feat: assorted improvements for CLI/daemon to be resilient and ergonomic

src/cocoindex_code/cli.py

@@ -32,7 +32,7 @@
 
 
 # ---------------------------------------------------------------------------
-# Shared CLI helpers (G1)
+# Shared CLI helpers
 # ---------------------------------------------------------------------------
 
 
@@ -70,7 +70,7 @@ def require_daemon_for_project() -> tuple[DaemonClient, str]:
 
 def resolve_default_path(project_root: Path) -> str | None:
     """Compute default ``--path`` filter from CWD relative to project root."""
-    cwd = Path.cwd()
+    cwd = Path.cwd().resolve()
     try:
         rel = cwd.relative_to(project_root)
     except ValueError:
@@ -120,8 +120,126 @@ def print_search_results(response: SearchResponse) -> None:
         _typer.echo(r.content)
 
 
+def _run_index_with_progress(client: DaemonClient, project_root: str) -> None:
+    """Run indexing with streaming progress display. Exits on failure."""
+    from rich.console import Console as _Console
+    from rich.live import Live as _Live
+    from rich.spinner import Spinner as _Spinner
+
+    err_console = _Console(stderr=True)
+    last_progress_line: str | None = None
+
+    with _Live(_Spinner("dots", "Indexing..."), console=err_console, transient=True) as live:
+
+        def _on_waiting() -> None:
+            live.update(
+                _Spinner(
+                    "dots",
+                    "Another indexing is ongoing, waiting for it to finish...",
+                )
+            )
+
+        def _on_progress(progress: IndexingProgress) -> None:
+            nonlocal last_progress_line
+            last_progress_line = f"Indexing: {_format_progress(progress)}"
+            live.update(_Spinner("dots", last_progress_line))
+
+        try:
+            resp = client.index(project_root, on_progress=_on_progress, on_waiting=_on_waiting)
+        except RuntimeError as e:
+            live.stop()
+            _typer.echo(f"Indexing failed: {e}", err=True)
+            raise _typer.Exit(code=1)
+
+    # Print the final progress line so it remains visible after the spinner clears
+    if last_progress_line is not None:
+        _typer.echo(last_progress_line, err=True)
+
+    if not resp.success:
+        _typer.echo(f"Indexing failed: {resp.message}", err=True)
+        raise _typer.Exit(code=1)
+
+
+_GITIGNORE_COMMENT = "# cocoindex-code"
+_GITIGNORE_ENTRY = "/.cocoindex_code/"
+
+
+def add_to_gitignore(project_root: Path) -> None:
+    """Add ``/.cocoindex_code/`` to ``.gitignore`` if ``.git`` exists.
+
+    Creates ``.gitignore`` if it doesn't exist.  Skips if the entry is already
+    present.
+    """
+    if not (project_root / ".git").is_dir():
+        return
+
+    gitignore = project_root / ".gitignore"
+    if gitignore.is_file():
+        content = gitignore.read_text()
+        if _GITIGNORE_ENTRY in content.splitlines():
+            return  # already present
+        # Ensure a trailing newline before appending
+        if content and not content.endswith("\n"):
+            content += "\n"
+        content += f"{_GITIGNORE_COMMENT}\n{_GITIGNORE_ENTRY}\n"
+        gitignore.write_text(content)
+    else:
+        gitignore.write_text(f"{_GITIGNORE_COMMENT}\n{_GITIGNORE_ENTRY}\n")
+
+
+def remove_from_gitignore(project_root: Path) -> None:
+    """Remove ``/.cocoindex_code/`` entry and its comment from ``.gitignore``."""
+    gitignore = project_root / ".gitignore"
+    if not gitignore.is_file():
+        return
+
+    lines = gitignore.read_text().splitlines(keepends=True)
+    new_lines: list[str] = []
+    i = 0
+    while i < len(lines):
+        stripped = lines[i].rstrip("\n\r")
+        if stripped == _GITIGNORE_ENTRY:
+            # Skip this line; also remove preceding comment if it matches
+            if new_lines and new_lines[-1].rstrip("\n\r") == _GITIGNORE_COMMENT:
+                new_lines.pop()
+            i += 1
+            continue
+        new_lines.append(lines[i])
+        i += 1
+    gitignore.write_text("".join(new_lines))
+
+
+def auto_init_project() -> Path:
+    """Auto-initialize project from CWD.
+
+    Runs core ``init`` logic without parent-directory confirmation and without
+    the "run ``ccc index``" prompt.  Returns the project root (CWD).
+    """
+    from .settings import project_settings_path
+
+    cwd = Path.cwd().resolve()
+    settings_file = project_settings_path(cwd)
+
+    if not settings_file.is_file():
+        # Create user settings if missing
+        user_path = user_settings_path()
+        if not user_path.is_file():
+            save_user_settings(default_user_settings())
+            _typer.echo(f"Created user settings: {user_path}")
+
+        # Create project settings
+        save_project_settings(cwd, default_project_settings())
+        _typer.echo(f"Created project settings: {settings_file}")
+        _typer.echo("You can edit the settings files to customize indexing behavior.")
+
+        # Update .gitignore
+        add_to_gitignore(cwd)
+
+    return cwd
+
+
 # ---------------------------------------------------------------------------
-# Commands (G2-G5)
+# Commands
 # ---------------------------------------------------------------------------
 
 
@@ -130,10 +248,10 @@ def init(
     force: bool = _typer.Option(False, "-f", "--force", help="Skip parent directory warning"),
 ) -> None:
     """Initialize a project for cocoindex-code."""
-    from .settings import project_settings_path
+    from .settings import project_settings_path as _project_settings_path
 
-    cwd = Path.cwd()
-    settings_file = project_settings_path(cwd)
+    cwd = Path.cwd().resolve()
+    settings_file = _project_settings_path(cwd)
 
     # Check if already initialized
     if settings_file.is_file():
@@ -160,49 +278,32 @@ def init(
     # Create project settings
     save_project_settings(cwd, default_project_settings())
     _typer.echo(f"Created project settings: {settings_file}")
-    _typer.echo("Project initialized. Run `ccc index` to build the index.")
+
+    # Add to .gitignore
+    add_to_gitignore(cwd)
+
+    _typer.echo("You can edit the settings files to customize indexing behavior.")
+    _typer.echo("Run `ccc index` to build the index.")
 
 
 @app.command()
 def index() -> None:
     """Create/update index for the codebase."""
-    from rich.console import Console as _Console
-    from rich.live import Live as _Live
-    from rich.spinner import Spinner as _Spinner
-
-    client, project_root = require_daemon_for_project()
-    err_console = _Console(stderr=True)
-    last_progress_line: str | None = None
-
-    with _Live(_Spinner("dots", "Indexing..."), console=err_console, transient=True) as live:
-
-        def _on_waiting() -> None:
-            live.update(
-                _Spinner(
-                    "dots",
-                    "Another indexing is ongoing, waiting for it to finish...",
-                )
-            )
-
-        def _on_progress(progress: IndexingProgress) -> None:
-            nonlocal last_progress_line
-            last_progress_line = f"Indexing: {_format_progress(progress)}"
-            live.update(_Spinner("dots", last_progress_line))
-
-        try:
-            resp = client.index(project_root, on_progress=_on_progress, on_waiting=_on_waiting)
-        except RuntimeError as e:
-            live.stop()
-            _typer.echo(f"Indexing failed: {e}", err=True)
-            raise _typer.Exit(code=1)
+    from .client import ensure_daemon
 
-    # Print the final progress line so it remains visible after the spinner clears
-    if last_progress_line is not None:
-        _typer.echo(last_progress_line, err=True)
+    # Auto-init if not in an initialized project
+    root = find_project_root(Path.cwd())
+    if root is None:
+        root = auto_init_project()
 
-    if not resp.success:
-        _typer.echo(f"Indexing failed: {resp.message}", err=True)
+    try:
+        client = ensure_daemon()
+    except Exception as e:
+        _typer.echo(f"Error: Failed to connect to daemon: {e}", err=True)
         raise _typer.Exit(code=1)
+    project_root = str(root)
+
+    _run_index_with_progress(client, project_root)
 
     status = client.project_status(project_root)
     print_index_stats(status)
@@ -221,6 +322,10 @@ def search(
     client, project_root = require_daemon_for_project()
     query_str = " ".join(query)
 
+    # Refresh index with progress display before searching
+    if refresh:
+        _run_index_with_progress(client, project_root)
+
     # Default path filter from CWD
     paths: list[str] | None = None
     if path is not None:
@@ -237,7 +342,7 @@ def search(
         paths=paths,
         limit=limit,
         offset=offset,
-        refresh=refresh,
+        refresh=False,
     )
     print_search_results(resp)
 
@@ -250,6 +355,82 @@ def status() -> None:
     print_index_stats(resp)
 
 
+@app.command()
+def reset(
+    all_: bool = _typer.Option(False, "--all", help="Also remove settings and .gitignore entry"),
+    force: bool = _typer.Option(False, "-f", "--force", help="Skip confirmation"),
+) -> None:
+    """Reset project databases and optionally remove settings."""
+    project_root = require_project_root()
+    cocoindex_dir = project_root / ".cocoindex_code"
+
+    db_files = [
+        cocoindex_dir / "cocoindex.db",
+        cocoindex_dir / "target_sqlite.db",
+    ]
+    settings_file = cocoindex_dir / "settings.yml"
+
+    # Determine what will be deleted
+    to_delete = [f for f in db_files if f.exists()]
+    if all_:
+        if settings_file.exists():
+            to_delete.append(settings_file)
+
+    if not to_delete and not all_:
+        _typer.echo("Nothing to reset.")
+        return
+
+    # Show what will be deleted
+    if to_delete:
+        _typer.echo("The following files will be deleted:")
+        for f in to_delete:
+            _typer.echo(f"  {f}")
+
+    # Confirm
+    if not force:
+        if not _typer.confirm("Proceed?"):
+            _typer.echo("Aborted.")
+            raise _typer.Exit(code=0)
+
+    # Remove project from daemon first so it releases file handles
+    try:
+        from .client import DaemonClient
+
+        client = DaemonClient.connect()
+        client.handshake()
+        client.remove_project(str(project_root))
+        client.close()
+    except (ConnectionRefusedError, OSError, RuntimeError):
+        pass  # Daemon not running — that's fine
+
+    # Delete files/directories
+    import shutil as _shutil
+
+    for f in to_delete:
+        if f.is_dir():
+            _shutil.rmtree(f)
+        else:
+            f.unlink(missing_ok=True)
+
+    if all_:
+        # Remove .cocoindex_code/ if empty
+        try:
+            cocoindex_dir.rmdir()
+        except OSError:
+            pass  # Not empty
+
+        # Remove from .gitignore
+        remove_from_gitignore(project_root)
+        _typer.echo("Project fully reset.")
+    else:
+        _typer.echo("Databases deleted.")
+        if settings_file.exists():
+            _typer.echo(
+                "Settings file still exists. Run `ccc reset --all` to remove it too,\n"
+                "or edit it manually."
+            )
+
+
 @app.command()
 def mcp() -> None:
     """Run as MCP server (stdio mode)."""
@@ -279,7 +460,7 @@ async def _bg_index(client, project_root: str) -> None:  # type: ignore[no-untyp
         pass
 
 
-# --- Daemon subcommands (G5) ---
+# --- Daemon subcommands ---
 
 
 @daemon_app.command("status")

src/cocoindex_code/client.py

@@ -26,6 +26,8 @@
     IndexWaitingNotice,
     ProjectStatusRequest,
     ProjectStatusResponse,
+    RemoveProjectRequest,
+    RemoveProjectResponse,
     Request,
     Response,
     SearchRequest,
@@ -72,7 +74,10 @@ def index(
         """Request indexing with streaming progress. Blocks until complete."""
         self._conn.send_bytes(encode_request(IndexRequest(project_root=project_root)))
         while True:
-            data = self._conn.recv_bytes()
+            try:
+                data = self._conn.recv_bytes()
+            except EOFError:
+                raise RuntimeError("Connection to daemon lost during indexing")
             resp = decode_response(data)
             if isinstance(resp, ErrorResponse):
                 raise RuntimeError(f"Daemon error: {resp.message}")
@@ -121,6 +126,11 @@ def daemon_status(self) -> DaemonStatusResponse:
 
         return self._send(DaemonStatusRequest())  # type: ignore[return-value]
 
+    def remove_project(self, project_root: str) -> RemoveProjectResponse:
+        return self._send(  # type: ignore[return-value]
+            RemoveProjectRequest(project_root=project_root)
+        )
+
     def stop(self) -> StopResponse:
         return self._send(StopRequest())  # type: ignore[return-value]
 
@@ -236,7 +246,7 @@ def stop_daemon() -> None:
         pass
 
 
-def _wait_for_daemon(timeout: float = 5.0) -> None:
+def _wait_for_daemon(timeout: float = 10.0) -> None:
     """Wait for the daemon socket/pipe to become available."""
     deadline = time.monotonic() + timeout
     while time.monotonic() < deadline: