diff --git a/docs/src/content/docs/reference/cli-commands.md b/docs/src/content/docs/reference/cli-commands.md
index 92707b591..d44c9f785 100644
--- a/docs/src/content/docs/reference/cli-commands.md
+++ b/docs/src/content/docs/reference/cli-commands.md
@@ -664,17 +664,27 @@ apm deps info design-guidelines
 Remove the entire `apm_modules/` directory and all installed APM packages.
 
 ```bash
-apm deps clean
+apm deps clean [OPTIONS]
 ```
 
+**Options:**
+- `--dry-run` - Show what would be removed without removing
+- `--yes`, `-y` - Skip confirmation prompt (for non-interactive/scripted use)
+
 **Examples:**
 ```bash
 # Remove all APM dependencies (with confirmation)
 apm deps clean
+
+# Preview what would be removed
+apm deps clean --dry-run
+
+# Remove without confirmation (e.g. in CI pipelines)
+apm deps clean --yes
 ```
 
 **Behavior:**
-- Shows confirmation prompt before deletion
+- Shows confirmation prompt before deletion (unless `--yes` is provided)
 - Removes entire `apm_modules/` directory
 - Displays count of packages that will be removed
 - Can be cancelled with Ctrl+C or 'n' response
@@ -684,11 +694,11 @@ apm deps clean
 Update installed APM dependencies to their latest versions.
 
 ```bash
-apm deps update [PACKAGE_NAME]
+apm deps update [PACKAGE]
 ```
 
 **Arguments:**
-- `PACKAGE_NAME` - Optional. Update specific package only
+- `PACKAGE` - Optional. Update specific package only
 
 **Examples:**
 ```bash
@@ -716,7 +726,7 @@ apm mcp list [OPTIONS]
 ```
 
 **Options:**
-- `--limit INTEGER` - Number of results to show
+- `--limit INTEGER` - Number of results to show (default: 20)
 
 **Examples:**
 ```bash
@@ -1189,7 +1199,7 @@ apm runtime remove [OPTIONS] {copilot|codex|llm}
 **Options:**
 - `--yes` - Confirm the action without prompting
 
-#### `apm runtime status` - Show runtime status
+#### `apm runtime status` - Show active runtime and preference order
 
 Display which runtime APM will use for execution and runtime preference order.
 
diff --git a/src/apm_cli/commands/deps/_utils.py b/src/apm_cli/commands/deps/_utils.py
index 8ab24f89a..16383cece 100644
--- a/src/apm_cli/commands/deps/_utils.py
+++ b/src/apm_cli/commands/deps/_utils.py
@@ -8,6 +8,29 @@
 from ...deps.github_downloader import GitHubPackageDownloader
 
 
+def _scan_installed_packages(apm_modules_dir: Path) -> list:
+    """Scan *apm_modules_dir* for installed package paths.
+
+    Walks the tree to find directories containing ``apm.yml`` or ``.apm``,
+    supporting GitHub (2-level), ADO (3-level), and subdirectory packages.
+
+    Returns:
+        List of ``"owner/repo"`` or ``"org/project/repo"`` path keys.
+    """
+    installed: list = []
+    if not apm_modules_dir.exists():
+        return installed
+    for candidate in apm_modules_dir.rglob("*"):
+        if not candidate.is_dir() or candidate.name.startswith("."):
+            continue
+        if not ((candidate / APM_YML_FILENAME).exists() or (candidate / APM_DIR).exists()):
+            continue
+        rel_parts = candidate.relative_to(apm_modules_dir).parts
+        if len(rel_parts) >= 2:
+            installed.append("/".join(rel_parts))
+    return installed
+
+
 def _is_nested_under_package(candidate: Path, apm_modules_path: Path) -> bool:
     """Check if *candidate* is a sub-directory of another installed package.
 
diff --git a/src/apm_cli/commands/deps/cli.py b/src/apm_cli/commands/deps/cli.py
index 2a3b65240..ac115ba48 100644
--- a/src/apm_cli/commands/deps/cli.py
+++ b/src/apm_cli/commands/deps/cli.py
@@ -397,7 +397,9 @@ def _add_children(parent_branch, parent_repo_url, depth=0):
 
 
 @deps.command(help="Remove all APM dependencies")
-def clean():
+@click.option("--dry-run", is_flag=True, default=False, help="Show what would be removed without removing")
+@click.option("--yes", "-y", is_flag=True, default=False, help="Skip confirmation prompt")
+def clean(dry_run: bool, yes: bool):
     """Remove entire apm_modules/ directory."""
     logger = CommandLogger("deps-clean")
 
@@ -408,21 +410,30 @@ def clean():
         logger.progress("No apm_modules/ directory found - already clean")
         return
     
-    # Show what will be removed
-    package_count = len([d for d in apm_modules_path.iterdir() if d.is_dir()])
+    # Count actual installed packages (not just top-level dirs like org namespaces or _local)
+    from ._utils import _scan_installed_packages
+    packages = _scan_installed_packages(apm_modules_path)
+    package_count = len(packages)
     
-    logger.warning(f"This will remove the entire apm_modules/ directory ({package_count} packages)")
+    if dry_run:
+        logger.progress(f"Dry run: would remove apm_modules/ ({package_count} package(s))")
+        for pkg in sorted(packages):
+            logger.progress(f"  - {pkg}")
+        return
     
-    # Confirmation prompt
-    try:
-        from rich.prompt import Confirm
-        confirm = Confirm.ask("Continue?")
-    except ImportError:
-        confirm = click.confirm("Continue?")
+    logger.warning(f"This will remove the entire apm_modules/ directory ({package_count} package(s))")
     
-    if not confirm:
-        logger.progress("Operation cancelled")
-        return
+    # Confirmation prompt (skip if --yes provided)
+    if not yes:
+        try:
+            from rich.prompt import Confirm
+            confirm = Confirm.ask("Continue?")
+        except ImportError:
+            confirm = click.confirm("Continue?")
+        
+        if not confirm:
+            logger.progress("Operation cancelled")
+            return
     
     try:
         shutil.rmtree(apm_modules_path)
diff --git a/src/apm_cli/commands/install.py b/src/apm_cli/commands/install.py
index ed5454850..71786f5e3 100644
--- a/src/apm_cli/commands/install.py
+++ b/src/apm_cli/commands/install.py
@@ -433,7 +433,7 @@ def _check_repo_fallback(token, git_env):
     "--dry-run", is_flag=True, help="Show what would be installed without installing"
 )
 @click.option("--force", is_flag=True, help="Overwrite locally-authored files on collision and deploy despite critical security findings")
-@click.option("--verbose", is_flag=True, help="Show detailed installation information")
+@click.option("--verbose", "-v", is_flag=True, help="Show detailed installation information")
 @click.option(
     "--trust-transitive-mcp",
     is_flag=True,
diff --git a/src/apm_cli/commands/mcp.py b/src/apm_cli/commands/mcp.py
index bac184d11..4db9f6e4e 100644
--- a/src/apm_cli/commands/mcp.py
+++ b/src/apm_cli/commands/mcp.py
@@ -292,7 +292,7 @@ def show(ctx, server_name, verbose):
 
 
 @mcp.command(help="List all available MCP servers")
-@click.option("--limit", default=20, help="Number of results to show")
+@click.option("--limit", default=20, show_default=True, help="Number of results to show")
 @click.option("--verbose", "-v", is_flag=True, help="Show detailed output")
 @click.pass_context
 def list(ctx, limit, verbose):
diff --git a/src/apm_cli/commands/pack.py b/src/apm_cli/commands/pack.py
index be89dcefc..90ae7e5b0 100644
--- a/src/apm_cli/commands/pack.py
+++ b/src/apm_cli/commands/pack.py
@@ -23,7 +23,7 @@
     "-t",
     type=click.Choice(["copilot", "vscode", "claude", "cursor", "opencode", "all"]),
     default=None,
-    help="Filter files by target (default: auto-detect). 'vscode' is an alias for 'copilot'.",
+    help="Filter files by target (default: auto-detect). 'copilot' is an alias for 'vscode'.",
 )
 @click.option("--archive", is_flag=True, default=False, help="Produce a .tar.gz archive.")
 @click.option(
diff --git a/src/apm_cli/commands/runtime.py b/src/apm_cli/commands/runtime.py
index fb2218fd9..40b0f01de 100644
--- a/src/apm_cli/commands/runtime.py
+++ b/src/apm_cli/commands/runtime.py
@@ -146,9 +146,9 @@ def remove(runtime_name):
         sys.exit(1)
 
 
-@runtime.command(help="Check which runtime will be used")
+@runtime.command(help="Show active runtime and preference order")
 def status():
-    """Show which runtime APM will use for execution."""
+    """Show active runtime and preference order."""
     logger = CommandLogger("runtime status")
     try:
         from ..runtime.manager import RuntimeManager
diff --git a/tests/unit/test_deps_clean_command.py b/tests/unit/test_deps_clean_command.py
new file mode 100644
index 000000000..bb12e6b1f
--- /dev/null
+++ b/tests/unit/test_deps_clean_command.py
@@ -0,0 +1,104 @@
+"""Tests for apm deps clean command --dry-run and --yes flags."""
+
+import contextlib
+import os
+import tempfile
+from pathlib import Path
+
+import pytest
+from click.testing import CliRunner
+
+from apm_cli.cli import cli
+
+
+class TestDepsCleanCommand:
+    """Tests for apm deps clean --dry-run and --yes flags."""
+
+    def setup_method(self):
+        self.runner = CliRunner()
+        try:
+            self.original_dir = os.getcwd()
+        except FileNotFoundError:
+            self.original_dir = str(Path(__file__).parent.parent.parent)
+            os.chdir(self.original_dir)
+
+    def teardown_method(self):
+        try:
+            os.chdir(self.original_dir)
+        except (FileNotFoundError, OSError):
+            repo_root = Path(__file__).parent.parent.parent
+            os.chdir(str(repo_root))
+
+    @contextlib.contextmanager
+    def _chdir_tmp(self):
+        """Create a temp dir, chdir into it, restore CWD on exit."""
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            try:
+                os.chdir(tmp_dir)
+                yield Path(tmp_dir)
+            finally:
+                os.chdir(self.original_dir)
+
+    def _create_fake_apm_modules(self, root: Path) -> Path:
+        """Create a fake apm_modules/ with one installed package."""
+        pkg_dir = root / "apm_modules" / "testorg" / "testrepo"
+        pkg_dir.mkdir(parents=True)
+        (pkg_dir / "apm.yml").write_text("name: testrepo\n")
+        return root / "apm_modules"
+
+    def test_dry_run_leaves_apm_modules_intact(self):
+        """--dry-run must not remove apm_modules/."""
+        with self._chdir_tmp() as tmp:
+            apm_modules = self._create_fake_apm_modules(tmp)
+
+            result = self.runner.invoke(cli, ["deps", "clean", "--dry-run"])
+
+            assert result.exit_code == 0
+            assert apm_modules.exists(), "apm_modules/ must not be removed in dry-run mode"
+            assert "Dry run" in result.output
+
+    def test_dry_run_lists_packages(self):
+        """--dry-run should show the packages that would be removed."""
+        with self._chdir_tmp() as tmp:
+            self._create_fake_apm_modules(tmp)
+
+            result = self.runner.invoke(cli, ["deps", "clean", "--dry-run"])
+
+            assert result.exit_code == 0
+            assert "testorg/testrepo" in result.output
+
+    def test_yes_flag_skips_confirmation(self):
+        """--yes must remove apm_modules/ without an interactive prompt."""
+        with self._chdir_tmp() as tmp:
+            apm_modules = self._create_fake_apm_modules(tmp)
+
+            result = self.runner.invoke(cli, ["deps", "clean", "--yes"])
+
+            assert result.exit_code == 0
+            assert not apm_modules.exists(), "apm_modules/ must be removed when --yes is used"
+
+    def test_yes_short_flag_skips_confirmation(self):
+        """-y short flag must also skip confirmation."""
+        with self._chdir_tmp() as tmp:
+            apm_modules = self._create_fake_apm_modules(tmp)
+
+            result = self.runner.invoke(cli, ["deps", "clean", "-y"])
+
+            assert result.exit_code == 0
+            assert not apm_modules.exists()
+
+    def test_no_apm_modules_reports_already_clean(self):
+        """When apm_modules/ does not exist the command should exit cleanly."""
+        with self._chdir_tmp():
+            result = self.runner.invoke(cli, ["deps", "clean"])
+
+            assert result.exit_code == 0
+            assert "already clean" in result.output
+
+    def test_dry_run_no_apm_modules_reports_already_clean(self):
+        """--dry-run with no apm_modules/ should also exit cleanly."""
+        with self._chdir_tmp():
+            result = self.runner.invoke(cli, ["deps", "clean", "--dry-run"])
+
+            assert result.exit_code == 0
+            assert "already clean" in result.output
diff --git a/uv.lock b/uv.lock
index 5ad4ef367..0683442d8 100644
--- a/uv.lock
+++ b/uv.lock
@@ -179,7 +179,7 @@ wheels = [
 
 [[package]]
 name = "apm-cli"
-version = "0.8.3"
+version = "0.8.4"
 source = { editable = "." }
 dependencies = [
     { name = "click" },