fix source file path searching

Author: Codegass

CHANGELOG.md

@@ -5,6 +5,27 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.3.2] - 2025-06-02
+
+### 🐛 Critical Bug Fix - Inner Class Source Resolution
+- **Fixed SOURCE_FILE_NOT_FOUND for Inner Classes**: Major fix for source file detection of inner classes
+  - **Problem**: Classes like `org.apache.commons.cli.HelpFormatter.Builder` were causing SOURCE_FILE_NOT_FOUND errors
+  - **Root Cause**: Method was searching for `org/apache/commons/cli/HelpFormatter/Builder.java` instead of `org/apache/commons/cli/HelpFormatter.java`
+  - **Solution**: Enhanced `getSourceFilePathForClass()` to detect inner classes and map them to their outer class source files
+  - **Impact**: Dramatically reduces SOURCE_FILE_NOT_FOUND errors in projects with inner classes
+
+### 🔧 Technical Improvements
+- **Smart Inner Class Detection**: Added logic to identify inner classes by uppercase naming patterns
+- **Outer Class Mapping**: Automatically strips inner class portions to find the correct source file
+- **Enhanced Debug Logging**: Added detailed logging for source file resolution process
+
+### 🧪 Verification
+- **commons-cli Project**: Tested on Apache Commons CLI project - eliminated most SOURCE_FILE_NOT_FOUND errors
+- **Before**: Multiple SOURCE_FILE_NOT_FOUND errors for `HelpFormatter.Builder` methods  
+- **After**: All inner class methods now correctly resolve to their source files
+
+This fix significantly improves analysis accuracy for projects using inner classes, which are common in Java projects.
+
 ## [1.3.1] - 2025-06-02
 
 ### 🐛 Bug Fixes - Windows Path Compatibility

build.gradle

@@ -17,7 +17,7 @@ application {
 }
 
 group = 'edu.stevens'
-version = '1.3.1'
+version = '1.3.2'
 
 dependencies {
     // Use JitPack dependency for release builds

src/main/java/edu/stevens/swe/research/java/cli/Main.java

@@ -16,7 +16,7 @@
 import edu.stevens.swe.research.java.cli.analyzer.ResultFormatter;
 import edu.stevens.swe.research.java.cli.analyzer.LogData;
 
-@Command(name = "analyzer", mixinStandardHelpOptions = true, version = "Analyzer CLI 1.3.1",
+@Command(name = "analyzer", mixinStandardHelpOptions = true, version = "Analyzer CLI 1.3.2",
         description = "Analyzes Java source code based on specified tasks.")
 public class Main implements Callable<Integer> {
 

src/main/java/edu/stevens/swe/research/java/cli/analyzer/core/TestCaseAnalyzer.java

@@ -405,7 +405,36 @@ private boolean isTestCode(String filePath) {
     // Utility from old MethodAnalyzer to find source file for a class.
     // This might need to be made more robust or use ProjectCtx information.
     public String getSourceFilePathForClass(String className, String sourceRootPath) {
-        String classPath = className.replace('.', File.separatorChar) + ".java";
+        // Handle inner classes: for inner classes like "com.example.Outer.Inner", 
+        // we need to find the file for "com.example.Outer.java"
+        String outerClassName = className;
+        if (className.contains(".") && Character.isUpperCase(className.charAt(className.lastIndexOf('.') + 1))) {
+            // This might be an inner class. Find the outer class.
+            // Look for pattern like "package.Class.InnerClass" where the last part starts with uppercase
+            String[] parts = className.split("\\.");
+            StringBuilder outerClassBuilder = new StringBuilder();
+            
+            for (int i = 0; i < parts.length; i++) {
+                if (i > 0 && Character.isUpperCase(parts[i].charAt(0))) {
+                    // Found first part that starts with uppercase, this might be the start of class names
+                    // Check if we already have a class name (outer class)
+                    if (outerClassBuilder.length() > 0 && Character.isUpperCase(parts[i-1].charAt(0))) {
+                        // Previous part was also a class name, so current part is inner class
+                        break;
+                    }
+                }
+                
+                if (outerClassBuilder.length() > 0) {
+                    outerClassBuilder.append(".");
+                }
+                outerClassBuilder.append(parts[i]);
+            }
+            outerClassName = outerClassBuilder.toString();
+        }
+        
+        System.out.println("DEBUG: Looking for source file - Original class: " + className + ", Outer class: " + outerClassName);
+        
+        String classPath = outerClassName.replace('.', File.separatorChar) + ".java";
         Path effectiveSourceRoot = Paths.get(sourceRootPath); 
 
         // Attempt to find in standard main/java or test/java if sourceRootPath is project root
@@ -434,13 +463,14 @@ public String getSourceFilePathForClass(String className, String sourceRootPath)
                         .collect(Collectors.toList());
                 if (!foundPaths.isEmpty()) {
                     // Prefer paths that match more closely or handle multiple matches if necessary
+                    System.out.println("DEBUG: Found source file: " + foundPaths.get(0).toString());
                     return foundPaths.get(0).toString(); 
                 }
             } catch (IOException e) {
                 System.err.println("Error walking path: " + root + " : " + e.getMessage());
             }
         }
-        System.err.println("Warning: Source file not found for class " + className + " under roots: " + potentialSourceRoots);
+        System.err.println("Warning: Source file not found for class " + className + " (searched as " + outerClassName + ") under roots: " + potentialSourceRoots);
         return null;
     }