refactor: unify data directory to .code-iq/ and --no-cache deletes DB

Directory consolidation:
- .code-intelligence → .code-iq/cache (H2 analysis cache)
- .osscodeiq/graph.db → .code-iq/graph/graph.db (Neo4j)
- .osscodeiq.yml → .code-iq.yml (project config, old name still supported)
- All data now under single .code-iq/ directory

--no-cache behavior:
- Now deletes the entire .code-iq/cache directory before re-indexing
  instead of just skipping cache reads (ensures fresh H2 schema)

Updated 12 test files + 8 source files for new paths.
Backward compat: .osscodeiq.yml still loaded as fallback config name.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: aksOps

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

@@ -90,7 +90,7 @@ public static void main(String[] args) {
             if (graphOverride != null) {
                 graphDbPath = java.nio.file.Path.of(graphOverride).toAbsolutePath().normalize();
             } else {
-                graphDbPath = root.resolve(".osscodeiq/graph.db");
+                graphDbPath = root.resolve(".code-iq/graph/graph.db");
             }
 
             // Point Neo4j config to the graph path (enriched or new empty db).

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

@@ -47,7 +47,7 @@ public class FileDiscovery {
             // Go / Rust
             "vendor",
             // Code-IQ own dirs
-            ".code-intelligence", ".osscodeiq"
+            ".code-iq", ".code-intelligence", ".osscodeiq"
     );
 
     /** Files to always skip (lock files, generated). */

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

@@ -105,7 +105,7 @@ public Integer call() {
         // Resolve paths
         Path neo4jDir = graphDirOption != null
                 ? graphDirOption.toAbsolutePath().normalize()
-                : root.resolve(".osscodeiq/graph.db");
+                : root.resolve(".code-iq/graph/graph.db");
         Path h2Dir = root.resolve(config.getCacheDir());
 
         // Validate Neo4j graph exists

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

@@ -78,8 +78,22 @@ public Integer call() {
         NumberFormat nf = NumberFormat.getIntegerInstance(Locale.US);
         int cores = parallelism != null ? parallelism : Runtime.getRuntime().availableProcessors();
 
-        // --no-cache overrides --incremental
+        // --no-cache overrides --incremental and deletes existing cache DB
         boolean useIncremental = incremental && !noCache;
+        if (noCache) {
+            Path cacheDir = root.resolve(config.getCacheDir());
+            if (java.nio.file.Files.exists(cacheDir)) {
+                try {
+                    try (var walk = java.nio.file.Files.walk(cacheDir)) {
+                        walk.sorted(java.util.Comparator.reverseOrder())
+                                .forEach(p -> { try { java.nio.file.Files.deleteIfExists(p); } catch (Exception ignored) {} });
+                    }
+                    CliOutput.info("  Deleted existing cache at " + cacheDir);
+                } catch (Exception e) {
+                    CliOutput.warn("  Could not delete cache: " + e.getMessage());
+                }
+            }
+        }
 
         CliOutput.step("[*]", "Indexing " + root + " ...");
         CliOutput.info("  (batch size: " + effectiveBatchSize + " files, "
@@ -112,7 +126,7 @@ public Integer call() {
         });
 
         CliOutput.printResultSummary(result, nf);
-        CliOutput.info("  Store:   H2 (.code-intelligence/analysis-cache)");
+        CliOutput.info("  Store:   H2 (.code-iq/cache/analysis-cache)");
 
         System.out.println();
         CliOutput.info("  Next step: code-iq enrich " + root);

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

@@ -344,7 +344,7 @@ public Integer call() {
                     private static final Set<String> SKIP_DIRS = Set.of(
                             "node_modules", ".git", "build", "target", "dist",
                             "__pycache__", "venv", ".venv", ".gradle",
-                            ".idea", ".vscode", ".code-intelligence");
+                            ".idea", ".vscode", ".code-iq", ".code-intelligence");
 
                     @Override
                     public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) {

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

@@ -20,8 +20,8 @@ public class CodeIqConfig {
     /** Root path of the codebase to analyze. */
     private String rootPath = ".";
 
-    /** Cache directory name (legacy name kept for backward compatibility). */
-    private String cacheDir = ".code-intelligence";
+    /** Cache directory relative to repo root. */
+    private String cacheDir = ".code-iq/cache";
 
     /** Maximum traversal depth for graph queries. */
     private int maxDepth = 10;
@@ -45,7 +45,7 @@ public class CodeIqConfig {
     private int maxSnippetLines = 50;
 
     public static class Graph {
-        private String path = ".osscodeiq/graph.db";
+        private String path = ".code-iq/graph/graph.db";
 
         public String getPath() { return path; }
         public void setPath(String path) { this.path = path; }

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

@@ -23,7 +23,7 @@
 public final class ProjectConfigLoader {
 
     private static final Logger log = LoggerFactory.getLogger(ProjectConfigLoader.class);
-    private static final String[] CONFIG_FILE_NAMES = {".osscodeiq.yml", ".osscodeiq.yaml"};
+    private static final String[] CONFIG_FILE_NAMES = {".code-iq.yml", ".code-iq.yaml", ".osscodeiq.yml", ".osscodeiq.yaml"};
 
     private ProjectConfigLoader() {
         // utility class

src/main/resources/application.yml

@@ -24,9 +24,9 @@ management:
 
 codeiq:
   root-path: "."
-  cache-dir: ".code-intelligence"
+  cache-dir: ".code-iq/cache"
   graph:
-    path: ".osscodeiq/graph.db"
+    path: ".code-iq/graph/graph.db"
   max-depth: 10
   max-radius: 10
   batch-size: 500

src/test/java/io/github/randomcodespace/iq/analyzer/BatchedStreamingTest.java

@@ -89,7 +89,7 @@ void batchedIndexWritesToH2() throws IOException {
         assertEquals(0, result.edgeCount());
 
         // Verify H2 has data
-        Path cachePath = tempDir.resolve(".code-intelligence").resolve("analysis-cache.db");
+        Path cachePath = tempDir.resolve(".code-iq/cache").resolve("analysis-cache.db");
         try (var cache = new AnalysisCache(cachePath)) {
             long nodeCount = cache.getNodeCount();
             assertEquals(10, nodeCount, "H2 should have 10 nodes");

src/test/java/io/github/randomcodespace/iq/analyzer/FileDiscoveryTest.java

@@ -215,12 +215,12 @@ void skipsOversizedConfigFiles() throws IOException {
 
     @Test
     void excludesCodeIqOwnDirs() throws IOException {
-        Path codeIntelDir = tempDir.resolve(".code-intelligence");
-        Path osscodeiqDir = tempDir.resolve(".osscodeiq");
-        Files.createDirectories(codeIntelDir);
-        Files.createDirectories(osscodeiqDir);
-        Files.writeString(codeIntelDir.resolve("cache.java"), "class Cache {}");
-        Files.writeString(osscodeiqDir.resolve("meta.java"), "class Meta {}");
+        Path codeIqDir = tempDir.resolve(".code-iq");
+        Files.createDirectories(codeIqDir);
+        Files.writeString(codeIqDir.resolve("cache.java"), "class Cache {}");
+        Path codeIqCacheDir = tempDir.resolve(".code-iq/cache");
+        Files.createDirectories(codeIqCacheDir);
+        Files.writeString(codeIqCacheDir.resolve("meta.java"), "class Meta {}");
         Files.writeString(tempDir.resolve("src.java"), "class Src {}");
 
         List<DiscoveredFile> files = discovery.discover(tempDir);