feat(exceptions): add typed exception hierarchy

02-Cybersecurity/Vulnerability-Detection-Agent-Java/dependency-parser-mcp-server/src/main/java/com/agent/parser/PipParser.java

@@ -13,57 +13,73 @@
 @Component
 public class PipParser {
 
-    // Matches: package==1.0, package>=1.0, package~=1.0, package<=1.0, package!=1.0
-    // Also handles inline comments like: requests==2.31.0  # HTTP library
-    private static final Pattern DEP_PATTERN =
-            Pattern.compile("^([A-Za-z0-9_.-]+)\\s*([><=!~]+)\\s*([A-Za-z0-9_.*+-]+)");
+    /**
+     * Matches a pip requirement line:
+     *   group 1 — package name  (letters, digits, -, _, .)
+     *   group 2 — optional extras e.g. [asyncio,security]  (captured but discarded)
+     *   group 3 — optional version specifier(s) e.g. >=1.0,<2.0  or  ~=1.4.4
+     *   (environment markers after ';' are stripped before matching)
+     *
+     * Examples handled:
+     *   requests==2.31.0
+     *   aiohttp>=3.11.18
+     *   sqlalchemy[asyncio]>=2.0.41
+     *   markitdown-no-magika[docx,xls,xlsx]>=0.1.2
+     *   audioop-lts ; python_full_version >= '3.13'
+     *   xinference-client          (no version)
+     *   chardet~=5.1.0
+     */
+    private static final Pattern DEP_PATTERN = Pattern.compile(
+            "^([A-Za-z0-9][A-Za-z0-9_.-]*)          # package name\n" +
+            "(\\[[^\\]]*\\])?                        # optional extras\n" +
+            "\\s*([><=!~,A-Za-z0-9_.*+\\-]*)\\s*$   # optional version spec(s)",
+            Pattern.COMMENTS
+    );
 
     public List<Dependency> parse(String content) {
-
         List<Dependency> deps = new ArrayList<>();
 
         if (content == null || content.isBlank()) {
             log.warn("[PipParser] Empty or null content received");
             return deps;
         }
 
-        String[] lines = content.split("\n");
+        // Normalise escaped newlines that appear when content travels through JSON
+        // e.g. "requests==2.31.0\naiohttp>=3.11.18" → real newlines
+        String normalised = content
+                .replace("\\r\\n", "\n")
+                .replace("\\n",    "\n")
+                .replace("\\r",    "\n");
 
-        for (String rawLine : lines) {
+        for (String rawLine : normalised.split("\n")) {
 
-            // Strip inline comments and whitespace
-            String line = rawLine.split("#")[0].trim();
+            // Strip inline comments and environment markers (everything after ';')
+            String line = rawLine.split("#")[0].split(";")[0].trim();
 
-            // Skip blank lines, comments, -r includes, -e editable installs
+            // Skip blank lines, options (-r, --index-url, -e editable installs, etc.)
             if (line.isEmpty() || line.startsWith("-")) {
                 continue;
             }
 
             Matcher matcher = DEP_PATTERN.matcher(line);
+            if (!matcher.matches()) {
+                log.debug("[PipParser] Line did not match: '{}'", line);
+                continue;
+            }
 
-            if (matcher.find()) {
-                String name    = matcher.group(1).trim();
-                String version = matcher.group(2).trim() + matcher.group(3).trim();
+            String name    = matcher.group(1).trim();
+            String version = matcher.group(3) == null ? "" : matcher.group(3).trim();
 
-                deps.add(Dependency.builder()
-                        .name(name)
-                        .version(version)
-                        .ecosystem("pip")
-                        .build());
-            } else {
-                // Package with no version pinned (e.g. just "requests")
-                if (!line.isEmpty()) {
-                    deps.add(Dependency.builder()
-                            .name(line.trim())
-                            .version("")
-                            .ecosystem("pip")
-                            .build());
-                }
-            }
+            if (name.isEmpty()) continue;
+
+            deps.add(Dependency.builder()
+                    .name(name)
+                    .version(version)
+                    .ecosystem("pip")
+                    .build());
         }
 
         log.info("[PipParser] Parsed {} dependencies", deps.size());
         return deps;
     }
-
 }

02-Cybersecurity/Vulnerability-Detection-Agent-Java/dependency-parser-mcp-server/src/main/java/com/agent/service/DependencyParserService.java

@@ -1,5 +1,7 @@
 package com.agent.service;
 
+import com.agent.service.IDependencyParserService;
+
 import com.agent.model.Dependency;
 import com.agent.parser.*;
 import lombok.RequiredArgsConstructor;
@@ -11,7 +13,7 @@
 @Slf4j
 @Service
 @RequiredArgsConstructor
-public class DependencyParserService {
+public class DependencyParserService implements IDependencyParserService {
 
     private final PomParser     pomParser;
     private final NpmParser     npmParser;

02-Cybersecurity/Vulnerability-Detection-Agent-Java/dependency-parser-mcp-server/src/main/java/com/agent/service/IDependencyParserService.java

@@ -0,0 +1,29 @@
+package com.agent.service;
+
+import com.agent.model.Dependency;
+
+import java.util.List;
+
+/**
+ * IDependencyParserService — contract for dependency file parsers.
+ *
+ * Extracted from the concrete class to enable mock injection in unit tests.
+ * Implementation: {@link impl.DependencyParserServiceImpl}
+ */
+public interface IDependencyParserService {
+
+    /** Parse Maven pom.xml content */
+    List<Dependency> parsePom(String content);
+
+    /** Parse npm package.json content */
+    List<Dependency> parsePackageJson(String content) throws Exception;
+
+    /** Parse pip requirements.txt content */
+    List<Dependency> parseRequirements(String content);
+
+    /** Parse Gradle build.gradle / build.gradle.kts content */
+    List<Dependency> parseGradle(String content);
+
+    /** Parse Flutter/Dart pubspec.yaml content */
+    List<Dependency> parsePubspec(String content);
+}

02-Cybersecurity/Vulnerability-Detection-Agent-Java/github-repo-mcp-server/src/main/java/com/agent/service/GithubRepoService.java

@@ -1,5 +1,7 @@
 package com.agent.service;
 
+import com.agent.service.IGithubRepoService;
+
 import com.agent.util.FileScannerUtil;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.stereotype.Service;
@@ -15,7 +17,7 @@
 
 @Slf4j
 @Service
-public class GithubRepoService {
+public class GithubRepoService implements IGithubRepoService {
 
     private static final String REPO_BASE_DIR = "/tmp/repos";
     private static final int CLONE_TIMEOUT_SECONDS = 120;

02-Cybersecurity/Vulnerability-Detection-Agent-Java/github-repo-mcp-server/src/main/java/com/agent/service/IGithubRepoService.java

@@ -0,0 +1,37 @@
+package com.agent.service;
+
+import java.io.IOException;
+import java.util.List;
+
+/**
+ * GithubRepoService — contract for repository access operations.
+ *
+ * Extracted from the concrete class to enable mock injection in unit tests.
+ * Implementation: {@link impl.GithubRepoServiceImpl}
+ */
+public interface IGithubRepoService {
+
+    /**
+     * Clone a GitHub repository to a local temp directory.
+     *
+     * @param repoUrl      full HTTPS GitHub URL
+     * @param forceReclone if true, delete and re-clone even if already present
+     * @return absolute path to the cloned repository root
+     */
+    String cloneRepository(String repoUrl, boolean forceReclone) throws Exception;
+
+    /**
+     * List all files recursively under repoPath (up to configured depth).
+     */
+    List<String> listRepositoryFiles(String repoPath) throws IOException;
+
+    /**
+     * Find dependency manifest files (pom.xml, package.json, etc.) under repoPath.
+     */
+    List<String> findDependencyFiles(String repoPath) throws IOException;
+
+    /**
+     * Read the content of a single file (path-traversal protected).
+     */
+    String readFileContent(String filePath) throws IOException;
+}