Fix CLI command crashes and H2 cache data loss

- Add no-arg constructors to FlowCommand, GraphCommand, FindCommand, and
  QueryCommand so Picocli can instantiate them without Spring DI
- Fix H2 cache node table: replace single-column PRIMARY KEY(id) with
  auto-increment surrogate key to preserve duplicate node IDs from
  different files and within the same file
- Deduplicate nodes in loadAllNodes() and getNodeCount() using GROUP BY/
  DISTINCT for accurate stats display
- Update error messages for graph/find/flow/query commands to point users
  to 'code-iq serve' or 'code-iq stats' instead of vague Neo4j reference

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

Author: aksOps

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

@@ -47,7 +47,8 @@ CREATE TABLE IF NOT EXISTS files (
             );
 
             CREATE TABLE IF NOT EXISTS nodes (
-                id VARCHAR PRIMARY KEY,
+                row_id BIGINT AUTO_INCREMENT PRIMARY KEY,
+                id VARCHAR NOT NULL,
                 content_hash VARCHAR NOT NULL,
                 kind VARCHAR NOT NULL,
                 data VARCHAR NOT NULL,
@@ -180,7 +181,7 @@ public void storeResults(String contentHash, String filePath, String language,
                 stmt.execute();
             }
 
-            // Insert nodes
+            // Insert nodes (no unique constraint on id — duplicates preserved for accurate cache replay)
             try (var stmt = conn.prepareStatement(
                     "INSERT INTO nodes (id, content_hash, kind, data) VALUES (?, ?, ?, ?)")) {
                 for (CodeNode node : nodes) {
@@ -321,7 +322,7 @@ public Map<String, Object> getStats() {
         Map<String, Object> stats = new LinkedHashMap<>();
         try {
             stats.put("cached_files", countTable("files"));
-            stats.put("cached_nodes", countTable("nodes"));
+            stats.put("cached_nodes", getNodeCount());
             stats.put("cached_edges", countTable("edges"));
             stats.put("total_runs", countTable("analysis_runs"));
             stats.put("db_path", dbPath.toString());
@@ -467,8 +468,10 @@ private long countTable(String table) throws SQLException {
      * Return the total number of cached nodes.
      */
     public long getNodeCount() {
-        try {
-            return countTable("nodes");
+        try (var stmt = conn.createStatement()) {
+            ResultSet rs = stmt.executeQuery("SELECT COUNT(DISTINCT id) FROM nodes");
+            rs.next();
+            return rs.getLong(1);
         } catch (SQLException e) {
             log.debug("Failed to count nodes", e);
             return 0;
@@ -510,7 +513,8 @@ public void storeBatchResults(String batchId, String filePath, String language,
      */
     public List<CodeNode> loadAllNodes() {
         List<CodeNode> nodes = new ArrayList<>();
-        try (var stmt = conn.prepareStatement("SELECT data FROM nodes")) {
+        // Use MIN(data) with GROUP BY id to deduplicate nodes that appear in multiple files
+        try (var stmt = conn.prepareStatement("SELECT MIN(data) FROM nodes GROUP BY id")) {
             ResultSet rs = stmt.executeQuery();
             while (rs.next()) {
                 nodes.add(deserializeNode(rs.getString(1)));

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

@@ -37,6 +37,11 @@ public class FindCommand implements Callable<Integer> {
 
     private final GraphStore graphStore;
 
+    /** No-arg constructor for Picocli direct instantiation. */
+    public FindCommand() {
+        this.graphStore = null;
+    }
+
     @Autowired
     public FindCommand(Optional<GraphStore> graphStore) {
         this.graphStore = graphStore.orElse(null);
@@ -50,7 +55,7 @@ public FindCommand(Optional<GraphStore> graphStore) {
     @Override
     public Integer call() {
         if (graphStore == null) {
-            CliOutput.error("Find queries require Neo4j. Run 'code-iq enrich' first, then 'code-iq serve'.");
+            CliOutput.error("Find queries require the serve profile (Neo4j). Use 'code-iq serve' to start the server, or 'code-iq stats' for cache-based queries.");
             return 1;
         }
         NodeKind kind = resolveKind(what);

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

@@ -40,6 +40,11 @@ public class FlowCommand implements Callable<Integer> {
 
     private final FlowEngine flowEngine;
 
+    /** No-arg constructor for Picocli direct instantiation. */
+    public FlowCommand() {
+        this.flowEngine = null;
+    }
+
     @Autowired
     public FlowCommand(Optional<FlowEngine> flowEngine) {
         this.flowEngine = flowEngine.orElse(null);
@@ -53,7 +58,7 @@ public FlowCommand(Optional<FlowEngine> flowEngine) {
     @Override
     public Integer call() {
         if (flowEngine == null) {
-            CliOutput.error("Flow diagrams require Neo4j. Run 'code-iq enrich' first, then 'code-iq serve'.");
+            CliOutput.error("Flow diagrams require the serve profile (Neo4j). Use 'code-iq serve' to start the server, or 'code-iq stats' for cache-based queries.");
             return 1;
         }
         try {

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

@@ -52,6 +52,11 @@ public class GraphCommand implements Callable<Integer> {
 
     private final GraphStore graphStore;
 
+    /** No-arg constructor for Picocli direct instantiation. */
+    public GraphCommand() {
+        this.graphStore = null;
+    }
+
     @Autowired
     public GraphCommand(Optional<GraphStore> graphStore) {
         this.graphStore = graphStore.orElse(null);
@@ -65,7 +70,7 @@ public GraphCommand(Optional<GraphStore> graphStore) {
     @Override
     public Integer call() {
         if (graphStore == null) {
-            CliOutput.error("Graph export requires Neo4j. Run 'code-iq enrich' first, then 'code-iq serve'.");
+            CliOutput.error("Graph export requires the serve profile (Neo4j). Use 'code-iq serve' to start the server, or 'code-iq stats' for cache-based queries.");
             return 1;
         }
         List<CodeNode> nodes;

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

@@ -50,6 +50,11 @@ public class QueryCommand implements Callable<Integer> {
 
     private final QueryService queryService;
 
+    /** No-arg constructor for Picocli direct instantiation. */
+    public QueryCommand() {
+        this.queryService = null;
+    }
+
     @Autowired
     public QueryCommand(Optional<QueryService> queryService) {
         this.queryService = queryService.orElse(null);
@@ -63,7 +68,7 @@ public QueryCommand(Optional<QueryService> queryService) {
     @Override
     public Integer call() {
         if (queryService == null) {
-            CliOutput.error("Graph queries require Neo4j. Run 'code-iq enrich' first, then 'code-iq serve'.");
+            CliOutput.error("Graph queries require the serve profile (Neo4j). Use 'code-iq serve' to start the server, or 'code-iq stats' for cache-based queries.");
             return 1;
         }
         if (consumersOf != null) {