Fix environment variable precedence for tenant configuration

Tenant-specific environment variables now properly override application.env
template variables. Previously, the application.env templates were applied
after tenant env vars, causing them to overwrite tenant-specific settings.

This ensures tenants can override default database paths and other settings
as needed.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: rubys

cmd/navigator/main.go

@@ -1678,11 +1678,6 @@ func ParseYAML(content []byte) (*Config, error) {
 			Hooks:            tenant.Hooks, // Copy tenant-specific hooks
 		}
 
-		// Copy tenant environment variables
-		for k, v := range tenant.Env {
-			location.EnvVars[k] = v
-		}
-
 		// Add variables from applications.env that need substitution (unless it's a special tenant)
 		if !tenant.Special {
 			for varName, template := range yamlConfig.Applications.Env {
@@ -1694,6 +1689,11 @@ func ParseYAML(content []byte) (*Config, error) {
 			}
 		}
 
+		// Copy tenant environment variables (these should override application env)
+		for k, v := range tenant.Env {
+			location.EnvVars[k] = v
+		}
+
 		if tenant.Root != "" {
 			location.Root = tenant.Root
 		} else if yamlConfig.Server.PublicDir != "" {