Fix: Only use template in keep run when --template flag is explicitly provided

The run command was incorrectly using templates when the --template option was not provided. Now it only uses templates when the user explicitly includes the --template flag.

Author: jszobody

docs/guide/deployment/runtime-injection.md

@@ -101,14 +101,14 @@ With Docker Compose, environment variables are automatically passed through when
 ## Template-Based Injection
 
 ```bash
-# Generate template from existing secrets
-keep template:add prod.env --stage=production
-
-# Use specific template
-keep run --vault=ssm --stage=production --template=env/prod.env -- npm start
+# Generate template from existing secrets in env/production.env
+keep template:add --stage=production
 
 # Auto-discover template (looks for env/{stage}.env)
 keep run --vault=ssm --stage=production --template -- npm start
+
+# Use specific template
+keep run --vault=ssm --stage=production --template=env/prod.env -- npm start
 ```
 
 See [Managing Templates](./templates.md) for detailed template documentation.

src/Commands/RunCommand.php

@@ -134,11 +134,11 @@ protected function buildEnvironment(string $stage, string $vaultSlug): array
         $inheritCurrent = !$this->option('no-inherit');
 
         // Handle template-based injection
-        // If --template is explicitly provided, use template mode
+        // Only use template if --template option is explicitly provided
         // But only if no filters are specified (filters only work in direct mode)
         $hasFilters = $this->option('only') || $this->option('except');
 
-        if (!$hasFilters && $this->hasOption('template') && $this->option('template') !== false) {
+        if (!$hasFilters && $templateOption !== null) {
             // If template value is empty string, it means auto-discovery
             $templatePath = $templateOption === '' ? null : $templateOption;
             return $this->buildFromTemplate($templatePath, $stage, $vaultSlug, $inheritCurrent);