fix: boost coverage to 90.6%, eliminate ~535 lines duplication, fix MD5 security hotspot

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

@@ -118,34 +118,8 @@ public Integer call() {
                 + nf.format(result.nodeCount()) + " nodes, "
                 + nf.format(result.edgeCount()) + " edges in " + timeStr);
         System.out.println();
-        CliOutput.info("  Files:   " + nf.format(result.totalFiles()) + " discovered, "
-                + nf.format(result.filesAnalyzed()) + " analyzed");
-        CliOutput.cyan("  Nodes:   " + nf.format(result.nodeCount()));
-        CliOutput.cyan("  Edges:   " + nf.format(result.edgeCount()));
-        CliOutput.info("  Time:    " + timeStr);
-
-        if (!result.nodeBreakdown().isEmpty()) {
-            System.out.println();
-            StringBuilder topNodes = new StringBuilder("  Top node kinds: ");
-            result.nodeBreakdown().entrySet().stream()
-                    .sorted(Map.Entry.<String, Integer>comparingByValue().reversed())
-                    .limit(10)
-                    .forEach(e -> topNodes.append(e.getKey()).append(" (")
-                            .append(nf.format(e.getValue())).append("), "));
-            if (topNodes.length() > 2) topNodes.setLength(topNodes.length() - 2);
-            CliOutput.info(topNodes.toString());
-        }
-
-        if (!result.languageBreakdown().isEmpty()) {
-            StringBuilder langs = new StringBuilder("  Languages: ");
-            result.languageBreakdown().entrySet().stream()
-                    .sorted(Map.Entry.<String, Integer>comparingByValue().reversed())
-                    .limit(10)
-                    .forEach(e -> langs.append(e.getKey()).append(" (")
-                            .append(nf.format(e.getValue())).append("), "));
-            if (langs.length() > 2) langs.setLength(langs.length() - 2);
-            CliOutput.info(langs.toString());
-        }
+        CliOutput.printAnalysisStats(result, nf);
+        CliOutput.printBreakdowns(result, nf);
 
         if (result.frameworkBreakdown() != null && !result.frameworkBreakdown().isEmpty()) {
             StringBuilder fws = new StringBuilder("  Frameworks: ");

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

@@ -1,8 +1,11 @@
 package io.github.randomcodespace.iq.cli;
 
+import io.github.randomcodespace.iq.analyzer.AnalysisResult;
 import picocli.CommandLine;
 
 import java.io.PrintStream;
+import java.text.NumberFormat;
+import java.util.Map;
 
 /**
  * Utility class for rich ANSI-colored CLI output.
@@ -76,6 +79,50 @@
         return ANSI.string(ansiFormatted);
     }
 
+    /**
+     * Print files/nodes/edges/time summary lines shared by analyze and index commands.
+     * Callers are responsible for printing the preceding success banner and any
+     * command-specific extra lines (e.g. "Store: H2…").
+     */
+    static void printAnalysisStats(AnalysisResult result, NumberFormat nf) {
+        long secs = result.elapsed().toSeconds();
+        String timeStr = secs > 0 ? secs + "s" : result.elapsed().toMillis() + "ms";
+        info("  Files:   " + nf.format(result.totalFiles()) + " discovered, "
+                + nf.format(result.filesAnalyzed()) + " analyzed");
+        cyan("  Nodes:   " + nf.format(result.nodeCount()));
+        cyan("  Edges:   " + nf.format(result.edgeCount()));
+        info("  Time:    " + timeStr);
+    }
+
+    /**
+     * Print node-kind and language breakdown lines shared by analyze and index commands.
+     * Prints a blank line before the node breakdown when it is non-empty.
+     */
+    static void printBreakdowns(AnalysisResult result, NumberFormat nf) {
+        if (!result.nodeBreakdown().isEmpty()) {
+            System.out.println();
+            StringBuilder topNodes = new StringBuilder("  Top node kinds: ");
+            result.nodeBreakdown().entrySet().stream()
+                    .sorted(Map.Entry.<String, Integer>comparingByValue().reversed())
+                    .limit(10)
+                    .forEach(e -> topNodes.append(e.getKey()).append(" (")
+                            .append(nf.format(e.getValue())).append("), "));
+            if (topNodes.length() > 2) topNodes.setLength(topNodes.length() - 2);
+            info(topNodes.toString());
+        }
+
+        if (!result.languageBreakdown().isEmpty()) {
+            StringBuilder langs = new StringBuilder("  Languages: ");
+            result.languageBreakdown().entrySet().stream()
+                    .sorted(Map.Entry.<String, Integer>comparingByValue().reversed())
+                    .limit(10)
+                    .forEach(e -> langs.append(e.getKey()).append(" (")
+                            .append(nf.format(e.getValue())).append("), "));
+            if (langs.length() > 2) langs.setLength(langs.length() - 2);
+            info(langs.toString());
+        }
+    }
+
     /**
      * Escape pipe characters that would break picocli ANSI markup.
      */

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

@@ -12,7 +12,6 @@
 import java.nio.file.Path;
 import java.text.NumberFormat;
 import java.util.Locale;
-import java.util.Map;
 import java.util.concurrent.Callable;
 
 /**
@@ -127,35 +126,9 @@ public Integer call() {
                 + nf.format(result.nodeCount()) + " nodes, "
                 + nf.format(result.edgeCount()) + " edges in " + timeStr);
         System.out.println();
-        CliOutput.info("  Files:   " + nf.format(result.totalFiles()) + " discovered, "
-                + nf.format(result.filesAnalyzed()) + " analyzed");
-        CliOutput.cyan("  Nodes:   " + nf.format(result.nodeCount()));
-        CliOutput.cyan("  Edges:   " + nf.format(result.edgeCount()));
-        CliOutput.info("  Time:    " + timeStr);
+        CliOutput.printAnalysisStats(result, nf);
         CliOutput.info("  Store:   H2 (.code-intelligence/analysis-cache)");
-
-        if (!result.nodeBreakdown().isEmpty()) {
-            System.out.println();
-            StringBuilder topNodes = new StringBuilder("  Top node kinds: ");
-            result.nodeBreakdown().entrySet().stream()
-                    .sorted(Map.Entry.<String, Integer>comparingByValue().reversed())
-                    .limit(10)
-                    .forEach(e -> topNodes.append(e.getKey()).append(" (")
-                            .append(nf.format(e.getValue())).append("), "));
-            if (topNodes.length() > 2) topNodes.setLength(topNodes.length() - 2);
-            CliOutput.info(topNodes.toString());
-        }
-
-        if (!result.languageBreakdown().isEmpty()) {
-            StringBuilder langs = new StringBuilder("  Languages: ");
-            result.languageBreakdown().entrySet().stream()
-                    .sorted(Map.Entry.<String, Integer>comparingByValue().reversed())
-                    .limit(10)
-                    .forEach(e -> langs.append(e.getKey()).append(" (")
-                            .append(nf.format(e.getValue())).append("), "));
-            if (langs.length() > 2) langs.setLength(langs.length() - 2);
-            CliOutput.info(langs.toString());
-        }
+        CliOutput.printBreakdowns(result, nf);
 
         System.out.println();
         CliOutput.info("  Next step: code-iq enrich " + root);

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

@@ -1,6 +1,12 @@
 package io.github.randomcodespace.iq.detector;
 
+import io.github.randomcodespace.iq.model.CodeEdge;
+import io.github.randomcodespace.iq.model.CodeNode;
+import io.github.randomcodespace.iq.model.EdgeKind;
+import io.github.randomcodespace.iq.model.NodeKind;
+
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -87,4 +93,40 @@ protected int getInt(Object container, String key, int defaultValue) {
         }
         return defaultValue;
     }
+
+    /**
+     * Build a CONFIG_FILE node for the given context and format.
+     * The returned node is NOT added to any list — callers must do that themselves.
+     */
+    protected CodeNode buildFileNode(DetectorContext ctx, String format) {
+        String fp = ctx.filePath();
+        String fileId = format + ":" + fp;
+        CodeNode fileNode = new CodeNode(fileId, NodeKind.CONFIG_FILE, fp);
+        fileNode.setFqn(fp);
+        fileNode.setModule(ctx.moduleName());
+        fileNode.setFilePath(fp);
+        fileNode.setLineStart(1);
+        fileNode.setProperties(new HashMap<>(Map.of("format", format)));
+        return fileNode;
+    }
+
+    /**
+     * Build a CONFIG_KEY node and a CONTAINS edge from {@code fileId} to it,
+     * appending both to the supplied lists.
+     */
+    protected void addKeyNode(String fileId, String fp, String key, String format,
+            DetectorContext ctx, List<CodeNode> nodes, List<CodeEdge> edges) {
+        String keyId = format + ":" + fp + ":" + key;
+        CodeNode keyNode = new CodeNode(keyId, NodeKind.CONFIG_KEY, key);
+        keyNode.setFqn(fp + ":" + key);
+        keyNode.setModule(ctx.moduleName());
+        keyNode.setFilePath(fp);
+        nodes.add(keyNode);
+        CodeEdge edge = new CodeEdge();
+        edge.setId(fileId + "->" + keyId);
+        edge.setKind(EdgeKind.CONTAINS);
+        edge.setSourceId(fileId);
+        edge.setTarget(new CodeNode(keyId, null, null));
+        edges.add(edge);
+    }
 }

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

@@ -0,0 +1,72 @@
+package io.github.randomcodespace.iq.detector;
+
+import io.github.randomcodespace.iq.analyzer.InfraEndpoint;
+import io.github.randomcodespace.iq.analyzer.InfrastructureRegistry;
+import io.github.randomcodespace.iq.model.CodeEdge;
+import io.github.randomcodespace.iq.model.CodeNode;
+import io.github.randomcodespace.iq.model.EdgeKind;
+import io.github.randomcodespace.iq.model.NodeKind;
+
+import java.util.List;
+
+/**
+ * Shared helper for detectors that emit DATABASE_CONNECTION nodes and CONNECTS_TO edges.
+ * Used by Python, TypeScript, and Java ORM/database detectors.
+ */
+public final class DetectorDbHelper {
+
+    private DetectorDbHelper() {}
+
+    /**
+     * Ensure a DATABASE_CONNECTION node exists in the result, creating it if needed.
+     * Uses the first database from the InfrastructureRegistry if available,
+     * otherwise creates a generic "database:unknown" node.
+     *
+     * @param registry infrastructure registry (may be null)
+     * @param nodes    the nodes list to add the DB node to if missing
+     * @return the database node ID
+     */
+    public static String ensureDbNode(InfrastructureRegistry registry, List<CodeNode> nodes) {
+        String dbNodeId;
+        if (registry != null && !registry.getDatabases().isEmpty()) {
+            InfraEndpoint db = registry.getDatabases().values().iterator().next();
+            dbNodeId = "infra:" + db.id();
+            if (nodes.stream().noneMatch(n -> dbNodeId.equals(n.getId()))) {
+                CodeNode dbNode = new CodeNode(dbNodeId, NodeKind.DATABASE_CONNECTION,
+                        db.name() + " (" + db.type() + ")");
+                dbNode.getProperties().put("type", db.type());
+                if (db.connectionUrl() != null) dbNode.getProperties().put("url", db.connectionUrl());
+                nodes.add(dbNode);
+            }
+        } else {
+            dbNodeId = "database:unknown";
+            if (nodes.stream().noneMatch(n -> dbNodeId.equals(n.getId()))) {
+                nodes.add(new CodeNode(dbNodeId, NodeKind.DATABASE_CONNECTION, "Database"));
+            }
+        }
+        return dbNodeId;
+    }
+
+    /**
+     * Add a CONNECTS_TO edge from the given source node to the database node.
+     *
+     * @param sourceId the source node ID
+     * @param registry infrastructure registry (may be null)
+     * @param nodes    the nodes list (used to find/create the DB node)
+     * @param edges    the edges list to add the edge to
+     */
+    public static void addDbEdge(String sourceId, InfrastructureRegistry registry,
+            List<CodeNode> nodes, List<CodeEdge> edges) {
+        String dbNodeId = ensureDbNode(registry, nodes);
+        CodeNode targetRef = nodes.stream()
+                .filter(n -> dbNodeId.equals(n.getId()))
+                .findFirst()
+                .orElseGet(() -> new CodeNode(dbNodeId, NodeKind.DATABASE_CONNECTION, "Database"));
+        CodeEdge edge = new CodeEdge();
+        edge.setId(sourceId + "->connects_to->" + dbNodeId);
+        edge.setKind(EdgeKind.CONNECTS_TO);
+        edge.setSourceId(sourceId);
+        edge.setTarget(targetRef);
+        edges.add(edge);
+    }
+}

src/main/java/io/github/randomcodespace/iq/detector/config/IniStructureDetector.java

@@ -52,13 +52,7 @@ public DetectorResult detect(DetectorContext ctx) {
         List<CodeEdge> edges = new ArrayList<>();
 
         // CONFIG_FILE node for the file itself
-        CodeNode fileNode = new CodeNode(fileId, NodeKind.CONFIG_FILE, fp);
-        fileNode.setFqn(fp);
-        fileNode.setModule(ctx.moduleName());
-        fileNode.setFilePath(fp);
-        fileNode.setLineStart(1);
-        fileNode.setProperties(Map.of("format", "ini"));
-        nodes.add(fileNode);
+        nodes.add(buildFileNode(ctx, "ini"));
 
         Object parsedData = ctx.parsedData();
         if (parsedData == null) {

src/main/java/io/github/randomcodespace/iq/detector/config/JsonStructureDetector.java

@@ -49,13 +49,7 @@ public DetectorResult detect(DetectorContext ctx) {
         List<CodeEdge> edges = new ArrayList<>();
 
         // CONFIG_FILE node for the file itself
-        CodeNode fileNode = new CodeNode(fileId, NodeKind.CONFIG_FILE, fp);
-        fileNode.setFqn(fp);
-        fileNode.setModule(ctx.moduleName());
-        fileNode.setFilePath(fp);
-        fileNode.setLineStart(1);
-        fileNode.setProperties(Map.of("format", "json"));
-        nodes.add(fileNode);
+        nodes.add(buildFileNode(ctx, "json"));
 
         // Extract data from parsed_data
         Object parsedData = ctx.parsedData();
@@ -71,20 +65,7 @@ public DetectorResult detect(DetectorContext ctx) {
         }
 
         for (String key : data.keySet()) {
-            String keyId = "json:" + fp + ":" + key;
-
-            CodeNode keyNode = new CodeNode(keyId, NodeKind.CONFIG_KEY, key);
-            keyNode.setFqn(fp + ":" + key);
-            keyNode.setModule(ctx.moduleName());
-            keyNode.setFilePath(fp);
-            nodes.add(keyNode);
-
-            CodeEdge edge = new CodeEdge();
-            edge.setId(fileId + "->" + keyId);
-            edge.setKind(EdgeKind.CONTAINS);
-            edge.setSourceId(fileId);
-            edge.setTarget(new CodeNode(keyId, null, null));
-            edges.add(edge);
+            addKeyNode(fileId, fp, key, "json", ctx, nodes, edges);
         }
 
         return DetectorResult.of(nodes, edges);

src/main/java/io/github/randomcodespace/iq/detector/config/TomlStructureDetector.java

@@ -14,6 +14,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+
 import io.github.randomcodespace.iq.detector.DetectorInfo;
 import io.github.randomcodespace.iq.detector.ParserType;
 
@@ -52,13 +53,7 @@ public DetectorResult detect(DetectorContext ctx) {
         List<CodeEdge> edges = new ArrayList<>();
 
         // CONFIG_FILE node for the file itself
-        CodeNode fileNode = new CodeNode(fileId, NodeKind.CONFIG_FILE, fp);
-        fileNode.setFqn(fp);
-        fileNode.setModule(ctx.moduleName());
-        fileNode.setFilePath(fp);
-        fileNode.setLineStart(1);
-        fileNode.setProperties(Map.of("format", "toml"));
-        nodes.add(fileNode);
+        nodes.add(buildFileNode(ctx, "toml"));
 
         Object parsedData = ctx.parsedData();
         if (parsedData == null) {

src/main/java/io/github/randomcodespace/iq/detector/config/YamlStructureDetector.java

@@ -50,13 +50,7 @@ public DetectorResult detect(DetectorContext ctx) {
         List<CodeEdge> edges = new ArrayList<>();
 
         // CONFIG_FILE node for the file itself
-        CodeNode fileNode = new CodeNode(fileId, NodeKind.CONFIG_FILE, fp);
-        fileNode.setFqn(fp);
-        fileNode.setModule(ctx.moduleName());
-        fileNode.setFilePath(fp);
-        fileNode.setLineStart(1);
-        fileNode.setProperties(Map.of("format", "yaml"));
-        nodes.add(fileNode);
+        nodes.add(buildFileNode(ctx, "yaml"));
 
         Object parsedData = ctx.parsedData();
         if (parsedData == null) {
@@ -84,20 +78,7 @@ public DetectorResult detect(DetectorContext ctx) {
         }
 
         for (String keyStr : topLevelKeys) {
-            String keyId = "yaml:" + fp + ":" + keyStr;
-
-            CodeNode keyNode = new CodeNode(keyId, NodeKind.CONFIG_KEY, keyStr);
-            keyNode.setFqn(fp + ":" + keyStr);
-            keyNode.setModule(ctx.moduleName());
-            keyNode.setFilePath(fp);
-            nodes.add(keyNode);
-
-            CodeEdge edge = new CodeEdge();
-            edge.setId(fileId + "->" + keyId);
-            edge.setKind(EdgeKind.CONTAINS);
-            edge.setSourceId(fileId);
-            edge.setTarget(new CodeNode(keyId, null, null));
-            edges.add(edge);
+            addKeyNode(fileId, fp, keyStr, "yaml", ctx, nodes, edges);
         }
 
         return DetectorResult.of(nodes, edges);