Fix PATH ordering to prioritize mvx-managed tools over system tools

- Store system PATH separately and append after tool directories
- Ensures mvx-managed Java 17 takes priority over system Java 21
- Fixes failing TestShellCommand/run_java_version test
- Tool directories are now added first, system directories appended
- Maintains backward compatibility with existing environment setup

This resolves the issue where system tools (like SDKMAN Java) were
taking priority over mvx-managed tools due to PATH ordering.

Author: gnodet

pkg/tools/environment.go

@@ -11,7 +11,7 @@ import (
 
 // EnvironmentManager provides safe environment variable management with special PATH handling
 type EnvironmentManager struct {
-	envVars map[string]string
+	envVars  map[string]string
 	pathDirs []string
 }
 
@@ -26,7 +26,7 @@ func NewEnvironmentManager() *EnvironmentManager {
 // NewEnvironmentManagerFromMap creates a new environment manager from an existing map
 func NewEnvironmentManagerFromMap(envVars map[string]string) *EnvironmentManager {
 	em := NewEnvironmentManager()
-	
+
 	for key, value := range envVars {
 		if key == "PATH" {
 			// Parse PATH into directories
@@ -37,7 +37,7 @@ func NewEnvironmentManagerFromMap(envVars map[string]string) *EnvironmentManager
 			em.envVars[key] = value
 		}
 	}
-	
+
 	return em
 }
 
@@ -64,18 +64,18 @@ func (em *EnvironmentManager) AddToPath(dir string) {
 	if dir == "" {
 		return
 	}
-	
+
 	// Clean the path
 	dir = filepath.Clean(dir)
-	
+
 	// Check if already present
 	for _, existing := range em.pathDirs {
 		if existing == dir {
 			util.LogVerbose("Directory %s already in PATH", dir)
 			return
 		}
 	}
-	
+
 	// Prepend to PATH
 	em.pathDirs = append([]string{dir}, em.pathDirs...)
 	util.LogVerbose("Added directory to PATH: %s", dir)
@@ -86,18 +86,18 @@ func (em *EnvironmentManager) AppendToPath(dir string) {
 	if dir == "" {
 		return
 	}
-	
+
 	// Clean the path
 	dir = filepath.Clean(dir)
-	
+
 	// Check if already present
 	for _, existing := range em.pathDirs {
 		if existing == dir {
 			util.LogVerbose("Directory %s already in PATH", dir)
 			return
 		}
 	}
-	
+
 	// Append to PATH
 	em.pathDirs = append(em.pathDirs, dir)
 	util.LogVerbose("Appended directory to PATH: %s", dir)
@@ -111,33 +111,33 @@ func (em *EnvironmentManager) GetPath() string {
 // ToMap converts the environment manager to a map[string]string
 func (em *EnvironmentManager) ToMap() map[string]string {
 	result := make(map[string]string)
-	
+
 	// Copy all environment variables
 	for key, value := range em.envVars {
 		result[key] = value
 	}
-	
+
 	// Add PATH
 	if len(em.pathDirs) > 0 {
 		result["PATH"] = em.GetPath()
 	}
-	
+
 	return result
 }
 
 // ToSlice converts the environment manager to []string in "KEY=VALUE" format
 func (em *EnvironmentManager) ToSlice() []string {
 	var result []string
-	
+
 	// Add all environment variables
 	for key, value := range em.envVars {
 		result = append(result, fmt.Sprintf("%s=%s", key, value))
 	}
-	
+
 	// Add PATH
 	if len(em.pathDirs) > 0 {
 		result = append(result, fmt.Sprintf("PATH=%s", em.GetPath()))
 	}
-	
+
 	return result
 }

pkg/tools/manager.go

@@ -849,20 +849,17 @@ func (m *Manager) EnsureTool(toolName string, cfg config.ToolConfig) (string, er
 
 // SetupEnvironment sets up environment variables for installed tools
 func (m *Manager) SetupEnvironment(cfg *config.Config) (map[string]string, error) {
-	// Create environment manager starting with system environment
+	// Create environment manager
 	envManager := NewEnvironmentManager()
 
-	// Add system environment variables first
+	// Add system environment variables first (except PATH - we'll handle that after tools)
+	var systemPath string
 	for _, envVar := range os.Environ() {
 		parts := strings.SplitN(envVar, "=", 2)
 		if len(parts) == 2 {
 			if parts[0] == "PATH" {
-				// Parse PATH into directories
-				if parts[1] != "" {
-					for _, dir := range strings.Split(parts[1], string(os.PathListSeparator)) {
-						envManager.AddToPath(dir)
-					}
-				}
+				// Store system PATH for later - we want tool paths to take priority
+				systemPath = parts[1]
 			} else {
 				envManager.SetEnv(parts[0], parts[1])
 			}
@@ -925,6 +922,15 @@ func (m *Manager) SetupEnvironment(cfg *config.Config) (map[string]string, error
 		}
 	}
 
+	// Add system PATH directories after tool directories (lower priority)
+	if systemPath != "" {
+		for _, dir := range strings.Split(systemPath, string(os.PathListSeparator)) {
+			if dir != "" {
+				envManager.AppendToPath(dir)
+			}
+		}
+	}
+
 	// Convert environment manager to map
 	return envManager.ToMap(), nil
 }