diff --git a/docs/src/content/docs/reference/cli-commands.md b/docs/src/content/docs/reference/cli-commands.md
index b89c1877..15c27d45 100644
--- a/docs/src/content/docs/reference/cli-commands.md
+++ b/docs/src/content/docs/reference/cli-commands.md
@@ -330,7 +330,7 @@ apm pack [OPTIONS]
 
 **Options:**
 - `-o, --output PATH` - Output directory (default: `./build`)
-- `-t, --target [copilot|vscode|claude|all]` - Filter files by target. Auto-detects from `apm.yml` if not specified. `vscode` is an alias for `copilot`
+- `-t, --target [vscode|copilot|claude|all]` - Filter files by target. Auto-detects from `apm.yml` if not specified. `copilot` is an alias for `vscode`
 - `--archive` - Produce a `.tar.gz` archive instead of a directory
 - `--dry-run` - List files that would be packed without writing anything
 - `--format [apm|plugin]` - Bundle format (default: `apm`)
@@ -567,17 +567,27 @@ 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
@@ -587,11 +597,11 @@ 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
@@ -619,7 +629,7 @@ apm mcp list [OPTIONS]
 ```
 
 **Options:**
-- `--limit INTEGER` - Number of results to show
+- `--limit INTEGER` - Number of results to show (default: 20)
 
 **Examples:**
 ```bash
@@ -1088,7 +1098,7 @@ 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.py b/src/apm_cli/commands/deps.py
index 17f4379f..8995f741 100644
--- a/src/apm_cli/commands/deps.py
+++ b/src/apm_cli/commands/deps.py
@@ -390,7 +390,9 @@ 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."""
     project_root = Path(".")
     apm_modules_path = project_root / "apm_modules"
@@ -399,21 +401,30 @@ def clean():
         _rich_info("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 ._helpers import _scan_installed_packages
+    packages = _scan_installed_packages(apm_modules_path)
+    package_count = len(packages)
     
-    _rich_warning(f"This will remove the entire apm_modules/ directory ({package_count} packages)")
+    if dry_run:
+        _rich_info(f"Dry run: would remove apm_modules/ ({package_count} package(s))")
+        for pkg in sorted(packages):
+            _rich_info(f"  - {pkg}")
+        return
     
-    # Confirmation prompt
-    try:
-        from rich.prompt import Confirm
-        confirm = Confirm.ask("Continue?")
-    except ImportError:
-        confirm = click.confirm("Continue?")
+    _rich_warning(f"This will remove the entire apm_modules/ directory ({package_count} package(s))")
     
-    if not confirm:
-        _rich_info("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:
+            _rich_info("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 f3881873..cdd102a1 100644
--- a/src/apm_cli/commands/install.py
+++ b/src/apm_cli/commands/install.py
@@ -300,7 +300,7 @@ def _validate_package_exists(package):
     "--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")
-@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 26a18f00..57afc6f1 100644
--- a/src/apm_cli/commands/mcp.py
+++ b/src/apm_cli/commands/mcp.py
@@ -288,7 +288,7 @@ def show(ctx, server_name):
 
 
 @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.pass_context
 def list(ctx, limit):
     """List all available MCP servers in the registry."""
diff --git a/src/apm_cli/commands/pack.py b/src/apm_cli/commands/pack.py
index 7b3833d4..4d3cdaf3 100644
--- a/src/apm_cli/commands/pack.py
+++ b/src/apm_cli/commands/pack.py
@@ -21,9 +21,9 @@
 @click.option(
     "--target",
     "-t",
-    type=click.Choice(["copilot", "vscode", "claude", "all"]),
+    type=click.Choice(["vscode", "copilot", "claude", "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 22bbadc8..8bd0fd18 100644
--- a/src/apm_cli/commands/runtime.py
+++ b/src/apm_cli/commands/runtime.py
@@ -147,9 +147,9 @@ 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."""
     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 00000000..bb12e6b1
--- /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 821fdafa..0026afbf 100644
--- a/uv.lock
+++ b/uv.lock
@@ -179,7 +179,7 @@ wheels = [
 
 [[package]]
 name = "apm-cli"
-version = "0.7.8"
+version = "0.7.9"
 source = { editable = "." }
 dependencies = [
     { name = "click" },