perf: replace in-memory stats with Cypher aggregations, add cache invalidation

- P1: QueryService.getStats() and getDetailedStats() now use GraphStore.computeAggregateStats()
  which runs Cypher COUNT/GROUP BY queries instead of loading all nodes into heap via findAll().
  This prevents OOM on large codebases (100K+ nodes).

- P2: Added POST /api/cache/invalidate endpoint that clears all Spring caches.
  Allows cache refresh after re-enrichment without server restart.

- P4: Wrapped Analyzer.runBatchedIndex() executor in try-with-resources to prevent
  thread leak on exception between creation (line 522) and close (line 639).

- Code cleanup: removed dead matchesAnyExclude() method, removed dead branches in
  ProjectConfigLoader.applyOverrides(), fixed AbstractJavaParserDetector ThreadLocal
  misuse (PARSER.remove() defeated pooling), removed unused ServeCommand.COMMAND_NAME,
  removed unused QueryService.statsService field and useNeo4j() method.

All 1431 tests pass.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: 3 people

src/main/java/io/github/randomcodespace/iq/analyzer/Analyzer.java

@@ -522,6 +522,7 @@ private AnalysisResult runBatchedWithCache(Path root, Integer parallelism, int b
         var batchExecutorService = parallelism != null && parallelism > 0
                 ? Executors.newFixedThreadPool(parallelism)
                 : Executors.newVirtualThreadPerTaskExecutor();
+        try (batchExecutorService) {
         List<DiscoveredFile> batch = new ArrayList<>(batchSize);
         for (int fileIdx = 0; fileIdx < files.size(); fileIdx++) {
             batch.add(files.get(fileIdx));
@@ -636,7 +637,7 @@ private AnalysisResult runBatchedWithCache(Path root, Integer parallelism, int b
                 batch.clear();
             }
         }
-        batchExecutorService.close();
+        } // close batchExecutorService
 
         if (cacheHits > 0) {
             report.accept("Cache hits: " + cacheHits + " / " + totalFiles + " files");
@@ -1290,15 +1291,6 @@ private static List<java.util.regex.Pattern> compileExcludePatterns(List<String>
                 .toList();
     }
 
-    /**
-     * Check whether a file path matches any of the given pre-compiled exclude patterns.
-     */
-    private static boolean matchesAnyExclude(String filePath, List<String> excludePatterns) {
-        if (excludePatterns == null) return false;
-        List<java.util.regex.Pattern> compiled = compileExcludePatterns(excludePatterns);
-        return matchesAnyCompiledExclude(filePath, compiled);
-    }
-
     /**
      * Check whether a file path matches any of the given pre-compiled patterns.
      */

src/main/java/io/github/randomcodespace/iq/api/GraphController.java

@@ -2,12 +2,14 @@
 
 import io.github.randomcodespace.iq.config.CodeIqConfig;
 import io.github.randomcodespace.iq.query.QueryService;
+import org.springframework.cache.CacheManager;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.context.annotation.Profile;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
@@ -30,11 +32,14 @@ public class GraphController {
 
     private final QueryService queryService;
     private final CodeIqConfig config;
+    private final CacheManager cacheManager;
 
     public GraphController(@org.springframework.beans.factory.annotation.Autowired(required = false) QueryService queryService,
-                           CodeIqConfig config) {
+                           CodeIqConfig config,
+                           @org.springframework.beans.factory.annotation.Autowired(required = false) CacheManager cacheManager) {
         this.queryService = queryService;
         this.config = config;
+        this.cacheManager = cacheManager;
     }
 
     @GetMapping("/stats")
@@ -196,13 +201,6 @@ public List<Map<String, Object>> searchGraph(
         return queryService.searchGraph(q, Math.min(limit, 1000));
     }
 
-    /**
-     * Check whether Neo4j (via QueryService) is available for queries.
-     */
-    private boolean useNeo4j() {
-        return queryService != null;
-    }
-
     private void requireQueryService() {
         if (queryService == null) {
             throw new ResponseStatusException(HttpStatus.SERVICE_UNAVAILABLE,
@@ -250,6 +248,21 @@ public ResponseEntity<String> readFile(
         }
     }
 
+    @PostMapping("/cache/invalidate")
+    public Map<String, Object> invalidateCache() {
+        int cleared = 0;
+        if (cacheManager != null) {
+            for (String name : cacheManager.getCacheNames()) {
+                var cache = cacheManager.getCache(name);
+                if (cache != null) {
+                    cache.clear();
+                    cleared++;
+                }
+            }
+        }
+        return Map.of("status", "ok", "caches_cleared", cleared);
+    }
+
     // POST /api/analyze removed — API/MCP server is read-only.
     // Analysis is done locally via CLI: code-iq analyze / code-iq index
     // Data is loaded into Neo4j on serve startup (auto-enrich).

src/main/java/io/github/randomcodespace/iq/cli/ServeCommand.java

@@ -30,8 +30,6 @@ public class ServeCommand implements Callable<Integer> {
 
     private static final Logger log = LoggerFactory.getLogger(ServeCommand.class);
 
-    public static final String COMMAND_NAME = "serve";
-
     @Parameters(index = "0", defaultValue = ".", description = "Path to analyzed codebase")
     private Path path;
 

src/main/java/io/github/randomcodespace/iq/config/ProjectConfigLoader.java

@@ -162,21 +162,8 @@ private static void applyOverrides(Map<String, Object> data, CodeIqConfig config
         if (data.containsKey("max_radius")) {
             config.setMaxRadius(toInt(data.get("max_radius"), config.getMaxRadius()));
         }
-        // Nested analysis section (matches Python config structure)
-        if (data.get("analysis") instanceof Map<?, ?> analysis) {
-            if (analysis.containsKey("parallelism")) {
-                // Stored for CLI to pick up; not directly in CodeIqConfig
-            }
-            if (analysis.containsKey("incremental")) {
-                // Available for future use
-            }
-        }
-        // Nested output section
-        if (data.get("output") instanceof Map<?, ?> output) {
-            if (output.containsKey("max_nodes")) {
-                // Available for future use
-            }
-        }
+        // Nested analysis/output sections are recognized but not yet mapped to CodeIqConfig.
+        // They are loaded and accessible via data map for CLI commands that need them.
     }
 
     private static int toInt(Object value, int defaultValue) {

src/main/java/io/github/randomcodespace/iq/detector/java/AbstractJavaParserDetector.java

@@ -29,8 +29,6 @@ protected Optional<CompilationUnit> parse(DetectorContext ctx) {
             // JavaParser may throw AssertionError for unrecognized token kinds
             // (e.g. newer Java syntax). Fall back to regex in those cases.
             return Optional.empty();
-        } finally {
-            PARSER.remove();
         }
     }