fix: reset skills array between runs and allow skill-only targets

- Reset this.skills and this.files in ManifestGenerator to prevent stale
  data when instance is reused across multiple manifest runs
- Allow targets with empty artifact_types to still install verbatim
  skills by checking skill_format before short-circuiting

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tools/cli/installers/lib/core/manifest-generator.js

@@ -105,6 +105,9 @@ class ManifestGenerator {
     // Filter out any undefined/null values from IDE list
     this.selectedIdes = resolvedIdes.filter((ide) => ide && typeof ide === 'string');
 
+    // Reset files list (defensive: prevent stale data if instance is reused)
+    this.files = [];
+
     // Collect workflow data
     await this.collectWorkflows(selectedModules);
 
@@ -144,6 +147,7 @@ class ManifestGenerator {
    */
   async collectWorkflows(selectedModules) {
     this.workflows = [];
+    this.skills = [];
 
     // Use updatedModules which already includes deduplicated 'core' + selectedModules
     for (const moduleName of this.updatedModules) {

tools/cli/installers/lib/ide/_config-driven.js

@@ -117,9 +117,10 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
   async installToTarget(projectDir, bmadDir, config, options) {
     const { target_dir, template_type, artifact_types } = config;
 
-    // Skip targets with explicitly empty artifact_types array
+    // Skip targets with explicitly empty artifact_types and no verbatim skills
     // This prevents creating empty directories when no artifacts will be written
-    if (Array.isArray(artifact_types) && artifact_types.length === 0) {
+    const skipStandardArtifacts = Array.isArray(artifact_types) && artifact_types.length === 0;
+    if (skipStandardArtifacts && !config.skill_format) {
       return { success: true, results: { agents: 0, workflows: 0, tasks: 0, tools: 0, skills: 0 } };
     }
 
@@ -129,6 +130,8 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
     const selectedModules = options.selectedModules || [];
     const results = { agents: 0, workflows: 0, tasks: 0, tools: 0, skills: 0 };
 
+    // Install standard artifacts (agents, workflows, tasks, tools)
+    if (!skipStandardArtifacts) {
       // Install agents
       if (!artifact_types || artifact_types.includes('agents')) {
         const agentGen = new AgentCommandGenerator(this.bmadFolderName);
@@ -151,6 +154,7 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
         results.tasks = taskToolResult.tasks || 0;
         results.tools = taskToolResult.tools || 0;
       }
+    }
 
     // Install verbatim skills (type: skill)
     if (config.skill_format) {