Add system dependencies support for tools

Tools can now declare system-level package dependencies (apt, brew, pacman, dnf)
that get checked and optionally installed when the tool is installed or run.

Features:
- SystemDependency dataclass with short form (string) and long form (dict)
- New system_deps.py module with platform detection and installation
- `cmdforge system-deps <tool>` command to check/install system packages
- `cmdforge check` now shows both CmdForge and system dependencies
- `cmdforge registry install` prompts for system dep installation
- GUI: System Dependencies section in Tool Builder with add/edit dialog
- Runner warns about missing system deps before execution
- Integration with project install (manifest and lock-based)

Also includes:
- Quote paths in wrapper scripts for spaces support
- Tests for value type preservation in code steps
- Unskip invalid tool name test

Co-Authored-By: Claude Opus 4.5 <[email protected]>

tests/test_runner.py

@@ -92,6 +92,21 @@ Line 3: {var1} again"""
         result = substitute_variables("Count: {n}", {"n": 42})
         assert result == "Count: 42"
 
+    def test_zero_value_preserved(self):
+        """Zero should be preserved, not converted to empty string."""
+        result = substitute_variables("Count: {n}", {"n": 0})
+        assert result == "Count: 0"
+
+    def test_false_value_preserved(self):
+        """False should be preserved, not converted to empty string."""
+        result = substitute_variables("Enabled: {flag}", {"flag": False})
+        assert result == "Enabled: False"
+
+    def test_true_value_preserved(self):
+        """True should be preserved as 'True'."""
+        result = substitute_variables("Enabled: {flag}", {"flag": True})
+        assert result == "Enabled: True"
+
 
 class TestExecutePromptStep:
     """Tests for prompt step execution."""
@@ -179,9 +194,10 @@ class TestExecuteCodeStep:
         outputs, success = execute_code_step(step, variables)
 
         assert success is True
-        assert outputs["a"] == "1"
-        assert outputs["b"] == "2"
-        assert outputs["c"] == "3"
+        # Code step outputs preserve original types (integers here)
+        assert outputs["a"] == 1
+        assert outputs["b"] == 2
+        assert outputs["c"] == 3
 
     def test_code_uses_variables(self):
         step = CodeStep(
@@ -242,7 +258,43 @@ class TestExecuteCodeStep:
         outputs, success = execute_code_step(step, variables)
 
         assert success is True
-        assert outputs["result"] == "3"
+        # Code step outputs preserve original types (integer here)
+        assert outputs["result"] == 3
+
+    def test_code_preserves_complex_types(self):
+        """Code step outputs preserve lists/dicts for code→code workflows."""
+        step = CodeStep(
+            code="data = [1, 2, 3]\ninfo = {'key': 'value'}",
+            output_var="data, info"
+        )
+        variables = {"input": ""}
+
+        outputs, success = execute_code_step(step, variables)
+
+        assert success is True
+        assert outputs["data"] == [1, 2, 3]
+        assert outputs["info"] == {"key": "value"}
+
+    def test_code_to_code_workflow(self):
+        """Test that complex types can flow between code steps."""
+        # First step creates a list
+        step1 = CodeStep(
+            code="numbers = [1, 2, 3, 4, 5]",
+            output_var="numbers"
+        )
+        variables = {"input": ""}
+        outputs1, _ = execute_code_step(step1, variables)
+        variables.update(outputs1)
+
+        # Second step uses the list directly (no re-parsing needed)
+        step2 = CodeStep(
+            code="total = sum(numbers)",
+            output_var="total"
+        )
+        outputs2, success = execute_code_step(step2, variables)
+
+        assert success is True
+        assert outputs2["total"] == 15
 
 
 class TestRunTool: