-#### **Package Dependencies**
-
-```cypher
-// Visualize package import relationships
-MATCH (p1:Package)-[:IMPORTS]->(p2:Package)
-WHERE p1.project_id = 'my-awesome-project'
-RETURN p1, p2
-```
-
-#### **Function Call Graph**
-
-```cypher
-// See function call relationships
-MATCH (f1:Function)-[:CALLS]->(f2:Function)
-WHERE f1.project_id = 'my-awesome-project'
-RETURN f1, f2
-LIMIT 100
-```
 
-#### **Architecture Overview**
-
-```cypher
-// High-level architecture view (packages and their relationships)
-MATCH path = (p1:Package)-[:IMPORTS*1..2]->(p2:Package)
-WHERE p1.project_id = 'my-awesome-project'
-  AND p2.project_id = 'my-awesome-project'
-RETURN path
-LIMIT 50
-```
-
-#### **Code Complexity Hotspots**
-
-```cypher
-// Find the most connected functions (potential complexity hotspots)
+// Find the most connected functions
 MATCH (f:Function)
 WHERE f.project_id = 'my-awesome-project'
-WITH f,
-     size((f)-[:CALLS]->()) as outgoing_calls,
-     size((f)<-[:CALLS]-()) as incoming_calls
-RETURN f.name, f.package, outgoing_calls, incoming_calls,
-       (outgoing_calls + incoming_calls) as total_connections
+OPTIONAL MATCH (f)-[:CALLS]->(called)
+WITH f, count(called) as outgoing_calls
+OPTIONAL MATCH (f)<-[:CALLS]-(caller)
+RETURN f.name, f.package, outgoing_calls, count(caller) as incoming_calls,
+       (outgoing_calls + count(caller)) as total_connections
 ORDER BY total_connections DESC
 LIMIT 20
 ```
@@ -253,63 +221,22 @@ LIMIT 20
 
 **Useful Browser Commands:**
 
-```cypher
-// Show node labels and relationship types
-CALL db.labels()
-CALL db.relationshipTypes()
-
-// Count nodes by type
-MATCH (n)
-WHERE n.project_id = 'my-awesome-project'
-RETURN labels(n)[0] as NodeType, count(n) as Count
-ORDER BY Count DESC
-
-// Find circular dependencies
-MATCH path = (p:Package)-[:IMPORTS*2..]->(p)
-WHERE p.project_id = 'my-awesome-project'
-RETURN path
-LIMIT 10
-```
+See [docs/QUERIES.md](docs/QUERIES.md) for more queries including:
+- Node and relationship type discovery
+- Circular dependency detection
+- Package dependency analysis
+- Test coverage analysis
+- And many more!
 
 ### 5. Advanced Analysis Examples
 
-```bash
-# Find unused functions
-gograph query "
-  MATCH (f:Function)
-  WHERE f.project_id = 'my-awesome-project'
-    AND NOT (f)<-[:CALLS]-()
-    AND NOT f.name = 'main'
-  RETURN f.name, f.package, f.file
-  ORDER BY f.package, f.name
-"
-
-# Analyze test coverage by package
-gograph query "
-  MATCH (p:Package)
-  WHERE p.project_id = 'my-awesome-project'
-  OPTIONAL MATCH (p)-[:CONTAINS]->(f:File)
-  WHERE f.name ENDS WITH '_test.go'
-  WITH p, count(f) as test_files
-  OPTIONAL MATCH (p)-[:CONTAINS]->(f2:File)
-  WHERE NOT f2.name ENDS WITH '_test.go'
-  RETURN p.name, count(f2) as source_files, test_files,
-         CASE WHEN count(f2) > 0
-              THEN round(100.0 * test_files / count(f2), 2)
-              ELSE 0 END as test_ratio
-  ORDER BY test_ratio DESC
-"
-
-# Find interface implementations
-gograph query "
-  MATCH (s:Struct)-[:IMPLEMENTS]->(i:Interface)
-  WHERE s.project_id = 'my-awesome-project'
-  RETURN i.name as Interface,
-         collect(s.name) as Implementations,
-         count(s) as ImplementationCount
-  ORDER BY ImplementationCount DESC
-"
-```
+For advanced analysis queries, see [docs/QUERIES.md](docs/QUERIES.md) which includes:
+- Finding unused functions
+- Analyzing test coverage by package  
+- Finding interface implementations
+- Detecting circular dependencies
+- Identifying code complexity hotspots
+- And many more analysis patterns!
 
 ### 6. Export and Share Results
 
@@ -569,33 +496,26 @@ export GOGRAPH_MCP_PORT=8080
 | `IMPLEMENTS` | Struct implements interface                               |
 | `HAS_METHOD` | Struct/interface has method                               |
 | `DEPENDS_ON` | File depends on another file                              |
-| `DECLARES`   | File declares function/struct/interface                   |
+| `DEFINES`    | File defines function/struct/interface                    |
 | `USES`       | Function uses variable/constant                           |
 
 ### Example Queries
 
-```cypher
--- Find all functions in a package
-MATCH (p:Package {name: "main"})-[:CONTAINS]->(f:File)-[:DECLARES]->(fn:Function)
-RETURN fn.name, fn.signature
-
--- Find circular dependencies
-MATCH path=(p1:Package)-[:IMPORTS*]->(p1)
-RETURN path
+For a comprehensive collection of Cypher queries organized by use case, see [docs/QUERIES.md](docs/QUERIES.md).
 
+Quick examples:
+```cypher
 -- Find most called functions
 MATCH (f:Function)<-[:CALLS]-(caller)
+WHERE f.project_id = 'my-project'
 RETURN f.name, count(caller) as call_count
 ORDER BY call_count DESC
+LIMIT 10
 
--- Find unused functions
-MATCH (f:Function)
-WHERE NOT (f)<-[:CALLS]-()
-RETURN f.name, f.package
-
--- Find interface implementations
+-- Find interface implementations  
 MATCH (s:Struct)-[:IMPLEMENTS]->(i:Interface)
-RETURN s.name, i.name
+WHERE s.project_id = 'my-project'
+RETURN i.name as Interface, collect(s.name) as Implementations
 ```
 
 ## 🤖 MCP Integration
@@ -817,6 +737,7 @@ Inspired by:
 ## 🔗 Links
 
 - [Documentation](docs/)
+- [Query Reference Guide](docs/QUERIES.md)
 - [MCP Integration Guide](docs/MCP_INTEGRATION.md)
 - [Issue Tracker](https://github.com/compozy/gograph/issues)
 - [Discussions](https://github.com/compozy/gograph/discussions)

cmd/gograph/commands/analyze.go

@@ -80,16 +80,22 @@ The resulting graph allows you to:
 
 			// Initialize parser configuration from config
 			parserConfig := &parser.Config{
-				IgnoreDirs:     cfg.Analysis.IgnoreDirs,
-				IgnoreFiles:    cfg.Analysis.IgnoreFiles,
-				IncludeTests:   cfg.Analysis.IncludeTests,
-				IncludeVendor:  cfg.Analysis.IncludeVendor,
-				MaxConcurrency: cfg.Analysis.MaxConcurrency,
+				IgnoreDirs:      cfg.Analysis.IgnoreDirs,
+				IgnoreFiles:     cfg.Analysis.IgnoreFiles,
+				IncludeTests:    cfg.Analysis.IncludeTests,
+				IncludeVendor:   cfg.Analysis.IncludeVendor,
+				EnableSSA:       true,
+				EnableCallGraph: true,
 			}
 
+			// Initialize analyzer configuration with defaults
 			// Initialize analyzer configuration with defaults
 			analyzerConfig := analyzer.DefaultAnalyzerConfig()
 
+			// Enable SSA for better analysis
+			parserConfig.EnableSSA = true
+			parserConfig.EnableCallGraph = true
+
 			// Initialize Neo4j configuration from config with fallback to defaults
 			neo4jURI := cfg.Neo4j.URI
 			if neo4jURI == "" {
@@ -150,8 +156,16 @@ func runAnalysisWithoutProgress(
 	if err != nil {
 		return fmt.Errorf("failed to parse project: %w", err)
 	}
+
+	// Count total files from packages
+	totalFiles := 0
+	for _, pkg := range parseResult.Packages {
+		totalFiles += len(pkg.Files)
+	}
+
 	logger.Info("parsing completed",
-		"files", len(parseResult.Files),
+		"packages", len(parseResult.Packages),
+		"files", totalFiles,
 		"duration_ms", parseResult.ParseTime)
 
 	// -----
@@ -160,8 +174,8 @@ func runAnalysisWithoutProgress(
 	logger.Info("analyzing project structure")
 	analyzerService := analyzer.NewAnalyzer(analyzerConfig)
 	analysisInput := &analyzer.AnalysisInput{
-		ProjectID: projectID.String(),
-		Files:     parseResult.Files,
+		ProjectID:   projectID.String(),
+		ParseResult: parseResult,
 	}
 	report, err := analyzerService.AnalyzeProject(ctx, analysisInput)
 	if err != nil {
@@ -255,9 +269,15 @@ func runAnalysisWithProgress(
 	// Success with detailed statistics
 	successMsg := "Analysis completed successfully!"
 
+	// Count total files from packages
+	totalFiles := 0
+	for _, pkg := range parseResult.Packages {
+		totalFiles += len(pkg.Files)
+	}
+
 	// Create detailed statistics
 	stats := progress.AnalysisStats{
-		Files:         len(parseResult.Files),
+		Files:         totalFiles,
 		Nodes:         len(graphResult.Nodes),
 		Relationships: len(graphResult.Relationships),
 		Interfaces:    len(report.InterfaceImplementations),
@@ -289,7 +309,17 @@ func runParsingPhase(
 		progressIndicator.Error(fmt.Errorf("failed to parse project: %w", err))
 		return nil, fmt.Errorf("failed to parse project: %w", err)
 	}
-	progressIndicator.UpdateProgress(0.25, fmt.Sprintf("Parsed %d files", len(parseResult.Files)))
+
+	// Count total files from packages
+	totalFiles := 0
+	for _, pkg := range parseResult.Packages {
+		totalFiles += len(pkg.Files)
+	}
+
+	progressIndicator.UpdateProgress(
+		0.25,
+		fmt.Sprintf("Parsed %d files in %d packages", totalFiles, len(parseResult.Packages)),
+	)
 	return parseResult, nil
 }
 
@@ -305,8 +335,8 @@ func runAnalysisPhase(
 
 	analyzerService := analyzer.NewAnalyzer(analyzerConfig)
 	analysisInput := &analyzer.AnalysisInput{
-		ProjectID: projectID.String(),
-		Files:     parseResult.Files,
+		ProjectID:   projectID.String(),
+		ParseResult: parseResult,
 	}
 	progressIndicator.UpdateProgress(0.4, "Analyzing structure and dependencies")