feat: shade JaCoCo into codeflash-runtime as one fat JAR

Merge JaCoCo agent and CLI into the runtime JAR instead of shipping 3
separate JARs. JaCoCo already self-shades its internals with a version
hash, so no relocation is needed.

- Add AgentDispatcher premain that routes to profiler (config=) or
  JaCoCo (destfile=) based on agent args
- Update shade plugin: Premain-Class → AgentDispatcher, add
  ServicesResourceTransformer and DontIncludeResourceTransformer
- Rewrite build_jacoco_agent_arg() and generate_jacoco_report() to use
  the runtime JAR instead of separate JaCoCo JARs
- Delete org.jacoco.agent-0.8.13-runtime.jar and
  org.jacoco.cli-0.8.13-nodeps.jar from resources/

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

codeflash-java-runtime/pom.xml

@@ -40,6 +40,7 @@
         <maven.compiler.source>11</maven.compiler.source>
         <maven.compiler.target>11</maven.compiler.target>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <jacoco.version>0.8.13</jacoco.version>
     </properties>
 
     <dependencies>
@@ -83,6 +84,22 @@
             <version>9.7.1</version>
         </dependency>
 
+        <!-- JaCoCo agent (coverage instrumentation at runtime) -->
+        <dependency>
+            <groupId>org.jacoco</groupId>
+            <artifactId>org.jacoco.agent</artifactId>
+            <version>${jacoco.version}</version>
+            <classifier>runtime</classifier>
+        </dependency>
+
+        <!-- JaCoCo CLI (report generation from .exec files) -->
+        <dependency>
+            <groupId>org.jacoco</groupId>
+            <artifactId>org.jacoco.cli</artifactId>
+            <version>${jacoco.version}</version>
+            <classifier>nodeps</classifier>
+        </dependency>
+
         <!-- JUnit 5 for testing -->
         <dependency>
             <groupId>org.junit.jupiter</groupId>
@@ -145,10 +162,14 @@
                                 <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                     <mainClass>com.codeflash.Comparator</mainClass>
                                     <manifestEntries>
-                                        <Premain-Class>com.codeflash.profiler.ProfilerAgent</Premain-Class>
+                                        <Premain-Class>com.codeflash.AgentDispatcher</Premain-Class>
                                         <Can-Retransform-Classes>true</Can-Retransform-Classes>
                                     </manifestEntries>
                                 </transformer>
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.DontIncludeResourceTransformer">
+                                    <resource>about.html</resource>
+                                </transformer>
                             </transformers>
                             <filters>
                                 <filter>

codeflash-java-runtime/src/main/java/com/codeflash/AgentDispatcher.java

@@ -0,0 +1,33 @@
+package com.codeflash;
+
+import java.lang.instrument.Instrumentation;
+
+/**
+ * Premain dispatcher that routes to either the CodeFlash line profiler or the
+ * JaCoCo coverage agent based on the agent arguments.
+ *
+ * <p>Detection logic:
+ * <ul>
+ *   <li>Args contain {@code config=} → line profiler mode → delegate to
+ *       {@link com.codeflash.profiler.ProfilerAgent}</li>
+ *   <li>Otherwise → JaCoCo mode → delegate to JaCoCo's PreMain</li>
+ * </ul>
+ *
+ * <p>This is reliable because our profiler always receives
+ * {@code config=/path/to/config.json} while JaCoCo always receives
+ * {@code destfile=/path/to/jacoco.exec}.
+ */
+public class AgentDispatcher {
+
+    static boolean isProfilerMode(String agentArgs) {
+        return agentArgs != null && agentArgs.contains("config=");
+    }
+
+    public static void premain(String agentArgs, Instrumentation inst) throws Exception {
+        if (isProfilerMode(agentArgs)) {
+            com.codeflash.profiler.ProfilerAgent.premain(agentArgs, inst);
+        } else {
+            org.jacoco.agent.rt.internal_0e20598.PreMain.premain(agentArgs, inst);
+        }
+    }
+}

codeflash-java-runtime/src/test/java/com/codeflash/AgentDispatcherTest.java

@@ -0,0 +1,33 @@
+package com.codeflash;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+import org.junit.jupiter.api.Test;
+
+class AgentDispatcherTest {
+
+    @Test
+    void profilerModeWhenConfigPresent() {
+        assertTrue(AgentDispatcher.isProfilerMode("config=/tmp/config.json"));
+    }
+
+    @Test
+    void profilerModeWithMultipleArgs() {
+        assertTrue(AgentDispatcher.isProfilerMode("config=/tmp/config.json,output=results"));
+    }
+
+    @Test
+    void jacocoModeWhenDestfilePresent() {
+        assertFalse(AgentDispatcher.isProfilerMode("destfile=/tmp/jacoco.exec"));
+    }
+
+    @Test
+    void jacocoModeWhenNullArgs() {
+        assertFalse(AgentDispatcher.isProfilerMode(null));
+    }
+
+    @Test
+    void jacocoModeWhenEmptyArgs() {
+        assertFalse(AgentDispatcher.isProfilerMode(""));
+    }
+}

codeflash/languages/java/build_tools.py

@@ -22,8 +22,6 @@ CODEFLASH_RUNTIME_VERSION = "1.0.0"
 CODEFLASH_RUNTIME_JAR_NAME = f"codeflash-runtime-{CODEFLASH_RUNTIME_VERSION}.jar"
 
 JACOCO_PLUGIN_VERSION = "0.8.13"
-JACOCO_AGENT_JAR = f"org.jacoco.agent-{JACOCO_PLUGIN_VERSION}-runtime.jar"
-JACOCO_CLI_JAR = f"org.jacoco.cli-{JACOCO_PLUGIN_VERSION}-nodeps.jar"
 
 _JAVA_RESOURCES_DIR = Path(__file__).parent / "resources"
 
@@ -72,21 +70,6 @@ def restore_all_pom_backups() -> None:
     _pom_backups.clear()
 
 
-def find_jacoco_agent_jar() -> Path | None:
-    """Find the bundled JaCoCo agent JAR in package resources."""
-    jar = _JAVA_RESOURCES_DIR / JACOCO_AGENT_JAR
-    if jar.exists():
-        return jar
-    return None
-
-
-def find_jacoco_cli_jar() -> Path | None:
-    """Find the bundled JaCoCo CLI JAR in package resources."""
-    jar = _JAVA_RESOURCES_DIR / JACOCO_CLI_JAR
-    if jar.exists():
-        return jar
-    return None
-
 
 # MVN_CENTRAL_TODO: Uncomment once codeflash-runtime is published to Maven Central.
 # Steps:

codeflash/languages/java/test_runner.py

@@ -28,8 +28,6 @@ from codeflash.languages.java.build_tools import (
     CODEFLASH_RUNTIME_VERSION,
     add_codeflash_dependency_to_pom,
     backup_pom,
-    find_jacoco_agent_jar,
-    find_jacoco_cli_jar,
     find_maven_executable,
     get_jacoco_xml_path,
     install_codeflash_runtime,
@@ -179,23 +177,29 @@ def _validate_java_class_name(class_name: str) -> bool:
 def build_jacoco_agent_arg(exec_dest: Path) -> str | None:
     """Build the -javaagent arg for standalone JaCoCo coverage collection.
 
-    Returns None if the bundled JaCoCo agent JAR is not found.
+    The codeflash-runtime JAR includes the shaded JaCoCo agent. The AgentDispatcher
+    routes to JaCoCo when the args contain ``destfile=`` (no ``config=``).
+
+    Returns None if the runtime JAR is not found.
     """
-    agent_jar = find_jacoco_agent_jar()
-    if agent_jar is None:
-        logger.warning("Bundled JaCoCo agent JAR not found — coverage will not be collected")
+    runtime_jar = _find_runtime_jar()
+    if runtime_jar is None:
+        logger.warning("codeflash-runtime JAR not found — coverage will not be collected")
         return None
-    return f"-javaagent:{agent_jar}=destfile={exec_dest}"
+    return f"-javaagent:{runtime_jar}=destfile={exec_dest}"
 
 
 def generate_jacoco_report(exec_file: Path, classfiles_dir: Path, sourcefiles_dir: Path, xml_output: Path) -> bool:
-    """Generate a JaCoCo XML report from a .exec file using the bundled CLI JAR.
+    """Generate a JaCoCo XML report from a .exec file.
+
+    Uses the JaCoCo CLI classes shaded into the codeflash-runtime JAR
+    (invoked via ``java -cp <runtime_jar> org.jacoco.cli.internal.Main``).
 
     Returns True if the report was generated successfully.
     """
-    cli_jar = find_jacoco_cli_jar()
-    if cli_jar is None:
-        logger.error("Bundled JaCoCo CLI JAR not found — cannot generate coverage report")
+    runtime_jar = _find_runtime_jar()
+    if runtime_jar is None:
+        logger.error("codeflash-runtime JAR not found — cannot generate coverage report")
         return False
 
     if not exec_file.exists():
@@ -206,8 +210,9 @@ def generate_jacoco_report(exec_file: Path, classfiles_dir: Path, sourcefiles_di
 
     cmd = [
         shutil.which("java") or "java",
-        "-jar",
-        str(cli_jar),
+        "-cp",
+        str(runtime_jar),
+        "org.jacoco.cli.internal.Main",
         "report",
         str(exec_file),
         "--classfiles",