merge: resolve conflict with main after PR #2019 merge

Take -cp first ordering from #2019, remove --app-args and mvn exec:java,
keep #2018's additions (Maven/Gradle test suites, multi-module, trace-only).

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

Author: mohamedashrraf222

codeflash/code_utils/code_utils.py

@@ -17,7 +17,7 @@
 
 from codeflash.cli_cmds.console import logger, paneled_text
 from codeflash.code_utils.config_parser import find_pyproject_toml, get_all_closest_config_files
-from codeflash.lsp.helpers import is_LSP_enabled
+from codeflash.lsp.helpers import is_LSP_enabled, is_subagent_mode
 
 _INVALID_CHARS_NT = {"<", ">", ":", '"', "|", "?", "*"}
 
@@ -471,6 +471,11 @@ def exit_with_message(message: str, *, error_on_exit: bool = False) -> None:
     if is_LSP_enabled():
         logger.error(message)
         return
+    if is_subagent_mode():
+        from xml.sax.saxutils import escape
+
+        sys.stdout.write(f"<codeflash-error>{escape(message)}</codeflash-error>\n")
+        sys.exit(1 if error_on_exit else 0)
     paneled_text(message, panel_args={"style": "red"})
 
     sys.exit(1 if error_on_exit else 0)

codeflash/languages/java/gradle_strategy.py

@@ -45,7 +45,8 @@
                 'spotbugsMain', 'spotbugsTest',
                 'pmdMain', 'pmdTest',
                 'rat', 'japicmp',
-                'jarHell', 'thirdPartyAudit'
+                'jarHell', 'thirdPartyAudit',
+                'spotlessCheck', 'spotlessApply', 'spotlessJava', 'spotlessKotlin', 'spotlessScala'
             ]
         }.configureEach {
             enabled = false

codeflash/languages/java/maven_strategy.py

@@ -43,6 +43,8 @@
     "-Denforcer.skip=true",
     "-Djapicmp.skip=true",
     "-Derrorprone.skip=true",
+    "-Dspotless.check.skip=true",
+    "-Dspotless.apply.skip=true",
     "-Dmaven.compiler.failOnWarning=false",
     "-Dmaven.compiler.showWarnings=false",
 ]

codeflash/languages/javascript/support.py

@@ -2268,7 +2268,10 @@ def get_module_path(self, source_file: Path, project_root: Path, tests_root: Pat
             source_without_ext = source_file_abs.with_suffix("")
 
             # Use os.path.relpath to compute relative path from tests_root to source file
-            rel_path = os.path.relpath(str(source_without_ext), str(tests_root_abs))
+            # Replace backslashes with forward slashes — JavaScript import/require paths
+            # must use forward slashes. Backslashes are escape chars in JS strings
+            # (e.g. \t → tab, \n → newline) and would break imports on Windows.
+            rel_path = os.path.relpath(str(source_without_ext), str(tests_root_abs)).replace("\\", "/")
 
             # For ESM, add .js extension (TypeScript convention)
             # TypeScript requires imports to reference the OUTPUT file extension (.js),

codeflash/languages/javascript/test_runner.py

@@ -369,7 +369,9 @@ def _create_runtime_jest_config(base_config_path: Path | None, project_root: Pat
 
     runtime_config_path = config_dir / f"jest.codeflash.runtime.config{config_ext}"
 
-    test_dirs_js = ", ".join(f"'{d}'" for d in sorted(test_dirs))
+    # Normalize to forward slashes — backslashes in JS strings are escape chars
+    # (e.g. \t → tab, \n → newline) and would corrupt paths on Windows.
+    test_dirs_js = ", ".join(f"'{d.replace(chr(92), '/')}'" for d in sorted(test_dirs))
 
     # In monorepos, add the root node_modules to moduleDirectories so Jest
     # can resolve workspace packages that are hoisted to the monorepo root.
@@ -382,6 +384,8 @@ def _create_runtime_jest_config(base_config_path: Path | None, project_root: Pat
     else:
         module_dirs_line_no_base = ""
 
+    project_root_posix = project_root.as_posix()
+
     # TypeScript configs (.ts) cannot be required from CommonJS modules
     # because Node.js cannot parse TypeScript syntax in require().
     # When the base config is TypeScript, we create a standalone config
@@ -403,7 +407,7 @@ def _create_runtime_jest_config(base_config_path: Path | None, project_root: Pat
     else:
         config_content = f"""// Auto-generated by codeflash - runtime config with test roots
 module.exports = {{
-  roots: ['{project_root}', {test_dirs_js}],
+  roots: ['{project_root_posix}', {test_dirs_js}],
   testMatch: ['**/*.test.ts', '**/*.test.js', '**/*.test.tsx', '**/*.test.jsx'],
 {module_dirs_line_no_base}}};
 """

codeflash/telemetry/posthog_cf.py

@@ -7,6 +7,7 @@
 
 from codeflash.api.cfapi import get_user_id
 from codeflash.cli_cmds.console import logger
+from codeflash.lsp.helpers import is_subagent_mode
 from codeflash.version import __version__
 
 _posthog = None
@@ -36,7 +37,7 @@ def ph(event: str, properties: dict[str, Any] | None = None) -> None:
         return
 
     properties = properties or {}
-    properties.update({"cli_version": __version__})
+    properties.update({"cli_version": __version__, "subagent": is_subagent_mode()})
 
     user_id = get_user_id()
 

codeflash/verification/coverage_utils.py

@@ -54,14 +54,17 @@ def load_from_jest_json(
             return CoverageData.create_empty(source_code_path, function_name, code_context)
 
         # Find the file entry in coverage data
-        # Jest uses absolute paths as keys
+        # Jest/Vitest always writes coverage keys with forward slashes (POSIX paths),
+        # so we normalize our paths to POSIX for comparison — critical on Windows
+        # where Path.resolve() and str(Path) produce backslash paths.
         file_coverage = None
-        source_path_str = str(source_code_path.resolve())
+        source_path_posix = source_code_path.resolve().as_posix()
+        source_relative_posix = source_code_path.as_posix()
 
         for file_path, file_data in coverage_data.items():
             # Match exact path or path ending with full relative path from src/
             # Avoid matching files with same name in different directories (e.g., db/utils.ts vs utils/utils.ts)
-            if file_path == source_path_str or file_path.endswith(str(source_code_path)):
+            if file_path == source_path_posix or file_path.endswith(source_relative_posix):
                 file_coverage = file_data
                 break
 

docs/codeflash-concepts/how-codeflash-works.mdx

@@ -3,20 +3,20 @@ title: "How Codeflash Works"
 description: "Understand Codeflash's generate-and-verify approach to code optimization and correctness verification"
 icon: "gear"
 sidebarTitle: "How It Works"
-keywords: ["architecture", "verification", "correctness", "testing", "optimization", "LLM", "benchmarking", "javascript", "typescript", "python"]
+keywords: ["architecture", "verification", "correctness", "testing", "optimization", "LLM", "benchmarking", "javascript", "typescript", "python", "java"]
 ---
 # How Codeflash Works
 
 Codeflash follows a "generate and verify" approach to optimize code. It uses LLMs to generate optimizations, then it rigorously verifies if those optimizations are indeed
 faster and if they have the same behavior. The basic unit of optimization is a function—Codeflash tries to speed up the function, and tries to ensure that it still behaves the same way. This way if you merge the optimized code, it simply runs faster without breaking any functionality.
 
-Codeflash supports **Python**, **JavaScript**, and **TypeScript** projects.
+Codeflash supports **Python**, **JavaScript**, **TypeScript**, and **Java** projects.
 
 ## Analysis of your code
 
 Codeflash scans your codebase to identify all available functions. It locates existing unit tests in your projects and maps which functions they test. When optimizing a function, Codeflash runs these discovered tests to verify nothing has broken.
 
-For Python, code analysis uses `libcst` and `jedi`. For JavaScript/TypeScript, it uses `tree-sitter` for AST parsing.
+For Python, code analysis uses `libcst` and `jedi`. For JavaScript/TypeScript and Java, it uses `tree-sitter` for AST parsing.
 
 #### What kind of functions can Codeflash optimize?
 
@@ -25,7 +25,7 @@ Codeflash supports optimizing async functions in all supported languages.
 
 #### Test Discovery
 
-Codeflash discovers tests that directly call the target function in their test body. For Python, it finds pytest and unittest tests. For JavaScript/TypeScript, it finds Jest and Vitest test files.
+Codeflash discovers tests that directly call the target function in their test body. For Python, it finds pytest and unittest tests. For JavaScript/TypeScript, it finds Jest and Vitest test files. For Java, it finds JUnit 5, JUnit 4, and TestNG test classes.
 
 To discover tests that indirectly call the function, you can use the Codeflash Tracer. The Tracer analyzes your test suite and identifies all tests that eventually call a function.
 
@@ -54,12 +54,12 @@ We recommend manually reviewing the optimized code since there might be importan
 
 Codeflash generates two types of tests:
 
-- **LLM Generated tests** - Codeflash uses LLMs to create several regression test cases that cover typical function usage, edge cases, and large-scale inputs to verify both correctness and performance. This works for Python, JavaScript, and TypeScript.
+- **LLM Generated tests** - Codeflash uses LLMs to create several regression test cases that cover typical function usage, edge cases, and large-scale inputs to verify both correctness and performance. This works for Python, JavaScript, TypeScript, and Java.
 - **Concolic coverage tests** - Codeflash uses state-of-the-art concolic testing with an SMT Solver (a theorem prover) to explore execution paths and generate function arguments. This aims to maximize code coverage for the function being optimized. Currently, this feature only supports Python (pytest).
 
 ## Code Execution
 
-Codeflash runs tests for the target function on your machine. For Python, it uses pytest or unittest. For JavaScript/TypeScript, it uses Jest or Vitest. Running on your machine ensures access to your environment and dependencies, and provides accurate performance measurements since runtime varies by system.
+Codeflash runs tests for the target function on your machine. For Python, it uses pytest or unittest. For JavaScript/TypeScript, it uses Jest or Vitest. For Java, it uses Maven Surefire or Gradle's test task. Running on your machine ensures access to your environment and dependencies, and provides accurate performance measurements since runtime varies by system.
 
 #### Performance benchmarking
 

docs/getting-started/java-installation.mdx

@@ -47,18 +47,72 @@ uv tool install codeflash
 ```
 
 </Step>
-<Step title="Initialize your project">
+<Step title="Authenticate with Codeflash">
+
+Codeflash uses cloud-hosted AI models. You need to authenticate before running any commands.
+
+**Option A: Browser login (recommended)**
+
+```bash
+codeflash auth login
+```
+
+This opens your browser to sign in with your GitHub account. Your API key is saved automatically to your shell profile.
+
+If you're on a remote server without a browser, a URL will be displayed that you can open on any device.
+
+**Option B: API key**
+
+1. Visit the [Codeflash Web App](https://app.codeflash.ai/) and sign up with your GitHub account (free tier available)
+2. Navigate to the [API Key](https://app.codeflash.ai/app/apikeys) page to generate your key
+3. Set it as an environment variable:
+
+```bash
+export CODEFLASH_API_KEY="your-api-key-here"
+```
+
+Add this to your shell profile (`~/.bashrc`, `~/.zshrc`) so it persists across sessions.
+
+<Info>
+If you skip this step, `codeflash init` will prompt you to authenticate interactively.
+</Info>
+
+</Step>
+<Step title="Initialize your project (recommended)">
 
 Navigate to your Java project root (where `pom.xml` or `build.gradle` is) and run:
 
 ```bash
 codeflash init
 ```
 
-This will:
-- Detect your build tool (Maven/Gradle)
-- Find your source and test directories
-- Write Codeflash configuration to your `pom.xml` properties (Maven) or `gradle.properties` (Gradle)
+The init command will:
+1. **Auto-detect your project** — find your build tool, source root (e.g., `src/main/java`), test root (e.g., `src/test/java`), and test framework
+2. **Confirm settings** — show the detected values and ask if you want to change anything
+3. **Configure formatter** — let you set up a code formatter (e.g., Spotless, google-java-format)
+4. **Install GitHub App** — offer to set up the [Codeflash GitHub App](https://github.com/apps/codeflash-ai/installations/select_target) for automatic PR creation (see next step)
+5. **Install GitHub Actions** — offer to add a CI workflow for automated optimization on PRs
+
+Only non-default settings are written to your `pom.xml` properties (Maven) or `gradle.properties` (Gradle). For standard layouts, no config changes are needed.
+
+<Info>
+**Can I skip init?** Yes. For standard Maven/Gradle projects, Codeflash auto-detects your project structure from `pom.xml` or `build.gradle` at runtime. If you're already authenticated and your project uses a standard layout (`src/main/java`, `src/test/java`), you can skip straight to optimizing.
+
+Init is recommended because it also sets up the GitHub App and Actions workflow, and lets you override paths for non-standard project layouts (e.g., multi-module projects where source is under `client/src/`).
+</Info>
+
+</Step>
+<Step title="Install the Codeflash GitHub App (recommended)">
+
+To have Codeflash create pull requests with optimizations automatically, install the GitHub App:
+
+[Install Codeflash GitHub App](https://github.com/apps/codeflash-ai/installations/select_target)
+
+Select the repositories you want Codeflash to optimize. This allows the codeflash-ai bot to open PRs with optimization suggestions in your repository.
+
+<Info>
+If you prefer to try Codeflash locally first, you can skip this step and use the `--no-pr` flag to apply optimizations directly to your local files (see next step).
+</Info>
 
 </Step>
 <Step title="Run your first optimization">
@@ -69,6 +123,12 @@ Optimize a specific function:
 codeflash --file src/main/java/com/example/Utils.java --function myMethod
 ```
 
+If you installed the GitHub App, Codeflash will create a pull request with the optimization. If you haven't installed the app yet, or prefer to review changes locally first, add `--no-pr`:
+
+```bash
+codeflash --file src/main/java/com/example/Utils.java --function myMethod --no-pr
+```
+
 Or optimize all functions in your project:
 
 ```bash
@@ -80,7 +140,7 @@ Codeflash will:
 2. Generate tests and optimization candidates using AI
 3. Verify correctness by running tests (JUnit 5, JUnit 4, or TestNG)
 4. Benchmark performance improvements
-5. Create a pull request with the optimization (if the GitHub App is installed)
+5. Create a pull request with the optimization (or apply locally with `--no-pr`)
 
 For advanced workflow tracing (profiling a running Java program), see [Trace & Optimize](/optimizing-with-codeflash/trace-and-optimize).
 

docs/optimizing-with-codeflash/codeflash-all.mdx

@@ -3,7 +3,7 @@ title: "Optimize Your Entire Codebase"
 description: "Automatically optimize all codepaths in your project with Codeflash's comprehensive analysis"
 icon: "database"
 sidebarTitle: "Optimize Entire Codebase"
-keywords: ["codebase optimization", "all functions", "batch optimization", "github app", "checkpoint", "recovery", "javascript", "typescript", "python"]
+keywords: ["codebase optimization", "all functions", "batch optimization", "github app", "checkpoint", "recovery", "javascript", "typescript", "python", "java"]
 ---
 
 # Optimize your entire codebase
@@ -45,6 +45,11 @@ codeflash --all path/to/dir
   codeflash optimize --trace-only --vitest ; codeflash --all
   ```
   </Tab>
+  <Tab title="Java">
+  ```bash
+  codeflash optimize --timeout 60 java -cp target/classes com.example.Main ; codeflash --all
+  ```
+  </Tab>
   </Tabs>
 
   This runs your test suite, traces all the code covered by your tests, ensuring higher correctness guarantees