features/resource_cli_flags_904.feature

@@ -0,0 +1,108 @@
+Feature: Resource and LSP CLI missing flags (issue #904)
+  As a CleverAgents user
+  I want the CLI to support all specification-defined flags
+  So that I can fully manage resources and LSP servers per the spec
+
+  # ---- resource add --update ----
+
+  Scenario: Add a resource with --update re-registers it
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    And I add a resource flags resource "git-checkout" named "local/upd-test" with path "/tmp/u1"
+    When I run resource flags add "git-checkout" "local/upd-test" with path "/tmp/u2" and update
+    Then the resource flags output should contain "Added resource"
+    And the resource flags output should contain "local/upd-test"
+
+  Scenario: Add with --update when resource does not yet exist
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    When I run resource flags add "git-checkout" "local/new-upd" with path "/tmp/nu" and update
+    Then the resource flags output should contain "Added resource"
+
+  # ---- resource add --mount (container types) ----
+
+  Scenario: Mount flag rejected for non-container type
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    When I run resource flags add "git-checkout" "local/bad-mount" with path "/tmp/bm" and mount "local/repo:/workspace"
+    Then the resource flags command should fail
+    And the resource flags output should contain "container types"
+
+  # ---- resource add --clone-into ----
+
+  Scenario: Clone-into flag rejected for non-container type
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    When I run resource flags add "git-checkout" "local/bad-clone" with path "/tmp/bc" and clone-into "https://example.com/repo.git:/workspace"
+    Then the resource flags command should fail
+    And the resource flags output should contain "container types"
+
+  Scenario: Clone-into flag with invalid format
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    When I run resource flags add "container-instance" "local/bad-fmt" with clone-into "no-colon-here"
+    Then the resource flags command should fail
+    And the resource flags output should contain "REPO_URL"
+
+  # ---- resource list --all ----
+
+  Scenario: Resource list default excludes auto-discovered resources
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    And a user-added resource flags resource "git-checkout" named "local/user-res" with path "/tmp/ur"
+    And an auto-discovered resource flags resource named "local/auto-res"
+    When I run resource flags list
+    Then the resource flags output should contain "local/user-res"
+    And the resource flags output should not contain "local/auto-res"
+
+  Scenario: Resource list --all includes auto-discovered resources
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    And a user-added resource flags resource "git-checkout" named "local/user-res2" with path "/tmp/ur2"
+    And an auto-discovered resource flags resource named "local/auto-res2"
+    When I run resource flags list with --all
+    Then the resource flags output should contain "local/user-res2"
+    And the resource flags output should contain "local/auto-res2"
+
+  # ---- resource tree --depth default ----
+
+  Scenario: Tree depth defaults to 3
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    And a resource flags resource "git-checkout" named "local/depth-root" with path "/tmp/dr"
+    When I run resource flags tree for "local/depth-root" with default depth
+    Then the resource flags tree depth used should be 3
+
+  # ---- resource type list [REGEX] ----
+
+  Scenario: Resource type list with regex filter
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    When I run resource flags type list with regex "git"
+    Then the resource flags output should contain "git-checkout"
+    And the resource flags output should not contain "fs-directory"
+
+  Scenario: Resource type list without regex shows all
+    Given a fresh resource flags test registry
+    And resource flags built-in types are bootstrapped
+    When I run resource flags type list without regex
+    Then the resource flags output should contain "git-checkout"
+    And the resource flags output should contain "fs-directory"
+
+  # ---- lsp list [REGEX] ----
+
+  Scenario: LSP list with regex filter
+    Given a clean LSP flags test environment
+    And a registered LSP flags server "local/pyright-test" for language "python"
+    And a registered LSP flags server "local/clangd-test" for language "cpp"
+    When I run lsp flags list with regex "pyright"
+    Then the lsp flags output should contain "local/pyright-test"
+    And the lsp flags output should not contain "local/clangd-test"
+
+  Scenario: LSP list without regex shows all
+    Given a clean LSP flags test environment
+    And a registered LSP flags server "local/pyright-test2" for language "python"
+    And a registered LSP flags server "local/clangd-test2" for language "cpp"
+    When I run lsp flags list without regex
+    Then the lsp flags output should contain "local/pyright-test2"
+    And the lsp flags output should contain "local/clangd-test2"

features/steps/coverage_boost_extra_steps.py

@@ -398,6 +398,8 @@ def step_run_resource_add_branch_only(
             branch=branch,
             description=None,
             read_only=False,
+            clone_into=None,
+            update=False,
             fmt="rich",
         )
         context.resource_cli_output = output

features/steps/resource_cli_flags_904_steps.py

@@ -0,0 +1,550 @@
+"""Step definitions for ``resource_cli_flags_904.feature`` (issue #904).
+
+Tests the new CLI flags:
+  - resource add --update, --mount (container types), --clone-into
+  - resource list --all
+  - resource tree --depth default changed to 3
+  - resource type list [REGEX]
+  - lsp list [REGEX]
+"""
+
+from __future__ import annotations
+
+from datetime import UTC, datetime
+from io import StringIO
+from typing import Any
+
+from behave import given, then, when
+from behave.runner import Context
+from rich.console import Console
+from sqlalchemy import create_engine, event
+from sqlalchemy.orm import sessionmaker
+
+from cleveragents.application.services.resource_registry_service import (
+    ResourceRegistryService,
+)
+from cleveragents.cli.commands.lsp import _reset_registry
+from cleveragents.infrastructure.database.models import Base, ResourceModel
+from cleveragents.lsp.models import LspCapability, LspServerConfig
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+
+def _make_flags_service(context: Context) -> ResourceRegistryService:
+    """Create or return a cached ResourceRegistryService for flags tests."""
+    if not hasattr(context, "flags_cli_service"):
+        engine = create_engine("sqlite:///:memory:", echo=False)
+
+        @event.listens_for(engine, "connect")
+        def _fk(conn: Any, _rec: Any) -> None:
+            conn.cursor().execute("PRAGMA foreign_keys=ON")
+
+        Base.metadata.create_all(engine)
+        factory = sessionmaker(bind=engine, expire_on_commit=False)
+        context.flags_cli_service = ResourceRegistryService(session_factory=factory)
+    return context.flags_cli_service
+
+
+def _capture_flags_output(func: Any, *args: Any, **kwargs: Any) -> tuple[str, bool]:
+    """Run a CLI function capturing its console output and success status."""
+    import contextlib
+
+    buf = StringIO()
+    console = Console(
+        file=buf, width=200, no_color=True, highlight=False, force_terminal=False
+    )
+
+    import cleveragents.cli.commands.resource as resource_mod
+
+    orig_console = resource_mod.console
+    resource_mod.console = console
+
+    failed = False
+    try:
+        with contextlib.redirect_stdout(buf):
+            func(*args, **kwargs)
+    except SystemExit:
+        failed = True
+    except Exception:
+        failed = True
+    finally:
+        resource_mod.console = orig_console
+
+    return buf.getvalue(), failed
+
+
+def _patch_flags_service(context: Context) -> Any:
+    """Monkey-patch the container to return our in-memory service."""
+    import cleveragents.cli.commands.resource as resource_mod
+
+    orig_fn = resource_mod._get_registry_service
+
+    def _mock_get() -> ResourceRegistryService:
+        return _make_flags_service(context)
+
+    resource_mod._get_registry_service = _mock_get
+    return orig_fn
+
+
+def _unpatch_flags_service(orig_fn: Any) -> None:
+    """Restore original service getter."""
+    import cleveragents.cli.commands.resource as resource_mod
+
+    resource_mod._get_registry_service = orig_fn
+
+
+# ---------------------------------------------------------------------------
+# Background / Given
+# ---------------------------------------------------------------------------
+
+
+@given("a fresh resource flags test registry")
+def step_fresh_flags_registry(context: Context) -> None:
+    engine = create_engine("sqlite:///:memory:", echo=False)
+
+    @event.listens_for(engine, "connect")
+    def _fk(conn: Any, _rec: Any) -> None:
+        conn.cursor().execute("PRAGMA foreign_keys=ON")
+
+    Base.metadata.create_all(engine)
+    factory = sessionmaker(bind=engine, expire_on_commit=False)
+    context.flags_cli_service = ResourceRegistryService(session_factory=factory)
+    context.flags_cli_output = ""
+    context.flags_cli_failed = False
+    context.flags_tree_depth_used = None
+
+
+@given("resource flags built-in types are bootstrapped")
+def step_flags_bootstrap(context: Context) -> None:
+    service = _make_flags_service(context)
+    service.bootstrap_builtin_types()
+
+
+@given(
+    'I add a resource flags resource "{type_name}" named "{name}" with path "{path}"'
+)
+def step_flags_add_resource_given(
+    context: Context, type_name: str, name: str, path: str
+) -> None:
+    from cleveragents.cli.commands.resource import resource_add
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(
+            resource_add,
+            type_name=type_name,
+            name=name,
+            path=path,
+            branch=None,
+            description=None,
+            read_only=False,
+            clone_into=None,
+            update=False,
+            fmt="rich",
+        )
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+@given('a resource flags resource "{type_name}" named "{name}" with path "{path}"')
+def step_flags_add_resource_given_alt(
+    context: Context, type_name: str, name: str, path: str
+) -> None:
+    service = _make_flags_service(context)
+    service.register_resource(
+        type_name=type_name,
+        name=name,
+        location=path,
+        description=None,
+        read_only=False,
+        properties={"path": path},
+    )
+
+
+@given(
+    'a user-added resource flags resource "{type_name}" named "{name}" with path "{path}"'
+)
+def step_flags_add_user_resource(
+    context: Context, type_name: str, name: str, path: str
+) -> None:
+    service = _make_flags_service(context)
+    service.register_resource(
+        type_name=type_name,
+        name=name,
+        location=path,
+        description=None,
+        read_only=False,
+        properties={"path": path},
+    )
+
+
+@given('an auto-discovered resource flags resource named "{name}"')
+def step_flags_add_auto_discovered(context: Context, name: str) -> None:
+    """Directly insert an auto-discovered resource into the DB."""
+    from ulid import ULID
+
+    service = _make_flags_service(context)
+    session = service._session()
+    try:
+        now_iso = datetime.now(tz=UTC).isoformat()
+        db_resource = ResourceModel(
+            resource_id=str(ULID()),
+            namespaced_name=name,
+            namespace=name.split("/", 1)[0] if "/" in name else None,
+            type_name="git-checkout",
+            resource_kind="physical",
+            location="/tmp/auto",
+            description="Auto-discovered",
+            read_only=False,
+            auto_discovered=True,
+            sandbox_strategy=None,
+            content_hash=None,
+            properties_json=None,
+            metadata_json=None,
+            created_at=now_iso,
+            updated_at=now_iso,
+        )
+        session.add(db_resource)
+        session.commit()
+    finally:
+        session.close()
+
+
+# ---------------------------------------------------------------------------
+# LSP Given
+# ---------------------------------------------------------------------------
+
+
+@given("a clean LSP flags test environment")
+def step_clean_lsp_flags(context: Context) -> None:
+    _reset_registry()
+    context.lsp_flags_output = ""
+    context.lsp_flags_failed = False
+
+
+@given('a registered LSP flags server "{name}" for language "{lang}"')
+def step_register_lsp_flags_server(context: Context, name: str, lang: str) -> None:
+    from cleveragents.cli.commands.lsp import _get_registry
+
+    registry = _get_registry()
+    config = LspServerConfig(
+        name=name,
+        command="test-server",
+        args=["--stdio"],
+        languages=[lang],
+        capabilities=[LspCapability.DIAGNOSTICS],
+    )
+    registry.register(config)
+
+
+# ---------------------------------------------------------------------------
+# When steps — resource add
+# ---------------------------------------------------------------------------
+
+
+@when('I run resource flags add "{type_name}" "{name}" with path "{path}" and update')
+def step_flags_add_update(
+    context: Context, type_name: str, name: str, path: str
+) -> None:
+    from cleveragents.cli.commands.resource import resource_add
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(
+            resource_add,
+            type_name=type_name,
+            name=name,
+            path=path,
+            branch=None,
+            description=None,
+            read_only=False,
+            clone_into=None,
+            update=True,
+            fmt="rich",
+        )
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+@when(
+    'I run resource flags add "{type_name}" "{name}" with path "{path}" and mount "{mount_spec}"'
+)
+def step_flags_add_mount(
+    context: Context, type_name: str, name: str, path: str, mount_spec: str
+) -> None:
+    from cleveragents.cli.commands.resource import resource_add
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(
+            resource_add,
+            type_name=type_name,
+            name=name,
+            path=path,
+            branch=None,
+            description=None,
+            read_only=False,
+            mount=[mount_spec],
+            clone_into=None,
+            update=False,
+            fmt="rich",
+        )
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+@when(
+    'I run resource flags add "{type_name}" "{name}" with path "{path}" and clone-into "{clone_spec}"'
+)
+def step_flags_add_clone_into(
+    context: Context, type_name: str, name: str, path: str, clone_spec: str
+) -> None:
+    from cleveragents.cli.commands.resource import resource_add
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(
+            resource_add,
+            type_name=type_name,
+            name=name,
+            path=path,
+            branch=None,
+            description=None,
+            read_only=False,
+            clone_into=clone_spec,
+            update=False,
+            fmt="rich",
+        )
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+@when('I run resource flags add "{type_name}" "{name}" with clone-into "{clone_spec}"')
+def step_flags_add_clone_into_no_path(
+    context: Context, type_name: str, name: str, clone_spec: str
+) -> None:
+    from cleveragents.cli.commands.resource import resource_add
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(
+            resource_add,
+            type_name=type_name,
+            name=name,
+            path=None,
+            branch=None,
+            description=None,
+            read_only=False,
+            clone_into=clone_spec,
+            update=False,
+            fmt="rich",
+        )
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+# ---------------------------------------------------------------------------
+# When steps — resource list
+# ---------------------------------------------------------------------------
+
+
+@when("I run resource flags list")
+def step_flags_list(context: Context) -> None:
+    from cleveragents.cli.commands.resource import resource_list
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(
+            resource_list, type_filter=None, show_all=False, fmt="rich"
+        )
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+@when("I run resource flags list with --all")
+def step_flags_list_all(context: Context) -> None:
+    from cleveragents.cli.commands.resource import resource_list
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(
+            resource_list, type_filter=None, show_all=True, fmt="rich"
+        )
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+# ---------------------------------------------------------------------------
+# When steps — resource tree
+# ---------------------------------------------------------------------------
+
+
+@when('I run resource flags tree for "{name}" with default depth')
+def step_flags_tree_default(context: Context, name: str) -> None:
+    """Run resource tree and capture the depth that was actually used."""
+    from cleveragents.cli.commands.resource import resource_tree
+
+    orig = _patch_flags_service(context)
+    try:
+        # We call resource_tree *without* passing depth so the default is used.
+        # We capture what depth the function uses by inspecting its default.
+        import inspect
+
+        sig = inspect.signature(resource_tree)
+        default_depth = sig.parameters["depth"].default
+        context.flags_tree_depth_used = default_depth
+
+        output, failed = _capture_flags_output(
+            resource_tree, resource=name, type_filter=None, fmt="rich"
+        )
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+# ---------------------------------------------------------------------------
+# When steps — resource type list [REGEX]
+# ---------------------------------------------------------------------------
+
+
+@when('I run resource flags type list with regex "{regex}"')
+def step_flags_type_list_regex(context: Context, regex: str) -> None:
+    from cleveragents.cli.commands.resource import type_list
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(type_list, regex=regex, fmt="rich")
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+@when("I run resource flags type list without regex")
+def step_flags_type_list_no_regex(context: Context) -> None:
+    from cleveragents.cli.commands.resource import type_list
+
+    orig = _patch_flags_service(context)
+    try:
+        output, failed = _capture_flags_output(type_list, regex=None, fmt="rich")
+        context.flags_cli_output = output
+        context.flags_cli_failed = failed
+    finally:
+        _unpatch_flags_service(orig)
+
+
+# ---------------------------------------------------------------------------
+# When steps — lsp list [REGEX]
+# ---------------------------------------------------------------------------
+
+
+def _capture_lsp_output(func: Any, *args: Any, **kwargs: Any) -> tuple[str, bool]:
+    """Run an LSP CLI function capturing its console output."""
+    import contextlib
+
+    buf = StringIO()
+    console = Console(
+        file=buf, width=200, no_color=True, highlight=False, force_terminal=False
+    )
+
+    import cleveragents.cli.commands.lsp as lsp_mod
+
+    orig_console = lsp_mod.console
+    lsp_mod.console = console
+
+    failed = False
+    try:
+        with contextlib.redirect_stdout(buf):
+            func(*args, **kwargs)
+    except SystemExit:
+        failed = True
+    except Exception:
+        failed = True
+    finally:
+        lsp_mod.console = orig_console
+
+    return buf.getvalue(), failed
+
+
+@when('I run lsp flags list with regex "{regex}"')
+def step_lsp_flags_list_regex(context: Context, regex: str) -> None:
+    from cleveragents.cli.commands.lsp import list_servers
+
+    output, failed = _capture_lsp_output(list_servers, regex=regex, fmt="rich")
+    context.lsp_flags_output = output
+    context.lsp_flags_failed = failed
+
+
+@when("I run lsp flags list without regex")
+def step_lsp_flags_list_no_regex(context: Context) -> None:
+    from cleveragents.cli.commands.lsp import list_servers
+
+    output, failed = _capture_lsp_output(list_servers, regex=None, fmt="rich")
+    context.lsp_flags_output = output
+    context.lsp_flags_failed = failed
+
+
+# ---------------------------------------------------------------------------
+# Then steps
+# ---------------------------------------------------------------------------
+
+
+@then('the resource flags output should contain "{text}"')
+def step_flags_output_contains(context: Context, text: str) -> None:
+    output = context.flags_cli_output
+    assert text.lower() in output.lower(), (
+        f"Expected '{text}' in output, got:\n{output}"
+    )
+
+
+@then('the resource flags output should not contain "{text}"')
+def step_flags_output_not_contains(context: Context, text: str) -> None:
+    output = context.flags_cli_output
+    assert text.lower() not in output.lower(), (
+        f"Did not expect '{text}' in output, got:\n{output}"
+    )
+
+
+@then("the resource flags command should fail")
+def step_flags_command_failed(context: Context) -> None:
+    assert context.flags_cli_failed, "Expected command to fail but it succeeded"
+
+
+@then("the resource flags tree depth used should be {expected_depth:d}")
+def step_flags_tree_depth(context: Context, expected_depth: int) -> None:
+    assert context.flags_tree_depth_used == expected_depth, (
+        f"Expected default depth {expected_depth}, got {context.flags_tree_depth_used}"
+    )
+
+
+@then('the lsp flags output should contain "{text}"')
+def step_lsp_flags_output_contains(context: Context, text: str) -> None:
+    output = context.lsp_flags_output
+    assert text.lower() in output.lower(), (
+        f"Expected '{text}' in output, got:\n{output}"
+    )
+
+
+@then('the lsp flags output should not contain "{text}"')
+def step_lsp_flags_output_not_contains(context: Context, text: str) -> None:
+    output = context.lsp_flags_output
+    assert text.lower() not in output.lower(), (
+        f"Did not expect '{text}' in output, got:\n{output}"
+    )

features/steps/resource_cli_steps.py

@@ -268,6 +268,8 @@ def _do_resource_add(context: Context, type_name: str, name: str, path: str) ->
             branch=None,
             description=None,
             read_only=False,
+            clone_into=None,
+            update=False,
             fmt="rich",
         )
         context.resource_cli_output = output
@@ -519,6 +521,8 @@ def step_run_resource_add_fmt(
             branch=None,
             description=None,
             read_only=False,
+            clone_into=None,
+            update=False,
             fmt=fmt,
         )
         context.resource_cli_output = output
@@ -552,6 +556,8 @@ def step_run_resource_add_branch_desc(
             branch=branch if branch else None,
             description=desc,
             read_only=False,
+            clone_into=None,
+            update=False,
             fmt="rich",
         )
         context.resource_cli_output = output
@@ -593,6 +599,8 @@ def step_add_resource_long_desc(context: Context) -> None:
             branch=None,
             description=long_desc,
             read_only=False,
+            clone_into=None,
+            update=False,
             fmt="rich",
         )
         context.resource_cli_output = output

features/steps/resource_type_bootstrap_fs_steps.py

@@ -141,6 +141,8 @@ def step_run_resource_add_fs(
             branch=None,
             description=None,
             image=None,
+            clone_into=None,
+            update=False,
             read_only=False,
             fmt="rich",
         )

features/steps/resource_type_bootstrap_git_steps.py

@@ -140,6 +140,8 @@ def step_run_resource_add_git(
             branch=branch,
             description=None,
             image=None,
+            clone_into=None,
+            update=False,
             read_only=False,
             fmt="rich",
         )

src/cleveragents/application/services/_resource_registry_ops.py

@@ -179,6 +179,7 @@ class ResourceInstanceMixin:
         type_name: str | None = None,
         *,
         exact: bool = False,
+        include_auto_discovered: bool = True,
     ) -> list[Resource]:
         """List registered resources.
 
@@ -188,6 +189,8 @@ class ResourceInstanceMixin:
                 include resources whose type is a **subtype** of
                 *type_name* (ADR-042 polymorphic listing).  When
                 ``True``, match only the exact type name.
+            include_auto_discovered: When ``False``, exclude resources
+                with ``auto_discovered=True`` (default shows all).
 
         Returns:
             List of ``Resource`` domain objects.
@@ -204,6 +207,8 @@ class ResourceInstanceMixin:
                     subtypes = find_subtypes(type_name, registry)
                     all_types = [type_name, *subtypes]
                     query = query.filter(ResourceModel.type_name.in_(all_types))
+            if not include_auto_discovered:
+                query = query.filter(ResourceModel.auto_discovered == False)  # noqa: E712
             query = query.order_by(ResourceModel.created_at)
             rows = query.all()
             return [db_resource_to_domain(row) for row in rows]

src/cleveragents/cli/commands/lsp.py

@@ -48,6 +48,7 @@ from __future__ import annotations
 import json
 import logging
 import os
+import re as _re
 from pathlib import Path
 from typing import Annotated, Any
 
@@ -237,6 +238,12 @@ def remove(
 
 @app.command("list")
 def list_servers(
+    regex: Annotated[
+        str | None,
+        typer.Argument(
+            help="Optional regex to filter server names",
+        ),
+    ] = None,
     namespace: Annotated[
         str | None,
         typer.Option("--namespace", "-n", help="Filter by namespace"),
@@ -252,8 +259,11 @@ def list_servers(
 ) -> None:
     """List registered LSP servers.
 
+    An optional positional REGEX argument filters server names.
+
     Examples:
         agents lsp list
+        agents lsp list "pyright.*"
         agents lsp list --namespace local
         agents lsp list --language python
         agents lsp list --format json
@@ -261,6 +271,15 @@ def list_servers(
     registry = _get_registry()
     servers = registry.list_servers(namespace=namespace, language=language)
 
+    # Apply optional regex filter on server names.
+    if regex is not None:
+        try:
+            pattern = _re.compile(regex)
+        except _re.error as re_exc:
+            console.print(f"[red]Invalid regex:[/red] {re_exc}")
+            raise typer.Abort() from re_exc
+        servers = [s for s in servers if pattern.search(s.name)]
+
     if not servers:
         console.print("[yellow]No LSP servers found.[/yellow]")
         console.print("Register one with 'agents lsp add --config <file>'")

src/cleveragents/cli/commands/resource.py

@@ -55,6 +55,7 @@ from __future__ import annotations
 
 import json
 import logging
+import re
 from pathlib import Path
 from typing import Annotated, Any
 
@@ -100,6 +101,9 @@ console = _get_console()
 
 _FORMAT_HELP = "Output format: json, yaml, plain, table, or rich (default: rich)"
 
+# Resource types that support --mount and --clone-into flags.
+_CONTAINER_TYPES = frozenset({"container-instance", "devcontainer-instance"})
+
 
 def _get_registry_service() -> ResourceRegistryService:
     """Get the ResourceRegistryService from the DI container."""
@@ -291,6 +295,12 @@ def type_remove(
 
 @type_app.command("list")
 def type_list(
+    regex: Annotated[
+        str | None,
+        typer.Argument(
+            help="Optional regex to filter type names",
+        ),
+    ] = None,
     fmt: Annotated[
         str,
         typer.Option("--format", "-f", help=_FORMAT_HELP),
@@ -298,14 +308,26 @@ def type_list(
 ) -> None:
     """List all registered resource types (built-in and custom).
 
+    An optional positional REGEX argument filters type names.
+
     Examples:
         agents resource type list
+        agents resource type list "git.*"
         agents resource type list --format json
     """
     try:
         service = _get_registry_service()
         types = service.list_types()
 
+        # Apply optional regex filter on type names.
+        if regex is not None:
+            try:
+                pattern = re.compile(regex)
+            except re.error as re_exc:
+                console.print(f"[red]Invalid regex:[/red] {re_exc}")
+                raise typer.Abort() from re_exc
+            types = [t for t in types if pattern.search(t.name)]
+
         if not types:
             console.print("[yellow]No resource types registered.[/yellow]")
             return
@@ -548,7 +570,7 @@ def resource_add(
         typer.Option(
             "--mount",
             help=(
-                "Mount specification for container-instance resources. "
+                "Mount specification for container types. "
                 "Formats: <resource>:<path> (resource-ref, rw) or "
                 "<host-path>:<container-path>:<mode> (host-path, mode=rw|ro). "
                 "Can be specified multiple times."
@@ -560,12 +582,19 @@ def resource_add(
         typer.Option(
             "--clone-into",
             help=(
-                "Clone a remote repository into the container at the specified "
-                "path. Format: REPO_URL:CONTAINER_PATH (e.g., "
-                "https://github.com/acme/api.git:/workspace)"
+                "Clone a repository into the container at a specified path. "
+                "Format: <REPO_URL>:<CONTAINER_PATH>. "
+                "Only valid for container types."
             ),
         ),
     ] = None,
+    update: Annotated[
+        bool,
+        typer.Option(
+            "--update",
+            help="Re-register an existing resource (remove and re-add).",
+        ),
+    ] = False,
     read_only: Annotated[
         bool,
         typer.Option("--read-only", help="Mark resource as read-only"),
@@ -577,15 +606,19 @@ def resource_add(
 ) -> None:
     """Add a new resource instance of the specified type.
 
+    Use ``--update`` to re-register an existing resource by name.
+
     Examples:
         agents resource add git-checkout local/my-repo --path /home/user/repo
         agents resource add fs-directory local/data --path /data --read-only
         agents resource add devcontainer-instance local/dc --path /project
         agents resource add container-instance local/ctr --image ubuntu:latest
-        agents resource add container-instance local/ctr --image node:18 \
-            --mount local/api-repo:/workspace \
+        agents resource add container-instance local/ctr --image node:18 \\
+            --mount local/api-repo:/workspace \\
             --mount /var/shared/config:/config:ro
-        agents resource add container-instance cloud/ci --clone-into https://github.com/acme/api.git:/workspace
+        agents resource add container-instance local/ctr --image node:18 \\
+            --clone-into https://github.com/org/repo.git:/workspace/repo
+        agents resource add git-checkout local/my-repo --path /tmp --update
     """
     try:
         # Validate --clone-into is only used with container resource types.
@@ -612,6 +645,36 @@ def resource_add(
 
         service = _get_registry_service()
 
+        # --update: remove existing resource before re-registering
+        if update:
+            try:
+                existing = service.show_resource(name)
+                # Remove the existing resource so we can re-register
+                session = service._session()
+                try:
+                    from cleveragents.infrastructure.database.models import (
+                        ResourceEdgeModel,
+                        ResourceModel,
+                    )
+
+                    # Remove edges first
+                    session.query(ResourceEdgeModel).filter(
+                        (ResourceEdgeModel.parent_id == existing.resource_id)
+                        | (ResourceEdgeModel.child_id == existing.resource_id)
+                    ).delete(synchronize_session="fetch")
+                    session.query(ResourceModel).filter_by(
+                        resource_id=existing.resource_id
+                    ).delete(synchronize_session="fetch")
+                    session.commit()
+                except Exception:
+                    session.rollback()
+                    raise
+                finally:
+                    session.close()
+            except NotFoundError:
+                # Resource doesn't exist yet — proceed with normal add
+                pass
+
         # Build properties from type-specific flags
         properties: dict[str, Any] = {}
         if path is not None:
@@ -621,15 +684,32 @@ def resource_add(
         if image is not None:
             properties["image"] = image
         if mount:
-            if type_name != "container-instance":
+            if type_name not in _CONTAINER_TYPES:
                 console.print(
                     "[red]Error:[/red] --mount is only valid for "
-                    "container-instance resources."
+                    "container types "
+                    f"({', '.join(sorted(_CONTAINER_TYPES))})."
                 )
                 raise typer.Abort()
             properties["mounts"] = json.dumps([_parse_mount_spec(m) for m in mount])
         if clone_into is not None:
-            properties["clone_into"] = clone_into
+            if type_name not in _CONTAINER_TYPES:
+                console.print(
+                    "[red]Error:[/red] --clone-into is only valid for "
+                    "container types "
+                    f"({', '.join(sorted(_CONTAINER_TYPES))})."
+                )
+                raise typer.Abort()
+            parts = clone_into.rsplit(":", 1)
+            if len(parts) != 2 or not parts[0] or not parts[1]:
+                console.print(
+                    "[red]Error:[/red] --clone-into must be in "
+                    "<REPO_URL>:<CONTAINER_PATH> format."
+                )
+                raise typer.Abort()
+            properties["clone_into"] = json.dumps(
+                {"repo_url": parts[0], "container_path": parts[1]}
+            )
 
         resource = service.register_resource(
             type_name=type_name,
@@ -672,6 +752,13 @@ def resource_list(
         str | None,
         typer.Option("--type", "-t", help="Filter by resource type"),
     ] = None,
+    show_all: Annotated[
+        bool,
+        typer.Option(
+            "--all",
+            help="Include auto-discovered child resources in the listing.",
+        ),
+    ] = False,
     fmt: Annotated[
         str,
         typer.Option("--format", "-f", help=_FORMAT_HELP),
@@ -679,14 +766,21 @@ def resource_list(
 ) -> None:
     """List registered resources.
 
+    By default only user-added (named) resources are shown. Use
+    ``--all`` to include auto-discovered children.
+
     Examples:
         agents resource list
+        agents resource list --all
         agents resource list --type git-checkout
         agents resource list --format json
     """
     try:
         service = _get_registry_service()
-        resources = service.list_resources(type_name=type_filter)
+        resources = service.list_resources(
+            type_name=type_filter,
+            include_auto_discovered=show_all,
+        )
 
         if not resources:
             console.print("[yellow]No resources found.[/yellow]")
@@ -806,7 +900,7 @@ def resource_tree(
     depth: Annotated[
         int,
         typer.Option("--depth", "-d", help="Maximum tree depth (-1 for unlimited)"),
-    ] = -1,
+    ] = 3,
     type_filter: Annotated[
         str | None,
         typer.Option("--type", "-t", help="Filter children by resource type"),