fix(spotbugs): eliminate 12 SpotBugs findings (RAN-23)

src/main/java/io/github/randomcodespace/iq/CodeIqApplication.java

@@ -54,8 +54,6 @@ public static void main(String[] args) {
                 .findFirst()
                 .orElse("");
         boolean isServe = "serve".equalsIgnoreCase(command);
-        boolean isIndex = "index".equalsIgnoreCase(command);
-        boolean isEnrich = "enrich".equalsIgnoreCase(command);
 
         if (isServe) {
             app.setAdditionalProfiles("serving");

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

@@ -15,9 +15,6 @@
 import io.github.randomcodespace.iq.detector.DetectorResult;
 import io.github.randomcodespace.iq.detector.DetectorUtils;
 import io.github.randomcodespace.iq.grammar.AntlrParserFactory;
-import io.github.randomcodespace.iq.intelligence.FileClassification;
-import io.github.randomcodespace.iq.intelligence.FileEntry;
-import io.github.randomcodespace.iq.intelligence.FileInventory;
 import io.github.randomcodespace.iq.intelligence.RepositoryIdentity;
 import io.github.randomcodespace.iq.model.CodeEdge;
 import io.github.randomcodespace.iq.model.CodeNode;
@@ -274,9 +271,8 @@ private AnalysisResult runWithCache(Path root, Integer parallelism, AnalysisCach
         int totalFiles = files.size();
         report.accept("Found " + totalFiles + " files");
 
-        // 1b. Resolve repository identity and build file inventory
+        // 1b. Resolve repository identity
         RepositoryIdentity repoIdentity = RepositoryIdentity.resolve(root);
-        FileInventory fileInventory = buildFileInventory(files, cache);
 
         // Compute language breakdown
         Map<String, Integer> languageBreakdown = new HashMap<>();
@@ -384,9 +380,12 @@ private AnalysisResult runWithCache(Path root, Integer parallelism, AnalysisCach
         report.accept("Linking cross-file relationships...");
         builder.runLinkers(linkers);
 
-        // Flush and collect deferred edges
-        GraphBuilder.FlushResult flushed = builder.flush();
-        List<io.github.randomcodespace.iq.model.CodeEdge> recoveredEdges = builder.flushDeferred();
+        // Flush buffered graph state and retry any deferred edges so the
+        // side effects (provenance stamping, edge validation, dropped-edge
+        // counters) still run even though we read the results straight off
+        // the builder below.
+        builder.flush();
+        builder.flushDeferred();
 
         // 5. Classify layers
         report.accept("Classifying layers...");
@@ -1619,22 +1618,6 @@ private DetectorResult analyzeFileRegexOnly(DiscoveredFile file, Path repoPath,
         return DetectorResult.of(allNodes, allEdges);
     }
 
-    /**
-     * Build a deterministic FileInventory from the list of discovered files.
-     * Content hashes are reused from {@code cache} when available (no re-read of files).
-     * Hashes remain null for files not yet present in the cache.
-     */
-    private static FileInventory buildFileInventory(List<DiscoveredFile> files, AnalysisCache cache) {
-        List<FileEntry> entries = new ArrayList<>(files.size());
-        for (DiscoveredFile f : files) {
-            String relPath = f.path().toString().replace('\\', '/');
-            FileClassification cls = FileEntry.classify(relPath, f.language());
-            String contentHash = cache != null ? cache.getHashForPath(relPath) : null;
-            entries.add(new FileEntry(relPath, f.language(), f.sizeBytes(), contentHash, cls));
-        }
-        return new FileInventory(entries);
-    }
-
     /**
      * Get the current git HEAD commit SHA, or null if not a git repo.
      */

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

@@ -165,6 +165,7 @@ private void addGitDiscoveredFile(Path root, List<DiscoveredFile> result, String
         try {
             size = Files.size(absPath);
         } catch (IOException e) {
+            log.debug("Skipping {} -- could not read size", absPath, e);
             return;
         }
         long maxSize = CONFIG_LANGUAGES.contains(language)

src/main/java/io/github/randomcodespace/iq/cache/AnalysisCache.java

@@ -35,7 +35,7 @@
  * Uses H2 in embedded mode — pure Java, no JNI, MVCC concurrency,
  * fully compatible with virtual threads.
  */
-public class AnalysisCache implements Closeable {
+public final class AnalysisCache implements Closeable {
 
     private static final Logger log = LoggerFactory.getLogger(AnalysisCache.class);
 

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

@@ -22,6 +22,7 @@
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Parameters;
 
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.text.NumberFormat;
@@ -125,7 +126,7 @@
         }
     }
 
     private int enrichFromCache(AnalysisCache cache, Path root, NumberFormat nf, Instant start) {
         // Load all nodes and edges from H2
         List<CodeNode> allNodes = cache.loadAllNodes();
         List<CodeEdge> allEdges = cache.loadAllEdges();
@@ -149,9 +150,12 @@
         builder.addEdges(allEdges);
         builder.runLinkers(linkers);
 
-        // Flush and collect valid edges
-        GraphBuilder.FlushResult flushed = builder.flush();
-        List<CodeEdge> recoveredEdges = builder.flushDeferred();
+        // Flush buffered graph state and retry any deferred edges so the
+        // side effects (provenance stamping, edge validation, dropped-edge
+        // counters) still run even though we read enriched nodes/edges
+        // straight off the builder below.
+        builder.flush();
+        builder.flushDeferred();
 
         List<CodeNode> enrichedNodes = new ArrayList<>(builder.getNodes());
         List<CodeEdge> enrichedEdges = new ArrayList<>(builder.getEdges());
@@ -422,7 +426,7 @@
 
             return 0;
 
-        } catch (Exception e) {
+        } catch (IOException | RuntimeException e) {
             log.error("Enrichment failed", e);
             CliOutput.error("Enrichment failed: " + e.getMessage());
             return 1;

src/main/java/io/github/randomcodespace/iq/detector/frontend/ReactComponentDetector.java

@@ -110,9 +110,6 @@ record ComponentEntry(String name, String sourceId, int matchStart) {}
 
         // RENDERS edges: scope JSX tag search to each component's body section.
         // A component's body is from its match position to the next component's position.
-        Set<String> allDetected = new HashSet<>(componentNames);
-        allDetected.addAll(hookNames);
-
         componentEntries.sort(Comparator.comparingInt(ComponentEntry::matchStart));
 
         for (int i = 0; i < componentEntries.size(); i++) {

src/main/java/io/github/randomcodespace/iq/detector/go/GoStructuresDetector.java

@@ -139,9 +139,7 @@ protected DetectorResult detectWithRegex(DetectorContext ctx) {
 
         // Methods
         Matcher mm = METHOD_RE.matcher(text);
-        Set<Integer> methodPositions = new HashSet<>();
         while (mm.find()) {
-            methodPositions.add(mm.start());
             String receiver = mm.group(1);
             String methodName = mm.group(2);
             boolean exported = Character.isUpperCase(methodName.charAt(0));

src/main/java/io/github/randomcodespace/iq/query/TopologyService.java

@@ -195,14 +195,12 @@ public Map<String, Object> serviceDependents(String serviceName, List<CodeNode>
     public Map<String, Object> blastRadius(String nodeId, List<CodeNode> nodes, List<CodeEdge> edges) {
         // Build adjacency for BFS
         Map<String, List<String>> adjacency = new HashMap<>();
-        Map<String, EdgeKind> edgeKinds = new HashMap<>();
         for (CodeEdge edge : edges) {
             if (!RUNTIME_EDGES.contains(edge.getKind())) continue;
             String src = edge.getSourceId();
             String tgt = edge.getTarget() != null ? edge.getTarget().getId() : null;
             if (src == null || tgt == null) continue;
             adjacency.computeIfAbsent(src, k -> new ArrayList<>()).add(tgt);
-            edgeKinds.put(src + "->" + tgt, edge.getKind());
         }
 
         // BFS from nodeId, max depth 5