projects/ui/serena-new/src/serena/cli.py

import glob
import json
import os
import shutil
import subprocess
import sys
from logging import Logger
from pathlib import Path
from typing import Any, Literal

import click
from sensai.util import logging
from sensai.util.logging import FileLoggerContext, datetime_tag
from tqdm import tqdm

from serena.agent import SerenaAgent
from serena.config.context_mode import SerenaAgentContext, SerenaAgentMode
from serena.config.serena_config import ProjectConfig, SerenaConfig, SerenaPaths
from serena.constants import (
    DEFAULT_CONTEXT,
    DEFAULT_MODES,
    PROMPT_TEMPLATES_DIR_IN_USER_HOME,
    PROMPT_TEMPLATES_DIR_INTERNAL,
    SERENA_LOG_FORMAT,
    SERENA_MANAGED_DIR_IN_HOME,
    SERENAS_OWN_CONTEXT_YAMLS_DIR,
    SERENAS_OWN_MODE_YAMLS_DIR,
    USER_CONTEXT_YAMLS_DIR,
    USER_MODE_YAMLS_DIR,
)
from serena.mcp import SerenaMCPFactory, SerenaMCPFactorySingleProcess
from serena.project import Project
from serena.tools import FindReferencingSymbolsTool, FindSymbolTool, GetSymbolsOverviewTool, SearchForPatternTool, ToolRegistry
from serena.util.logging import MemoryLogHandler
from solidlsp.ls_config import Language
from solidlsp.util.subprocess_util import subprocess_kwargs

log = logging.getLogger(__name__)

# --------------------- Utilities -------------------------------------


def _open_in_editor(path: str) -> None:
    """Open the given file in the system's default editor or viewer."""
    editor = os.environ.get("EDITOR")
    run_kwargs = subprocess_kwargs()
    try:
        if editor:
            subprocess.run([editor, path], check=False, **run_kwargs)
        elif sys.platform.startswith("win"):
            try:
                os.startfile(path)
            except OSError:
                subprocess.run(["notepad.exe", path], check=False, **run_kwargs)
        elif sys.platform == "darwin":
            subprocess.run(["open", path], check=False, **run_kwargs)
        else:
            subprocess.run(["xdg-open", path], check=False, **run_kwargs)
    except Exception as e:
        print(f"Failed to open {path}: {e}")


class ProjectType(click.ParamType):
    """ParamType allowing either a project name or a path to a project directory."""

    name = "[PROJECT_NAME|PROJECT_PATH]"

    def convert(self, value: str, param: Any, ctx: Any) -> str:
        path = Path(value).resolve()
        if path.exists() and path.is_dir():
            return str(path)
        return value


PROJECT_TYPE = ProjectType()


class AutoRegisteringGroup(click.Group):
    """
    A click.Group subclass that automatically registers any click.Command
    attributes defined on the class into the group.

    After initialization, it inspects its own class for attributes that are
    instances of click.Command (typically created via @click.command) and
    calls self.add_command(cmd) on each. This lets you define your commands
    as static methods on the subclass for IDE-friendly organization without
    manual registration.
    """

    def __init__(self, name: str, help: str):
        super().__init__(name=name, help=help)
        # Scan class attributes for click.Command instances and register them.
        for attr in dir(self.__class__):
            cmd = getattr(self.__class__, attr)
            if isinstance(cmd, click.Command):
                self.add_command(cmd)


class TopLevelCommands(AutoRegisteringGroup):
    """Root CLI group containing the core Serena commands."""

    def __init__(self) -> None:
        super().__init__(name="serena", help="Serena CLI commands. You can run `<command> --help` for more info on each command.")

    @staticmethod
    @click.command("start-mcp-server", help="Starts the Serena MCP server.")
    @click.option("--project", "project", type=PROJECT_TYPE, default=None, help="Path or name of project to activate at startup.")
    @click.option("--project-file", "project", type=PROJECT_TYPE, default=None, help="[DEPRECATED] Use --project instead.")
    @click.argument("project_file_arg", type=PROJECT_TYPE, required=False, default=None, metavar="")
    @click.option(
        "--context", type=str, default=DEFAULT_CONTEXT, show_default=True, help="Built-in context name or path to custom context YAML."
    )
    @click.option(
        "--mode",
        "modes",
        type=str,
        multiple=True,
        default=DEFAULT_MODES,
        show_default=True,
        help="Built-in mode names or paths to custom mode YAMLs.",
    )
    @click.option("--transport", type=click.Choice(["stdio", "sse"]), default="stdio", show_default=True, help="Transport protocol.")
    @click.option("--host", type=str, default="0.0.0.0", show_default=True)
    @click.option("--port", type=int, default=8000, show_default=True)
    @click.option("--enable-web-dashboard", type=bool, is_flag=False, default=None, help="Override dashboard setting in config.")
    @click.option("--enable-gui-log-window", type=bool, is_flag=False, default=None, help="Override GUI log window setting in config.")
    @click.option(
        "--log-level",
        type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]),
        default=None,
        help="Override log level in config.",
    )
    @click.option("--trace-lsp-communication", type=bool, is_flag=False, default=None, help="Whether to trace LSP communication.")
    @click.option("--tool-timeout", type=float, default=None, help="Override tool execution timeout in config.")
    def start_mcp_server(
        project: str | None,
        project_file_arg: str | None,
        context: str,
        modes: tuple[str, ...],
        transport: Literal["stdio", "sse"],
        host: str,
        port: int,
        enable_web_dashboard: bool | None,
        enable_gui_log_window: bool | None,
        log_level: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] | None,
        trace_lsp_communication: bool | None,
        tool_timeout: float | None,
    ) -> None:
        # initialize logging, using INFO level initially (will later be adjusted by SerenaAgent according to the config)
        #   * memory log handler (for use by GUI/Dashboard)
        #   * stream handler for stderr (for direct console output, which will also be captured by clients like Claude Desktop)
        #   * file handler
        # (Note that stdout must never be used for logging, as it is used by the MCP server to communicate with the client.)
        Logger.root.setLevel(logging.INFO)
        formatter = logging.Formatter(SERENA_LOG_FORMAT)
        memory_log_handler = MemoryLogHandler()
        Logger.root.addHandler(memory_log_handler)
        stderr_handler = logging.StreamHandler(stream=sys.stderr)
        stderr_handler.formatter = formatter
        Logger.root.addHandler(stderr_handler)
        log_path = SerenaPaths().get_next_log_file_path("mcp")
        file_handler = logging.FileHandler(log_path, mode="w")
        file_handler.formatter = formatter
        Logger.root.addHandler(file_handler)

        log.info("Initializing Serena MCP server")
        log.info("Storing logs in %s", log_path)
        project_file = project_file_arg or project
        factory = SerenaMCPFactorySingleProcess(context=context, project=project_file, memory_log_handler=memory_log_handler)
        server = factory.create_mcp_server(
            host=host,
            port=port,
            modes=modes,
            enable_web_dashboard=enable_web_dashboard,
            enable_gui_log_window=enable_gui_log_window,
            log_level=log_level,
            trace_lsp_communication=trace_lsp_communication,
            tool_timeout=tool_timeout,
        )
        if project_file_arg:
            log.warning(
                "Positional project arg is deprecated; use --project instead. Used: %s",
                project_file,
            )
        log.info("Starting MCP server …")
        server.run(transport=transport)

    @staticmethod
    @click.command("print-system-prompt", help="Print the system prompt for a project.")
    @click.argument("project", type=click.Path(exists=True), default=os.getcwd(), required=False)
    @click.option(
        "--log-level",
        type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]),
        default="WARNING",
        help="Log level for prompt generation.",
    )
    @click.option("--only-instructions", is_flag=True, help="Print only the initial instructions, without prefix/postfix.")
    @click.option(
        "--context", type=str, default=DEFAULT_CONTEXT, show_default=True, help="Built-in context name or path to custom context YAML."
    )
    @click.option(
        "--mode",
        "modes",
        type=str,
        multiple=True,
        default=DEFAULT_MODES,
        show_default=True,
        help="Built-in mode names or paths to custom mode YAMLs.",
    )
    def print_system_prompt(project: str, log_level: str, only_instructions: bool, context: str, modes: tuple[str, ...]) -> None:
        prefix = "You will receive access to Serena's symbolic tools. Below are instructions for using them, take them into account."
        postfix = "You begin by acknowledging that you understood the above instructions and are ready to receive tasks."
        from serena.tools.workflow_tools import InitialInstructionsTool

        lvl = logging.getLevelNamesMapping()[log_level.upper()]
        logging.configure(level=lvl)
        context_instance = SerenaAgentContext.load(context)
        mode_instances = [SerenaAgentMode.load(mode) for mode in modes]
        agent = SerenaAgent(
            project=os.path.abspath(project),
            serena_config=SerenaConfig(web_dashboard=False, log_level=lvl),
            context=context_instance,
            modes=mode_instances,
        )
        tool = agent.get_tool(InitialInstructionsTool)
        instr = tool.apply()
        if only_instructions:
            print(instr)
        else:
            print(f"{prefix}\n{instr}\n{postfix}")


class ModeCommands(AutoRegisteringGroup):
    """Group for 'mode' subcommands."""

    def __init__(self) -> None:
        super().__init__(name="mode", help="Manage Serena modes. You can run `mode <command> --help` for more info on each command.")

    @staticmethod
    @click.command("list", help="List available modes.")
    def list() -> None:
        mode_names = SerenaAgentMode.list_registered_mode_names()
        max_len_name = max(len(name) for name in mode_names) if mode_names else 20
        for name in mode_names:
            mode_yml_path = SerenaAgentMode.get_path(name)
            is_internal = Path(mode_yml_path).is_relative_to(SERENAS_OWN_MODE_YAMLS_DIR)
            descriptor = "(internal)" if is_internal else f"(at {mode_yml_path})"
            name_descr_string = f"{name:<{max_len_name + 4}}{descriptor}"
            click.echo(name_descr_string)

    @staticmethod
    @click.command("create", help="Create a new mode or copy an internal one.")
    @click.option(
        "--name",
        "-n",
        type=str,
        default=None,
        help="Name for the new mode. If --from-internal is passed may be left empty to create a mode of the same name, which will then override the internal mode.",
    )
    @click.option("--from-internal", "from_internal", type=str, default=None, help="Copy from an internal mode.")
    def create(name: str, from_internal: str) -> None:
        if not (name or from_internal):
            raise click.UsageError("Provide at least one of --name or --from-internal.")
        mode_name = name or from_internal
        dest = os.path.join(USER_MODE_YAMLS_DIR, f"{mode_name}.yml")
        src = (
            os.path.join(SERENAS_OWN_MODE_YAMLS_DIR, f"{from_internal}.yml")
            if from_internal
            else os.path.join(SERENAS_OWN_MODE_YAMLS_DIR, "mode.template.yml")
        )
        if not os.path.exists(src):
            raise FileNotFoundError(
                f"Internal mode '{from_internal}' not found in {SERENAS_OWN_MODE_YAMLS_DIR}. Available modes: {SerenaAgentMode.list_registered_mode_names()}"
            )
        os.makedirs(os.path.dirname(dest), exist_ok=True)
        shutil.copyfile(src, dest)
        click.echo(f"Created mode '{mode_name}' at {dest}")
        _open_in_editor(dest)

    @staticmethod
    @click.command("edit", help="Edit a custom mode YAML file.")
    @click.argument("mode_name")
    def edit(mode_name: str) -> None:
        path = os.path.join(USER_MODE_YAMLS_DIR, f"{mode_name}.yml")
        if not os.path.exists(path):
            if mode_name in SerenaAgentMode.list_registered_mode_names(include_user_modes=False):
                click.echo(
                    f"Mode '{mode_name}' is an internal mode and cannot be edited directly. "
                    f"Use 'mode create --from-internal {mode_name}' to create a custom mode that overrides it before editing."
                )
            else:
                click.echo(f"Custom mode '{mode_name}' not found. Create it with: mode create --name {mode_name}.")
            return
        _open_in_editor(path)

    @staticmethod
    @click.command("delete", help="Delete a custom mode file.")
    @click.argument("mode_name")
    def delete(mode_name: str) -> None:
        path = os.path.join(USER_MODE_YAMLS_DIR, f"{mode_name}.yml")
        if not os.path.exists(path):
            click.echo(f"Custom mode '{mode_name}' not found.")
            return
        os.remove(path)
        click.echo(f"Deleted custom mode '{mode_name}'.")


class ContextCommands(AutoRegisteringGroup):
    """Group for 'context' subcommands."""

    def __init__(self) -> None:
        super().__init__(
            name="context", help="Manage Serena contexts. You can run `context <command> --help` for more info on each command."
        )

    @staticmethod
    @click.command("list", help="List available contexts.")
    def list() -> None:
        context_names = SerenaAgentContext.list_registered_context_names()
        max_len_name = max(len(name) for name in context_names) if context_names else 20
        for name in context_names:
            context_yml_path = SerenaAgentContext.get_path(name)
            is_internal = Path(context_yml_path).is_relative_to(SERENAS_OWN_CONTEXT_YAMLS_DIR)
            descriptor = "(internal)" if is_internal else f"(at {context_yml_path})"
            name_descr_string = f"{name:<{max_len_name + 4}}{descriptor}"
            click.echo(name_descr_string)

    @staticmethod
    @click.command("create", help="Create a new context or copy an internal one.")
    @click.option(
        "--name",
        "-n",
        type=str,
        default=None,
        help="Name for the new context. If --from-internal is passed may be left empty to create a context of the same name, which will then override the internal context",
    )
    @click.option("--from-internal", "from_internal", type=str, default=None, help="Copy from an internal context.")
    def create(name: str, from_internal: str) -> None:
        if not (name or from_internal):
            raise click.UsageError("Provide at least one of --name or --from-internal.")
        ctx_name = name or from_internal
        dest = os.path.join(USER_CONTEXT_YAMLS_DIR, f"{ctx_name}.yml")
        src = (
            os.path.join(SERENAS_OWN_CONTEXT_YAMLS_DIR, f"{from_internal}.yml")
            if from_internal
            else os.path.join(SERENAS_OWN_CONTEXT_YAMLS_DIR, "context.template.yml")
        )
        if not os.path.exists(src):
            raise FileNotFoundError(
                f"Internal context '{from_internal}' not found in {SERENAS_OWN_CONTEXT_YAMLS_DIR}. Available contexts: {SerenaAgentContext.list_registered_context_names()}"
            )
        os.makedirs(os.path.dirname(dest), exist_ok=True)
        shutil.copyfile(src, dest)
        click.echo(f"Created context '{ctx_name}' at {dest}")
        _open_in_editor(dest)

    @staticmethod
    @click.command("edit", help="Edit a custom context YAML file.")
    @click.argument("context_name")
    def edit(context_name: str) -> None:
        path = os.path.join(USER_CONTEXT_YAMLS_DIR, f"{context_name}.yml")
        if not os.path.exists(path):
            if context_name in SerenaAgentContext.list_registered_context_names(include_user_contexts=False):
                click.echo(
                    f"Context '{context_name}' is an internal context and cannot be edited directly. "
                    f"Use 'context create --from-internal {context_name}' to create a custom context that overrides it before editing."
                )
            else:
                click.echo(f"Custom context '{context_name}' not found. Create it with: context create --name {context_name}.")
            return
        _open_in_editor(path)

    @staticmethod
    @click.command("delete", help="Delete a custom context file.")
    @click.argument("context_name")
    def delete(context_name: str) -> None:
        path = os.path.join(USER_CONTEXT_YAMLS_DIR, f"{context_name}.yml")
        if not os.path.exists(path):
            click.echo(f"Custom context '{context_name}' not found.")
            return
        os.remove(path)
        click.echo(f"Deleted custom context '{context_name}'.")


class SerenaConfigCommands(AutoRegisteringGroup):
    """Group for 'config' subcommands."""

    def __init__(self) -> None:
        super().__init__(name="config", help="Manage Serena configuration.")

    @staticmethod
    @click.command(
        "edit", help="Edit serena_config.yml in your default editor. Will create a config file from the template if no config is found."
    )
    def edit() -> None:
        config_path = os.path.join(SERENA_MANAGED_DIR_IN_HOME, "serena_config.yml")
        if not os.path.exists(config_path):
            SerenaConfig.generate_config_file(config_path)
        _open_in_editor(config_path)


class ProjectCommands(AutoRegisteringGroup):
    """Group for 'project' subcommands."""

    def __init__(self) -> None:
        super().__init__(
            name="project", help="Manage Serena projects. You can run `project <command> --help` for more info on each command."
        )

    @staticmethod
    @click.command("generate-yml", help="Generate a project.yml file.")
    @click.argument("project_path", type=click.Path(exists=True, file_okay=False), default=os.getcwd())
    @click.option("--language", type=str, default=None, help="Programming language; inferred if not specified.")
    def generate_yml(project_path: str, language: str | None = None) -> None:
        yml_path = os.path.join(project_path, ProjectConfig.rel_path_to_project_yml())
        if os.path.exists(yml_path):
            raise FileExistsError(f"Project file {yml_path} already exists.")
        lang_inst = None
        if language:
            try:
                lang_inst = Language[language.upper()]
            except KeyError:
                all_langs = [l.name.lower() for l in Language.iter_all(include_experimental=True)]
                raise ValueError(f"Unknown language '{language}'. Supported: {all_langs}")
        generated_conf = ProjectConfig.autogenerate(project_root=project_path, project_language=lang_inst)
        print(f"Generated project.yml with language {generated_conf.language.value} at {yml_path}.")

    @staticmethod
    @click.command("index", help="Index a project by saving symbols to the LSP cache.")
    @click.argument("project", type=click.Path(exists=True), default=os.getcwd(), required=False)
    @click.option(
        "--log-level",
        type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]),
        default="WARNING",
        help="Log level for indexing.",
    )
    @click.option("--timeout", type=float, default=10, help="Timeout for indexing a single file.")
    def index(project: str, log_level: str, timeout: float) -> None:
        ProjectCommands._index_project(project, log_level, timeout=timeout)

    @staticmethod
    @click.command("index-deprecated", help="Deprecated alias for 'serena project index'.")
    @click.argument("project", type=click.Path(exists=True), default=os.getcwd(), required=False)
    @click.option("--log-level", type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]), default="WARNING")
    @click.option("--timeout", type=float, default=10, help="Timeout for indexing a single file.")
    def index_deprecated(project: str, log_level: str, timeout: float) -> None:
        click.echo("Deprecated! Use `serena project index` instead.")
        ProjectCommands._index_project(project, log_level, timeout=timeout)

    @staticmethod
    def _index_project(project: str, log_level: str, timeout: float) -> None:
        lvl = logging.getLevelNamesMapping()[log_level.upper()]
        logging.configure(level=lvl)
        proj = Project.load(os.path.abspath(project))
        click.echo(f"Indexing symbols in project {project}…")
        ls = proj.create_language_server(log_level=lvl, ls_timeout=timeout)
        log_file = os.path.join(project, ".serena", "logs", "indexing.txt")

        collected_exceptions: list[Exception] = []
        files_failed = []
        with ls.start_server():
            files = proj.gather_source_files()
            for i, f in enumerate(tqdm(files, desc="Indexing")):
                try:
                    ls.request_document_symbols(f, include_body=False)
                    ls.request_document_symbols(f, include_body=True)
                except Exception as e:
                    log.error(f"Failed to index {f}, continuing.")
                    collected_exceptions.append(e)
                    files_failed.append(f)
                if (i + 1) % 10 == 0:
                    ls.save_cache()
            ls.save_cache()
        click.echo(f"Symbols saved to {ls.cache_path}")
        if len(files_failed) > 0:
            os.makedirs(os.path.dirname(log_file), exist_ok=True)
            with open(log_file, "w") as f:
                for file, exception in zip(files_failed, collected_exceptions, strict=True):
                    f.write(f"{file}\n")
                    f.write(f"{exception}\n")
            click.echo(f"Failed to index {len(files_failed)} files, see:\n{log_file}")

    @staticmethod
    @click.command("is_ignored_path", help="Check if a path is ignored by the project configuration.")
    @click.argument("path", type=click.Path(exists=False, file_okay=True, dir_okay=True))
    @click.argument("project", type=click.Path(exists=True, file_okay=False, dir_okay=True), default=os.getcwd())
    def is_ignored_path(path: str, project: str) -> None:
        """
        Check if a given path is ignored by the project configuration.

        :param path: The path to check.
        :param project: The path to the project directory, defaults to the current working directory.
        """
        proj = Project.load(os.path.abspath(project))
        if os.path.isabs(path):
            path = os.path.relpath(path, start=proj.project_root)
        is_ignored = proj.is_ignored_path(path)
        click.echo(f"Path '{path}' IS {'ignored' if is_ignored else 'IS NOT ignored'} by the project configuration.")

    @staticmethod
    @click.command("index-file", help="Index a single file by saving its symbols to the LSP cache.")
    @click.argument("file", type=click.Path(exists=True, file_okay=True, dir_okay=False))
    @click.argument("project", type=click.Path(exists=True, file_okay=False, dir_okay=True), default=os.getcwd())
    @click.option("--verbose", "-v", is_flag=True, help="Print detailed information about the indexed symbols.")
    def index_file(file: str, project: str, verbose: bool) -> None:
        """
        Index a single file by saving its symbols to the LSP cache, useful for debugging.
        :param file: path to the file to index, must be inside the project directory.
        :param project: path to the project directory, defaults to the current working directory.
        :param verbose: if set, prints detailed information about the indexed symbols.
        """
        proj = Project.load(os.path.abspath(project))
        if os.path.isabs(file):
            file = os.path.relpath(file, start=proj.project_root)
        if proj.is_ignored_path(file, ignore_non_source_files=True):
            click.echo(f"'{file}' is ignored or declared as non-code file by the project configuration, won't index.")
            exit(1)
        ls = proj.create_language_server()
        with ls.start_server():
            symbols, _ = ls.request_document_symbols(file, include_body=False)
            ls.request_document_symbols(file, include_body=True)
            if verbose:
                click.echo(f"Symbols in file '{file}':")
                for symbol in symbols:
                    click.echo(f"  - {symbol['name']} at line {symbol['selectionRange']['start']['line']} of kind {symbol['kind']}")
            ls.save_cache()
            click.echo(f"Successfully indexed file '{file}', {len(symbols)} symbols saved to {ls.cache_path}.")

    @staticmethod
    @click.command("health-check", help="Perform a comprehensive health check of the project's tools and language server.")
    @click.argument("project", type=click.Path(exists=True, file_okay=False, dir_okay=True), default=os.getcwd())
    def health_check(project: str) -> None:
        """
        Perform a comprehensive health check of the project's tools and language server.

        :param project: path to the project directory, defaults to the current working directory.
        """
        # NOTE: completely written by Claude Code, only functionality was reviewed, not implementation
        logging.configure(level=logging.INFO)
        project_path = os.path.abspath(project)
        proj = Project.load(project_path)

        # Create log file with timestamp
        timestamp = datetime_tag()
        log_dir = os.path.join(project_path, ".serena", "logs", "health-checks")
        os.makedirs(log_dir, exist_ok=True)
        log_file = os.path.join(log_dir, f"health_check_{timestamp}.log")

        with FileLoggerContext(log_file, append=False, enabled=True):
            log.info("Starting health check for project: %s", project_path)

            try:
                # Create SerenaAgent with dashboard disabled
                log.info("Creating SerenaAgent with disabled dashboard...")
                config = SerenaConfig(gui_log_window_enabled=False, web_dashboard=False)
                agent = SerenaAgent(project=project_path, serena_config=config)
                log.info("SerenaAgent created successfully")

                # Find first non-empty file that can be analyzed
                log.info("Searching for analyzable files...")
                files = proj.gather_source_files()
                target_file = None

                for file_path in files:
                    try:
                        full_path = os.path.join(project_path, file_path)
                        if os.path.getsize(full_path) > 0:
                            target_file = file_path
                            log.info("Found analyzable file: %s", target_file)
                            break
                    except (OSError, FileNotFoundError):
                        continue

                if not target_file:
                    log.error("No analyzable files found in project")
                    click.echo("❌ Health check failed: No analyzable files found")
                    click.echo(f"Log saved to: {log_file}")
                    return

                # Get tools from agent
                overview_tool = agent.get_tool(GetSymbolsOverviewTool)
                find_symbol_tool = agent.get_tool(FindSymbolTool)
                find_refs_tool = agent.get_tool(FindReferencingSymbolsTool)
                search_pattern_tool = agent.get_tool(SearchForPatternTool)

                # Test 1: Get symbols overview
                log.info("Testing GetSymbolsOverviewTool on file: %s", target_file)
                overview_result = agent.execute_task(lambda: overview_tool.apply(target_file))
                overview_data = json.loads(overview_result)
                log.info("GetSymbolsOverviewTool returned %d symbols", len(overview_data))

                if not overview_data:
                    log.error("No symbols found in file %s", target_file)
                    click.echo("❌ Health check failed: No symbols found in target file")
                    click.echo(f"Log saved to: {log_file}")
                    return

                # Extract suitable symbol (prefer class or function over variables)
                # LSP symbol kinds: 5=class, 12=function, 6=method, 9=constructor
                preferred_kinds = [5, 12, 6, 9]  # class, function, method, constructor

                selected_symbol = None
                for symbol in overview_data:
                    if symbol.get("kind") in preferred_kinds:
                        selected_symbol = symbol
                        break

                # If no preferred symbol found, use first available
                if not selected_symbol:
                    selected_symbol = overview_data[0]
                    log.info("No class or function found, using first available symbol")

                symbol_name = selected_symbol.get("name_path", "unknown")
                symbol_kind = selected_symbol.get("kind", "unknown")
                log.info("Using symbol for testing: %s (kind: %d)", symbol_name, symbol_kind)

                # Test 2: FindSymbolTool
                log.info("Testing FindSymbolTool for symbol: %s", symbol_name)
                find_symbol_result = agent.execute_task(
                    lambda: find_symbol_tool.apply(symbol_name, relative_path=target_file, include_body=True)
                )
                find_symbol_data = json.loads(find_symbol_result)
                log.info("FindSymbolTool found %d matches for symbol %s", len(find_symbol_data), symbol_name)

                # Test 3: FindReferencingSymbolsTool
                log.info("Testing FindReferencingSymbolsTool for symbol: %s", symbol_name)
                try:
                    find_refs_result = agent.execute_task(lambda: find_refs_tool.apply(symbol_name, relative_path=target_file))
                    find_refs_data = json.loads(find_refs_result)
                    log.info("FindReferencingSymbolsTool found %d references for symbol %s", len(find_refs_data), symbol_name)
                except Exception as e:
                    log.warning("FindReferencingSymbolsTool failed for symbol %s: %s", symbol_name, str(e))
                    find_refs_data = []

                # Test 4: SearchForPatternTool to verify references
                log.info("Testing SearchForPatternTool for pattern: %s", symbol_name)
                try:
                    search_result = agent.execute_task(
                        lambda: search_pattern_tool.apply(substring_pattern=symbol_name, restrict_search_to_code_files=True)
                    )
                    search_data = json.loads(search_result)
                    pattern_matches = sum(len(matches) for matches in search_data.values())
                    log.info("SearchForPatternTool found %d pattern matches for %s", pattern_matches, symbol_name)
                except Exception as e:
                    log.warning("SearchForPatternTool failed for pattern %s: %s", symbol_name, str(e))
                    pattern_matches = 0

                # Verify tools worked as expected
                tools_working = True
                if not find_symbol_data:
                    log.error("FindSymbolTool returned no results")
                    tools_working = False

                if len(find_refs_data) == 0 and pattern_matches == 0:
                    log.warning("Both FindReferencingSymbolsTool and SearchForPatternTool found no matches - this might indicate an issue")

                log.info("Health check completed successfully")

                if tools_working:
                    click.echo("✅ Health check passed - All tools working correctly")
                else:
                    click.echo("⚠️  Health check completed with warnings - Check log for details")

            except Exception as e:
                log.exception("Health check failed with exception: %s", str(e))
                click.echo(f"❌ Health check failed: {e!s}")

            finally:
                click.echo(f"Log saved to: {log_file}")


class ToolCommands(AutoRegisteringGroup):
    """Group for 'tool' subcommands."""

    def __init__(self) -> None:
        super().__init__(
            name="tools",
            help="Commands related to Serena's tools. You can run `serena tools <command> --help` for more info on each command.",
        )

    @staticmethod
    @click.command(
        "list",
        help="Prints an overview of the tools that are active by default (not just the active ones for your project). For viewing all tools, pass `--all / -a`",
    )
    @click.option("--quiet", "-q", is_flag=True)
    @click.option("--all", "-a", "include_optional", is_flag=True, help="List all tools, including those not enabled by default.")
    @click.option("--only-optional", is_flag=True, help="List only optional tools (those not enabled by default).")
    def list(quiet: bool = False, include_optional: bool = False, only_optional: bool = False) -> None:
        tool_registry = ToolRegistry()
        if quiet:
            if only_optional:
                tool_names = tool_registry.get_tool_names_optional()
            elif include_optional:
                tool_names = tool_registry.get_tool_names()
            else:
                tool_names = tool_registry.get_tool_names_default_enabled()
            for tool_name in tool_names:
                click.echo(tool_name)
        else:
            ToolRegistry().print_tool_overview(include_optional=include_optional, only_optional=only_optional)

    @staticmethod
    @click.command(
        "description",
        help="Print the description of a tool, optionally with a specific context (the latter may modify the default description).",
    )
    @click.argument("tool_name", type=str)
    @click.option("--context", type=str, default=None, help="Context name or path to context file.")
    def description(tool_name: str, context: str | None = None) -> None:
        # Load the context
        serena_context = None
        if context:
            serena_context = SerenaAgentContext.load(context)

        agent = SerenaAgent(
            project=None,
            serena_config=SerenaConfig(web_dashboard=False, log_level=logging.INFO),
            context=serena_context,
        )
        tool = agent.get_tool_by_name(tool_name)
        mcp_tool = SerenaMCPFactory.make_mcp_tool(tool)
        click.echo(mcp_tool.description)


class PromptCommands(AutoRegisteringGroup):
    def __init__(self) -> None:
        super().__init__(name="prompts", help="Commands related to Serena's prompts that are outside of contexts and modes.")

    @staticmethod
    def _get_user_prompt_yaml_path(prompt_yaml_name: str) -> str:
        os.makedirs(PROMPT_TEMPLATES_DIR_IN_USER_HOME, exist_ok=True)
        return os.path.join(PROMPT_TEMPLATES_DIR_IN_USER_HOME, prompt_yaml_name)

    @staticmethod
    @click.command("list", help="Lists yamls that are used for defining prompts.")
    def list() -> None:
        serena_prompt_yaml_names = [os.path.basename(f) for f in glob.glob(PROMPT_TEMPLATES_DIR_INTERNAL + "/*.yml")]
        for prompt_yaml_name in serena_prompt_yaml_names:
            user_prompt_yaml_path = PromptCommands._get_user_prompt_yaml_path(prompt_yaml_name)
            if os.path.exists(user_prompt_yaml_path):
                click.echo(f"{user_prompt_yaml_path} merged with default prompts in {prompt_yaml_name}")
            else:
                click.echo(prompt_yaml_name)

    @staticmethod
    @click.command("create-override", help="Create an override of an internal prompts yaml for customizing Serena's prompts")
    @click.argument("prompt_yaml_name")
    def create_override(prompt_yaml_name: str) -> None:
        """
        :param prompt_yaml_name: The yaml name of the prompt you want to override. Call the `list` command for discovering valid prompt yaml names.
        :return:
        """
        # for convenience, we can pass names without .yml
        if not prompt_yaml_name.endswith(".yml"):
            prompt_yaml_name = prompt_yaml_name + ".yml"
        user_prompt_yaml_path = PromptCommands._get_user_prompt_yaml_path(prompt_yaml_name)
        if os.path.exists(user_prompt_yaml_path):
            raise FileExistsError(f"{user_prompt_yaml_path} already exists.")
        serena_prompt_yaml_path = os.path.join(PROMPT_TEMPLATES_DIR_INTERNAL, prompt_yaml_name)
        shutil.copyfile(serena_prompt_yaml_path, user_prompt_yaml_path)
        _open_in_editor(user_prompt_yaml_path)

    @staticmethod
    @click.command("edit-override", help="Edit an existing prompt override file")
    @click.argument("prompt_yaml_name")
    def edit_override(prompt_yaml_name: str) -> None:
        """
        :param prompt_yaml_name: The yaml name of the prompt override to edit.
        :return:
        """
        # for convenience, we can pass names without .yml
        if not prompt_yaml_name.endswith(".yml"):
            prompt_yaml_name = prompt_yaml_name + ".yml"
        user_prompt_yaml_path = PromptCommands._get_user_prompt_yaml_path(prompt_yaml_name)
        if not os.path.exists(user_prompt_yaml_path):
            click.echo(f"Override file '{prompt_yaml_name}' not found. Create it with: prompts create-override {prompt_yaml_name}")
            return
        _open_in_editor(user_prompt_yaml_path)

    @staticmethod
    @click.command("list-overrides", help="List existing prompt override files")
    def list_overrides() -> None:
        os.makedirs(PROMPT_TEMPLATES_DIR_IN_USER_HOME, exist_ok=True)
        serena_prompt_yaml_names = [os.path.basename(f) for f in glob.glob(PROMPT_TEMPLATES_DIR_INTERNAL + "/*.yml")]
        override_files = glob.glob(os.path.join(PROMPT_TEMPLATES_DIR_IN_USER_HOME, "*.yml"))
        for file_path in override_files:
            if os.path.basename(file_path) in serena_prompt_yaml_names:
                click.echo(file_path)

    @staticmethod
    @click.command("delete-override", help="Delete a prompt override file")
    @click.argument("prompt_yaml_name")
    def delete_override(prompt_yaml_name: str) -> None:
        """

        :param prompt_yaml_name:  The yaml name of the prompt override to delete."
        :return:
        """
        # for convenience, we can pass names without .yml
        if not prompt_yaml_name.endswith(".yml"):
            prompt_yaml_name = prompt_yaml_name + ".yml"
        user_prompt_yaml_path = PromptCommands._get_user_prompt_yaml_path(prompt_yaml_name)
        if not os.path.exists(user_prompt_yaml_path):
            click.echo(f"Override file '{prompt_yaml_name}' not found.")
            return
        os.remove(user_prompt_yaml_path)
        click.echo(f"Deleted override file '{prompt_yaml_name}'.")


# Expose groups so we can reference them in pyproject.toml
mode = ModeCommands()
context = ContextCommands()
project = ProjectCommands()
config = SerenaConfigCommands()
tools = ToolCommands()
prompts = PromptCommands()

# Expose toplevel commands for the same reason
top_level = TopLevelCommands()
start_mcp_server = top_level.start_mcp_server
index_project = project.index_deprecated

# needed for the help script to work - register all subcommands to the top-level group
for subgroup in (mode, context, project, config, tools, prompts):
    top_level.add_command(subgroup)


def get_help() -> str:
    """Retrieve the help text for the top-level Serena CLI."""
    return top_level.get_help(click.Context(top_level, info_name="serena"))