feat: sync CLI from main with Java additions

Adds subagent mode, config display, and main's CLI refactoring.
Preserves omni-java's NullHighlighter, Java test root detection,
and Java project root detection (pom.xml/build.gradle).

codeflash/cli_cmds/cli.py

@@ -130,9 +130,18 @@ def parse_args() -> Namespace:
         "--reset-config", action="store_true", help="Remove codeflash configuration from project config file."
     )
     parser.add_argument("-y", "--yes", action="store_true", help="Skip confirmation prompts (useful for CI/scripts).")
+    parser.add_argument(
+        "--subagent",
+        action="store_true",
+        help="Subagent mode: skip all interactive prompts with sensible defaults. Designed for AI agent integrations.",
+    )
 
     args, unknown_args = parser.parse_known_args()
     sys.argv[:] = [sys.argv[0], *unknown_args]
+    if args.subagent:
+        args.yes = True
+        args.no_pr = True
+        args.worktree = True
     return process_and_validate_cmd_args(args)
 
 
@@ -237,7 +246,18 @@ def process_pyproject_config(args: Namespace) -> Namespace:
         set_current_test_framework(pyproject_config["test_framework"])
 
     if args.tests_root is None:
-        if is_js_ts_project:
+        if is_java_project:
+            # Try standard Maven/Gradle test directories
+            for test_dir in ["src/test/java", "test", "tests"]:
+                test_path = Path(args.module_root).parent / test_dir if "/" in test_dir else Path(test_dir)
+                if not test_path.is_absolute():
+                    test_path = Path.cwd() / test_path
+                if test_path.is_dir():
+                    args.tests_root = str(test_path)
+                    break
+            if args.tests_root is None:
+                args.tests_root = str(Path.cwd() / "src" / "test" / "java")
+        elif is_js_ts_project:
             # Try common JS test directories at project root first
             for test_dir in ["test", "tests", "__tests__"]:
                 if Path(test_dir).is_dir():
@@ -256,17 +276,6 @@ def process_pyproject_config(args: Namespace) -> Namespace:
             # In such cases, the user should explicitly configure testsRoot in package.json
             if args.tests_root is None:
                 args.tests_root = args.module_root
-        elif is_java_project:
-            # Try standard Maven/Gradle test directories
-            for test_dir in ["src/test/java", "test", "tests"]:
-                test_path = Path(args.module_root).parent / test_dir if "/" in test_dir else Path(test_dir)
-                if not test_path.is_absolute():
-                    test_path = Path.cwd() / test_path
-                if test_path.is_dir():
-                    args.tests_root = str(test_path)
-                    break
-            if args.tests_root is None:
-                args.tests_root = str(Path.cwd() / "src" / "test" / "java")
         else:
             raise AssertionError("--tests-root must be specified")
     assert Path(args.tests_root).is_dir(), f"--tests-root {args.tests_root} must be a valid directory"
@@ -327,7 +336,6 @@ def project_root_from_module_root(module_root: Path, pyproject_file_path: Path)
             return current.resolve()
         if (current / "build.gradle").exists() or (current / "build.gradle.kts").exists():
             return current.resolve()
-        # Check for config file (pyproject.toml for Python, codeflash.toml for other languages)
         if (current / "codeflash.toml").exists():
             return current.resolve()
         current = current.parent
@@ -378,32 +386,52 @@ def _handle_show_config() -> None:
     from codeflash.setup.detector import detect_project, has_existing_config
 
     project_root = Path.cwd()
-    detected = detect_project(project_root)
+    config_exists, _ = has_existing_config(project_root)
 
-    # Check if config exists or is auto-detected
-    config_exists, config_file = has_existing_config(project_root)
-    status = "Saved config" if config_exists else "Auto-detected (not saved)"
+    if config_exists:
+        from codeflash.code_utils.config_parser import parse_config_file
 
-    console.print()
-    console.print(f"[bold]Codeflash Configuration[/bold] ({status})")
-    if config_exists and config_file:
-        console.print(f"[dim]Config file: {project_root / config_file}[/dim]")
-    console.print()
+        config, config_file_path = parse_config_file()
+        status = "Saved config"
 
-    table = Table(show_header=True, header_style="bold cyan")
-    table.add_column("Setting", style="dim")
-    table.add_column("Value")
+        console.print()
+        console.print(f"[bold]Codeflash Configuration[/bold] ({status})")
+        console.print(f"[dim]Config file: {config_file_path}[/dim]")
+        console.print()
 
-    table.add_row("Language", detected.language)
-    table.add_row("Project root", str(detected.project_root))
-    table.add_row("Module root", str(detected.module_root))
-    table.add_row("Tests root", str(detected.tests_root) if detected.tests_root else "(not detected)")
-    table.add_row("Test runner", detected.test_runner or "(not detected)")
-    table.add_row("Formatter", ", ".join(detected.formatter_cmds) if detected.formatter_cmds else "(not detected)")
-    table.add_row(
-        "Ignore paths", ", ".join(str(p) for p in detected.ignore_paths) if detected.ignore_paths else "(none)"
-    )
-    table.add_row("Confidence", f"{detected.confidence:.0%}")
+        table = Table(show_header=True, header_style="bold cyan")
+        table.add_column("Setting", style="dim")
+        table.add_column("Value")
+
+        table.add_row("Project root", str(project_root))
+        table.add_row("Module root", config.get("module_root", "(not set)"))
+        table.add_row("Tests root", config.get("tests_root", "(not set)"))
+        table.add_row("Test runner", config.get("test_framework", config.get("pytest_cmd", "(not set)")))
+        table.add_row("Formatter", ", ".join(config["formatter_cmds"]) if config.get("formatter_cmds") else "(not set)")
+        ignore_paths = config.get("ignore_paths", [])
+        table.add_row("Ignore paths", ", ".join(str(p) for p in ignore_paths) if ignore_paths else "(none)")
+    else:
+        detected = detect_project(project_root)
+        status = "Auto-detected (not saved)"
+
+        console.print()
+        console.print(f"[bold]Codeflash Configuration[/bold] ({status})")
+        console.print()
+
+        table = Table(show_header=True, header_style="bold cyan")
+        table.add_column("Setting", style="dim")
+        table.add_column("Value")
+
+        table.add_row("Language", detected.language)
+        table.add_row("Project root", str(detected.project_root))
+        table.add_row("Module root", str(detected.module_root))
+        table.add_row("Tests root", str(detected.tests_root) if detected.tests_root else "(not detected)")
+        table.add_row("Test runner", detected.test_runner or "(not detected)")
+        table.add_row("Formatter", ", ".join(detected.formatter_cmds) if detected.formatter_cmds else "(not detected)")
+        table.add_row(
+            "Ignore paths", ", ".join(str(p) for p in detected.ignore_paths) if detected.ignore_paths else "(none)"
+        )
+        table.add_row("Confidence", f"{detected.confidence:.0%}")
 
     console.print(table)
     console.print()
@@ -436,7 +464,7 @@ def _handle_reset_config(confirm: bool = True) -> None:
         console.print("[bold]This will remove Codeflash configuration from your project.[/bold]")
         console.print()
 
-        config_file = {"python": "pyproject.toml", "java": "codeflash.toml"}.get(detected.language, "package.json")
+        config_file = "pyproject.toml" if detected.language == "python" else "package.json"
         console.print(f"  Config file: {project_root / config_file}")
         console.print()
 

codeflash/cli_cmds/console.py

@@ -22,7 +22,7 @@ from rich.progress import (
 
 from codeflash.cli_cmds.console_constants import SPINNER_TYPES
 from codeflash.cli_cmds.logging_config import BARE_LOGGING_FORMAT
-from codeflash.lsp.helpers import is_LSP_enabled
+from codeflash.lsp.helpers import is_LSP_enabled, is_subagent_mode
 from codeflash.lsp.lsp_logger import enhanced_log
 from codeflash.lsp.lsp_message import LspCodeMessage, LspTextMessage
 
@@ -35,42 +35,69 @@ if TYPE_CHECKING:
     from codeflash.discovery.functions_to_optimize import FunctionToOptimize
     from codeflash.languages.base import DependencyResolver, IndexResult
     from codeflash.lsp.lsp_message import LspMessage
+    from codeflash.models.models import TestResults
 
 DEBUG_MODE = logging.getLogger().getEffectiveLevel() == logging.DEBUG
 
 console = Console(highlighter=NullHighlighter())
 
-if is_LSP_enabled():
+if is_LSP_enabled() or is_subagent_mode():
     console.quiet = True
 
-logging.basicConfig(
-    level=logging.INFO,
-    handlers=[
-        RichHandler(
-            rich_tracebacks=True,
-            markup=False,
-            highlighter=NullHighlighter(),
-            console=console,
-            show_path=False,
-            show_time=False,
-        )
-    ],
-    format=BARE_LOGGING_FORMAT,
-)
+if is_subagent_mode():
+    import re
+    import sys
+
+    _lsp_prefix_re = re.compile(r"^(?:!?lsp,?|h[2-4]|loading)\|")
+    _subagent_drop_patterns = (
+        "Test log -",
+        "Test failed to load",
+        "Examining file ",
+        "Generated ",
+        "Add custom marker",
+        "Disabling all autouse",
+        "Reverting code and helpers",
+    )
+
+    class _AgentLogFilter(logging.Filter):
+        def filter(self, record: logging.LogRecord) -> bool:
+            record.msg = _lsp_prefix_re.sub("", str(record.msg))
+            msg = record.getMessage()
+            return not any(msg.startswith(p) for p in _subagent_drop_patterns)
+
+    _agent_handler = logging.StreamHandler(sys.stderr)
+    _agent_handler.addFilter(_AgentLogFilter())
+    logging.basicConfig(level=logging.INFO, handlers=[_agent_handler], format="%(levelname)s: %(message)s")
+else:
+    logging.basicConfig(
+        level=logging.INFO,
+        handlers=[
+            RichHandler(
+                rich_tracebacks=True,
+                markup=False,
+                highlighter=NullHighlighter(),
+                console=console,
+                show_path=False,
+                show_time=False,
+            )
+        ],
+        format=BARE_LOGGING_FORMAT,
+    )
 
 logger = logging.getLogger("rich")
 logging.getLogger("parso").setLevel(logging.WARNING)
 
 # override the logger to reformat the messages for the lsp
-for level in ("info", "debug", "warning", "error"):
-    real_fn = getattr(logger, level)
-    setattr(
-        logger,
-        level,
-        lambda msg, *args, _real_fn=real_fn, _level=level, **kwargs: enhanced_log(
-            msg, _real_fn, _level, *args, **kwargs
-        ),
-    )
+if not is_subagent_mode():
+    for level in ("info", "debug", "warning", "error"):
+        real_fn = getattr(logger, level)
+        setattr(
+            logger,
+            level,
+            lambda msg, *args, _real_fn=real_fn, _level=level, **kwargs: enhanced_log(
+                msg, _real_fn, _level, *args, **kwargs
+            ),
+        )
 
 
 class DummyTask:
@@ -97,6 +124,8 @@ def paneled_text(
     text: str, panel_args: dict[str, str | bool] | None = None, text_args: dict[str, str] | None = None
 ) -> None:
     """Print text in a panel."""
+    if is_subagent_mode():
+        return
     from rich.panel import Panel
     from rich.text import Text
 
@@ -125,6 +154,8 @@ def code_print(
         language: Programming language for syntax highlighting ('python', 'javascript', 'typescript')
 
     """
+    if is_subagent_mode():
+        return
     if is_LSP_enabled():
         lsp_log(
             LspCodeMessage(code=code_str, file_name=file_name, function_name=function_name, message_id=lsp_message_id)
@@ -162,6 +193,10 @@ def progress_bar(
     """
     global _progress_bar_active
 
+    if is_subagent_mode():
+        yield DummyTask().id
+        return
+
     if is_LSP_enabled():
         lsp_log(LspTextMessage(text=message, takes_time=True))
         yield
@@ -193,6 +228,10 @@ def progress_bar(
 @contextmanager
 def test_files_progress_bar(total: int, description: str) -> Generator[tuple[Progress, TaskID], None, None]:
     """Progress bar for test files."""
+    if is_subagent_mode():
+        yield DummyProgress(), DummyTask().id
+        return
+
     if is_LSP_enabled():
         lsp_log(LspTextMessage(text=description, takes_time=True))
         dummy_progress = DummyProgress()
@@ -226,6 +265,10 @@ def call_graph_live_display(
     from rich.text import Text
     from rich.tree import Tree
 
+    if is_subagent_mode():
+        yield lambda _: None
+        return
+
     if is_LSP_enabled():
         lsp_log(LspTextMessage(text="Building call graph", takes_time=True))
         yield lambda _: None
@@ -333,6 +376,9 @@ def call_graph_summary(call_graph: DependencyResolver, file_to_funcs: dict[Path,
     if not total_functions:
         return
 
+    if is_subagent_mode():
+        return
+
     # Build the mapping expected by the dependency resolver
     file_items = file_to_funcs.items()
     mapping = {file_path: {func.qualified_name for func in funcs} for file_path, funcs in file_items}
@@ -359,3 +405,92 @@ def call_graph_summary(call_graph: DependencyResolver, file_to_funcs: dict[Path,
         return
 
     console.print(Panel(summary, title="Call Graph Summary", border_style="cyan"))
+
+
+def subagent_log_optimization_result(
+    function_name: str,
+    file_path: Path,
+    perf_improvement_line: str,
+    original_runtime_ns: int,
+    best_runtime_ns: int,
+    raw_explanation: str,
+    original_code: dict[Path, str],
+    new_code: dict[Path, str],
+    review: str,
+    test_results: TestResults,
+) -> None:
+    import sys
+    from xml.sax.saxutils import escape
+
+    from codeflash.code_utils.code_utils import unified_diff_strings
+    from codeflash.code_utils.time_utils import humanize_runtime
+    from codeflash.models.test_type import TestType
+
+    diff_parts = []
+    for path in original_code:
+        old = original_code.get(path, "")
+        new = new_code.get(path, "")
+        if old != new:
+            diff = unified_diff_strings(old, new, fromfile=str(path), tofile=str(path))
+            if diff:
+                diff_parts.append(diff)
+
+    diff_str = "\n".join(diff_parts)
+
+    original_runtime = humanize_runtime(original_runtime_ns)
+    optimized_runtime = humanize_runtime(best_runtime_ns)
+
+    report = test_results.get_test_pass_fail_report_by_type()
+    verification_rows = []
+    for test_type in TestType:
+        if test_type is TestType.INIT_STATE_TEST:
+            continue
+        name = test_type.to_name()
+        if not name:
+            continue
+        passed = report[test_type]["passed"]
+        failed = report[test_type]["failed"]
+        if passed == 0 and failed == 0:
+            status = "None Found"
+        elif failed > 0:
+            status = f"{failed} Failed, {passed} Passed"
+        else:
+            status = f"{passed} Passed"
+        verification_rows.append(f'    <test type="{escape(name)}" status="{escape(status)}"/>')
+
+    xml = [
+        "<codeflash-optimization>",
+        f"  <function>{escape(function_name)}</function>",
+        f"  <file>{escape(str(file_path))}</file>",
+        f"  <performance>{escape(perf_improvement_line)}</performance>",
+        f"  <original-runtime>{escape(original_runtime)}</original-runtime>",
+        f"  <optimized-runtime>{escape(optimized_runtime)}</optimized-runtime>",
+    ]
+    if review:
+        xml.append(f"  <reviewer-confidence>{escape(review)}</reviewer-confidence>")
+    xml.append(f"  <explanation>{escape(raw_explanation.strip())}</explanation>")
+    xml.append("  <verification>")
+    xml.extend(verification_rows)
+    xml.append("  </verification>")
+    if diff_str:
+        xml.append(f"  <diff>{escape(diff_str)}</diff>")
+    for path in new_code:
+        if new_code[path] != original_code.get(path, ""):
+            xml.append(f'  <optimized-code file="{escape(str(path))}">{escape(new_code[path])}</optimized-code>')
+    xml.append("  <action>")
+    xml.append("    First, present a short summary: function name, performance improvement, and explanation.")
+    xml.append("    If you are running inside an IDE (VS Code, Cursor, Windsurf, etc.):")
+    xml.append("      For each optimized-code element, use the Write tool to write the optimized code to the file.")
+    xml.append("      This will surface the diff in the IDE's native diff view for the user to accept or reject.")
+    xml.append("    If you are running in a terminal without an IDE connection:")
+    xml.append("      Present this optimization to the user using AskUserQuestion.")
+    xml.append("      Show the function name, performance improvement, and explanation as the question text.")
+    xml.append("      Provide two options: 'Apply' (write the optimized code to the file) and 'Reject' (do nothing).")
+    xml.append(
+        "      Put the full diff in the 'Apply' option's markdown preview so the user can review the exact changes."
+    )
+    xml.append("      If the user chooses 'Apply', write the content from optimized-code to the corresponding file.")
+    xml.append("  </action>")
+    xml.append("</codeflash-optimization>")
+
+    sys.stdout.write("\n".join(xml) + "\n")

codeflash/cli_cmds/logging_config.py

@@ -5,8 +5,18 @@ BARE_LOGGING_FORMAT = "%(message)s"
 
 def set_level(level: int, *, echo_setting: bool = True) -> None:
     import logging
+    import sys
     import time
 
+    from codeflash.lsp.helpers import is_subagent_mode
+
+    if is_subagent_mode():
+        logging.basicConfig(
+            level=level, handlers=[logging.StreamHandler(sys.stderr)], format="%(levelname)s: %(message)s", force=True
+        )
+        logging.getLogger().setLevel(level)
+        return
+
     from rich.highlighter import NullHighlighter
     from rich.logging import RichHandler