diff --git a/src/modules/bmm/workflows/1-analysis/brainstorm-game/workflow.yaml b/src/modules/bmm/workflows/1-analysis/brainstorm-game/workflow.yaml
index 0bf71ab5..854501c9 100644
--- a/src/modules/bmm/workflows/1-analysis/brainstorm-game/workflow.yaml
+++ b/src/modules/bmm/workflows/1-analysis/brainstorm-game/workflow.yaml
@@ -25,6 +25,8 @@ web_bundle:
   name: "brainstorm-game"
   description: "Facilitate game brainstorming sessions by orchestrating the CIS brainstorming workflow with game-specific context, guidance, and additional game design techniques."
   author: "BMad"
+  instructions: "bmad/bmm/workflows/1-analysis/brainstorm-game/instructions.md"
+  template: false
   use_advanced_elicitation: true
   web_bundle_files:
     - "bmad/bmm/workflows/1-analysis/brainstorm-game/instructions.md"
diff --git a/src/modules/bmm/workflows/1-analysis/brainstorm-project/workflow.yaml b/src/modules/bmm/workflows/1-analysis/brainstorm-project/workflow.yaml
index 43b81da9..eeb2a0e4 100644
--- a/src/modules/bmm/workflows/1-analysis/brainstorm-project/workflow.yaml
+++ b/src/modules/bmm/workflows/1-analysis/brainstorm-project/workflow.yaml
@@ -24,6 +24,8 @@ web_bundle:
   name: "brainstorm-project"
   description: "Facilitate project brainstorming sessions by orchestrating the CIS brainstorming workflow with project-specific context and guidance."
   author: "BMad"
+  instructions: "bmad/bmm/workflows/1-analysis/brainstorm-project/instructions.md"
+  template: false
   use_advanced_elicitation: true
   web_bundle_files:
     - "bmad/bmm/workflows/1-analysis/brainstorm-project/instructions.md"
diff --git a/src/modules/bmm/workflows/1-analysis/game-brief/workflow.yaml b/src/modules/bmm/workflows/1-analysis/game-brief/workflow.yaml
index 601373c0..42fa84f7 100644
--- a/src/modules/bmm/workflows/1-analysis/game-brief/workflow.yaml
+++ b/src/modules/bmm/workflows/1-analysis/game-brief/workflow.yaml
@@ -34,6 +34,9 @@ web_bundle:
   name: "game-brief"
   description: "Interactive game brief creation workflow that guides users through defining their game vision with multiple input sources and conversational collaboration"
   author: "BMad"
+  instructions: "bmad/bmm/workflows/1-analysis/product-brief/instructions.md"
+  validation: "bmad/bmm/workflows/1-analysis/product-brief/checklist.md"
+  template: "bmad/bmm/workflows/1-analysis/game-brief/template.md"
   use_advanced_elicitation: true
   web_bundle_files:
     - "bmad/bmm/workflows/1-analysis/game-brief/template.md"
diff --git a/src/modules/bmm/workflows/1-analysis/product-brief/workflow.yaml b/src/modules/bmm/workflows/1-analysis/product-brief/workflow.yaml
index 5aa5fde2..f82eb7fe 100644
--- a/src/modules/bmm/workflows/1-analysis/product-brief/workflow.yaml
+++ b/src/modules/bmm/workflows/1-analysis/product-brief/workflow.yaml
@@ -33,6 +33,9 @@ web_bundle:
   name: "product-brief"
   description: "Interactive product brief creation workflow that guides users through defining their product vision with multiple input sources and conversational collaboration"
   author: "BMad"
+  instructions: "bmad/bmm/workflows/1-analysis/product-brief/instructions.md"
+  validation: "bmad/bmm/workflows/1-analysis/product-brief/checklist.md"
+  template: "bmad/bmm/workflows/1-analysis/product-brief/template.md"
   use_advanced_elicitation: true
   web_bundle_files:
     - "bmad/bmm/workflows/1-analysis/product-brief/template.md"
diff --git a/src/modules/bmm/workflows/1-analysis/research/workflow.yaml b/src/modules/bmm/workflows/1-analysis/research/workflow.yaml
index d463720a..1c0a9915 100644
--- a/src/modules/bmm/workflows/1-analysis/research/workflow.yaml
+++ b/src/modules/bmm/workflows/1-analysis/research/workflow.yaml
@@ -152,6 +152,8 @@ web_bundle:
   name: "research"
   description: "Adaptive research workflow supporting multiple research types: market research, deep research prompt generation, technical/architecture evaluation, competitive intelligence, user research, and domain analysis"
   author: "BMad"
+  instructions: "bmad/bmm/workflows/1-analysis/research/instructions-router.md" # Router loads specific instruction sets
+  validation: "bmad/bmm/workflows/1-analysis/research/checklist.md"
   use_advanced_elicitation: true
   web_bundle_files:
     - "bmad/bmm/workflows/1-analysis/research/instructions-router.md"
@@ -162,3 +164,82 @@ web_bundle:
     - "bmad/bmm/workflows/1-analysis/research/template-deep-prompt.md"
     - "bmad/bmm/workflows/1-analysis/research/template-technical.md"
     - "bmad/bmm/workflows/1-analysis/research/checklist.md"
+  # Workflow configuration
+  interactive: true # User checkpoints throughout
+  autonomous: false # Requires user input
+  allow_parallel: true # Can run research tasks in parallel
+
+  # Research frameworks available (context dependent)
+  frameworks:
+    market:
+      - "TAM/SAM/SOM Analysis"
+      - "Porter's Five Forces"
+      - "Jobs-to-be-Done"
+      - "Technology Adoption Lifecycle"
+      - "SWOT Analysis"
+      - "Value Chain Analysis"
+    technical:
+      - "Trade-off Analysis"
+      - "Architecture Decision Records (ADR)"
+      - "Technology Radar"
+      - "Comparison Matrix"
+      - "Cost-Benefit Analysis"
+    deep_prompt:
+      - "ChatGPT Deep Research Best Practices"
+      - "Gemini Deep Research Framework"
+      - "Grok DeepSearch Optimization"
+      - "Claude Projects Methodology"
+      - "Iterative Prompt Refinement"
+
+  # Data sources (for web research)
+  data_sources:
+    - "Industry reports and publications"
+    - "Government statistics and databases"
+    - "Financial reports and SEC filings"
+    - "News articles and press releases"
+    - "Academic research papers"
+    - "Technical documentation and RFCs"
+    - "GitHub repositories and discussions"
+    - "Stack Overflow and developer forums"
+    - "Market research firm reports"
+    - "Social media and communities"
+    - "Patent databases"
+    - "Benchmarking studies"
+  # Research types supported
+  research_types:
+    market:
+      name: "Market Research"
+      description: "Comprehensive market analysis with TAM/SAM/SOM"
+      instructions: "bmad/bmm/workflows/1-analysis/research/instructions-market.md"
+      template: "bmad/bmm/workflows/1-analysis/research/template-market.md"
+      output: "{market_output}"
+    deep_prompt:
+      name: "Deep Research Prompt Generator"
+      description: "Generate optimized prompts for AI research platforms"
+      instructions: "bmad/bmm/workflows/1-analysis/research/instructions-deep-prompt.md"
+      template: "bmad/bmm/workflows/1-analysis/research/template-deep-prompt.md"
+      output: "{deep_prompt_output}"
+    technical:
+      name: "Technical/Architecture Research"
+      description: "Technology evaluation and architecture pattern research"
+      instructions: "bmad/bmm/workflows/1-analysis/research/instructions-technical.md"
+      template: "bmad/bmm/workflows/1-analysis/research/template-technical.md"
+      output: "{technical_output}"
+    competitive:
+      name: "Competitive Intelligence"
+      description: "Deep competitor analysis"
+      instructions: "bmad/bmm/workflows/1-analysis/research/instructions-market.md" # Uses market with competitive focus
+      template: "bmad/bmm/workflows/1-analysis/research/template-market.md"
+      output: "{output_folder}/competitive-intelligence-{{date}}.md"
+    user:
+      name: "User Research"
+      description: "Customer insights and persona development"
+      instructions: "bmad/bmm/workflows/1-analysis/research/instructions-market.md" # Uses market with user focus
+      template: "bmad/bmm/workflows/1-analysis/research/template-market.md"
+      output: "{output_folder}/user-research-{{date}}.md"
+    domain:
+      name: "Domain/Industry Research"
+      description: "Industry and domain deep dives"
+      instructions: "bmad/bmm/workflows/1-analysis/research/instructions-market.md" # Uses market with domain focus
+      template: "bmad/bmm/workflows/1-analysis/research/template-market.md"
+      output: "{output_folder}/domain-research-{{date}}.md"
diff --git a/src/modules/bmm/workflows/2-plan/workflow.yaml b/src/modules/bmm/workflows/2-plan/workflow.yaml
index ddebeda7..45f5c6ce 100644
--- a/src/modules/bmm/workflows/2-plan/workflow.yaml
+++ b/src/modules/bmm/workflows/2-plan/workflow.yaml
@@ -64,6 +64,30 @@ web_bundle:
   description: "Scale-adaptive project planning workflow for all project levels (0-4). Automatically adjusts outputs based on project scope - from single atomic changes (Level 0: tech-spec only) to enterprise platforms (Level 4: full PRD + epics). Level 2-4 route to 3-solutioning workflow for architecture and tech specs. Generates appropriate planning artifacts for each level."
   author: "BMad"
   use_advanced_elicitation: true
+  # Do not load these directly - instructions-router.md will load the proper file based on project type/level when needed
+  instructions_sm: "bmad/bmm/workflows/2-plan/tech-spec/instructions-sm.md"
+  instructions_med: "bmad/bmm/workflows/2-plan/prd/instructions-med.md"
+  instructions_lg: "bmad/bmm/workflows/2-plan/prd/instructions-lg.md"
+  instructions_ux: "bmad/bmm/workflows/2-plan/ux/instructions-ux.md"
+  instructions_gdd: "bmad/bmm/workflows/2-plan/gdd/instructions-gdd.md"
+  instructions_narrative: "bmad/bmm/workflows/2-plan/narrative/instructions-narrative.md"
+  validation: "bmad/bmm/workflows/2-plan/checklist.md"
+  # Templates - Load these only when the instructions request loading them
+  prd_template: "{installed_path}/prd/prd-template.md"
+  analysis_template: "{installed_path}/prd/analysis-template.md"
+  epics_template: "{installed_path}/prd/epics-template.md"
+  tech_spec_template: "{installed_path}/tech-spec/tech-spec-template.md"
+  ux_spec_template: "{installed_path}/ux/ux-spec-template.md"
+  gdd_template: "{installed_path}/gdd/gdd-template.md"
+  game_types_csv: "{installed_path}/gdd/game-types.csv"
+  narrative_template: "{installed_path}/narrative/narrative-template.md"
+  # Scale parameters - adaptive by project level
+  scale_parameters:
+    level_0: "Single atomic change, tech-spec only"
+    level_1: "1-10 stories, 1 epic, minimal PRD + tech-spec"
+    level_2: "5-15 stories, 1-2 epics, focused PRD + tech-spec"
+    level_3: "12-40 stories, 2-5 epics, full PRD + architect handoff"
+    level_4: "40+ stories, 5+ epics, enterprise PRD + architect handoff"
   web_bundle_files:
     - "bmad/bmm/workflows/2-plan/instructions-router.md"
     - "bmad/bmm/workflows/2-plan/tech-spec/instructions-sm.md"
diff --git a/src/modules/bmm/workflows/3-solutioning/workflow.yaml b/src/modules/bmm/workflows/3-solutioning/workflow.yaml
index c7bf9e3a..46479543 100644
--- a/src/modules/bmm/workflows/3-solutioning/workflow.yaml
+++ b/src/modules/bmm/workflows/3-solutioning/workflow.yaml
@@ -59,12 +59,18 @@ project_types_questions: "{installed_path}/project-types"
 default_output_file: "{output_folder}/solution-architecture.md"
 
 # Additional workflow dependencies
-tech_spec_workflow: "{project-root}/bmad/bmm/workflows/3-solutioning/tech-spec"
+tech_spec_workflow: "{project-root}/bmad/bmm/workflows/3-solutioning/tech-spec/workflow.yaml"
 
 web_bundle:
   name: "solution-architecture"
   description: "Scale-adaptive solution architecture generation with dynamic template sections. Replaces legacy HLA workflow with modern BMAD Core compliance."
   author: "BMad Builder"
+  instructions: "bmad/bmm/workflows/3-solutioning/instructions.md"
+  validation: "bmad/bmm/workflows/3-solutioning/checklist.md"
+  tech_spec_workflow: "bmad/bmm/workflows/3-solutioning/tech-spec/workflow.yaml"
+  # Reference data files
+  architecture_registry: "bmad/bmm/workflows/3-solutioning/templates/registry.csv"
+  project_types_questions: "bmad/bmm/workflows/3-solutioning/project-types"
   web_bundle_files:
     - "bmad/bmm/workflows/3-solutioning/instructions.md"
     - "bmad/bmm/workflows/3-solutioning/checklist.md"
diff --git a/src/modules/bmm/workflows/4-implementation/correct-course/workflow.yaml b/src/modules/bmm/workflows/4-implementation/correct-course/workflow.yaml
index db8a4242..26d9129c 100644
--- a/src/modules/bmm/workflows/4-implementation/correct-course/workflow.yaml
+++ b/src/modules/bmm/workflows/4-implementation/correct-course/workflow.yaml
@@ -34,10 +34,4 @@ execution_modes:
   - incremental: "Recommended - Refine each edit with user collaboration"
   - batch: "Present all changes at once for review"
 
-web_bundle:
-  name: "correct-course"
-  description: "Navigate significant changes during sprint execution by analyzing impact, proposing solutions, and routing for implementation"
-  author: "BMad Method"
-  web_bundle_files:
-    - "bmad/bmm/workflows/4-implementation/correct-course/instructions.md"
-    - "bmad/bmm/workflows/4-implementation/correct-course/checklist.md"
+web_bundle: false
diff --git a/src/modules/bmm/workflows/4-implementation/create-story/workflow.yaml b/src/modules/bmm/workflows/4-implementation/create-story/workflow.yaml
index b3590b16..27017313 100644
--- a/src/modules/bmm/workflows/4-implementation/create-story/workflow.yaml
+++ b/src/modules/bmm/workflows/4-implementation/create-story/workflow.yaml
@@ -71,12 +71,4 @@ execution_hints:
   autonomous: true
   iterative: true
 
-web_bundle:
-  name: "create-story"
-  description: "Create the next user story markdown from epics/PRD and architecture, using a standard template and saving to the stories folder"
-  author: "BMad"
-  use_advanced_elicitation: true
-  web_bundle_files:
-    - "bmad/bmm/workflows/create-story/template.md"
-    - "bmad/bmm/workflows/create-story/instructions.md"
-    - "bmad/bmm/workflows/create-story/checklist.md"
+web_bundle: false
diff --git a/src/modules/bmm/workflows/4-implementation/dev-story/workflow.yaml b/src/modules/bmm/workflows/4-implementation/dev-story/workflow.yaml
index f165c173..dc84240f 100644
--- a/src/modules/bmm/workflows/4-implementation/dev-story/workflow.yaml
+++ b/src/modules/bmm/workflows/4-implementation/dev-story/workflow.yaml
@@ -52,11 +52,4 @@ execution_hints:
   autonomous: true # Proceed without user input unless blocked
   iterative: true
 
-web_bundle:
-  name: "dev-story"
-  description: "Execute a story by implementing tasks/subtasks, writing tests, validating, and updating the story file per acceptance criteria"
-  author: "BMad"
-  use_advanced_elicitation: true
-  web_bundle_files:
-    - "bmad/bmm/workflows/dev-story/instructions.md"
-    - "bmad/bmm/workflows/dev-story/checklist.md"
+web_bundle: false
diff --git a/src/modules/bmm/workflows/4-implementation/retrospective/workflow.yaml b/src/modules/bmm/workflows/4-implementation/retrospective/workflow.yaml
index 94e03a11..eff2d837 100644
--- a/src/modules/bmm/workflows/4-implementation/retrospective/workflow.yaml
+++ b/src/modules/bmm/workflows/4-implementation/retrospective/workflow.yaml
@@ -40,10 +40,4 @@ validation_required:
   - technical_health: "Is codebase in stable, maintainable state?"
   - blocker_resolution: "Any unresolved blockers that will impact next epic?"
 
-web_bundle:
-  name: "retrospective"
-  description: "Run after epic completion to review overall success, extract lessons learned, and explore if new information emerged that might impact the next epic"
-  author: "BMad"
-  use_advanced_elicitation: true
-  web_bundle_files:
-    - "bmad/bmm/workflows/4-implementation/retrospective/instructions.md"
+web_bundle: false
diff --git a/src/modules/bmm/workflows/4-implementation/review-story/workflow.yaml b/src/modules/bmm/workflows/4-implementation/review-story/workflow.yaml
index 4942eb20..f0daa0fe 100644
--- a/src/modules/bmm/workflows/4-implementation/review-story/workflow.yaml
+++ b/src/modules/bmm/workflows/4-implementation/review-story/workflow.yaml
@@ -98,11 +98,4 @@ execution_hints:
   autonomous: true # Proceed without user input unless blocked
   iterative: true
 
-web_bundle:
-  name: "review-story"
-  description: "Perform a Senior Developer Review on a completed story flagged Ready for Review, leveraging story-context, epic tech-spec, repo docs, MCP servers for latest best-practices, and web search as fallback. Appends structured review notes to the story."
-  author: "BMad"
-  use_advanced_elicitation: true
-  web_bundle_files:
-    - "bmad/bmm/workflows/review-story/instructions.md"
-    - "bmad/bmm/workflows/review-story/checklist.md"
+web_bundle: false
diff --git a/src/modules/bmm/workflows/4-implementation/story-context/workflow.yaml b/src/modules/bmm/workflows/4-implementation/story-context/workflow.yaml
index 6cdcfa6f..4de8f47a 100644
--- a/src/modules/bmm/workflows/4-implementation/story-context/workflow.yaml
+++ b/src/modules/bmm/workflows/4-implementation/story-context/workflow.yaml
@@ -55,12 +55,4 @@ execution_hints:
   autonomous: true
   iterative: true
 
-web_bundle:
-  name: "story-context"
-  description: "Assemble a dynamic Story Context XML by pulling latest documentation and existing code/library artifacts relevant to a drafted story"
-  author: "BMad"
-  use_advanced_elicitation: true
-  web_bundle_files:
-    - "bmad/bmm/workflows/story-context/context-template.xml"
-    - "bmad/bmm/workflows/story-context/instructions.md"
-    - "bmad/bmm/workflows/story-context/checklist.md"
+web_bundle: false
diff --git a/tools/cli/bundlers/web-bundler.js b/tools/cli/bundlers/web-bundler.js
index 407842ba..a97ae724 100644
--- a/tools/cli/bundlers/web-bundler.js
+++ b/tools/cli/bundlers/web-bundler.js
@@ -173,12 +173,17 @@ class WebBundler {
 
     // Resolve dependencies with warning tracking
     const dependencyWarnings = [];
-    const dependencies = await this.resolveAgentDependencies(agentXml, moduleName, dependencyWarnings);
+    const { dependencies, skippedWorkflows } = await this.resolveAgentDependencies(agentXml, moduleName, dependencyWarnings);
 
     if (dependencyWarnings.length > 0) {
       this.stats.warnings.push({ agent: agentName, warnings: dependencyWarnings });
     }
 
+    // Remove commands for skipped workflows from agent XML
+    if (skippedWorkflows.length > 0) {
+      agentXml = this.removeSkippedWorkflowCommands(agentXml, skippedWorkflows);
+    }
+
     // Build the bundle (no manifests for individual agents)
     const bundle = this.buildAgentBundle(agentXml, dependencies);
 
@@ -266,6 +271,7 @@ class WebBundler {
   async resolveAgentDependencies(agentXml, moduleName, warnings = []) {
     const dependencies = new Map();
     const processed = new Set();
+    const skippedWorkflows = [];
 
     // Extract file references from agent XML
     const { refs, workflowRefs } = this.extractFileReferences(agentXml);
@@ -277,10 +283,13 @@ class WebBundler {
 
     // Process workflow references with special handling
     for (const workflowRef of workflowRefs) {
-      await this.processWorkflowDependency(workflowRef, dependencies, processed, moduleName, warnings);
+      const result = await this.processWorkflowDependency(workflowRef, dependencies, processed, moduleName, warnings);
+      if (result && result.skipped) {
+        skippedWorkflows.push(workflowRef);
+      }
     }
 
-    return dependencies;
+    return { dependencies, skippedWorkflows };
   }
 
   /**
@@ -330,6 +339,27 @@ class WebBundler {
     return { refs: [...refs], workflowRefs: [...workflowRefs] };
   }
 
+  /**
+   * Remove commands from agent XML that reference skipped workflows
+   */
+  removeSkippedWorkflowCommands(agentXml, skippedWorkflows) {
+    let modifiedXml = agentXml;
+
+    // For each skipped workflow, find and remove the corresponding <c> command
+    for (const workflowPath of skippedWorkflows) {
+      // Match: <c cmd="..." run-workflow="workflowPath">...</c>
+      // Need to escape special regex characters in the path
+      const escapedPath = workflowPath.replaceAll(/[.*+?^${}()|[\]\\]/g, String.raw`\$&`);
+
+      // Pattern to match the command line with this workflow
+      const pattern = new RegExp(`\\s*<c\\s+cmd="[^"]*"\\s+run-workflow="[^"]*${escapedPath}"[^>]*>.*?</c>\\s*`, 'gs');
+
+      modifiedXml = modifiedXml.replace(pattern, '');
+    }
+
+    return modifiedXml;
+  }
+
   /**
    * Process a file dependency recursively
    */
@@ -504,7 +534,7 @@ class WebBundler {
   async processWorkflowDependency(workflowPath, dependencies, processed, moduleName, warnings = []) {
     // Skip if already processed
     if (processed.has(workflowPath)) {
-      return;
+      return { skipped: false };
     }
     processed.add(workflowPath);
 
@@ -513,7 +543,7 @@ class WebBundler {
 
     if (!actualPath || !(await fs.pathExists(actualPath))) {
       warnings.push(workflowPath);
-      return;
+      return { skipped: true };
     }
 
     // Read and parse YAML file
@@ -524,12 +554,28 @@ class WebBundler {
       workflowConfig = yaml.load(yamlContent);
     } catch (error) {
       warnings.push(`${workflowPath} (invalid YAML: ${error.message})`);
-      return;
+      return { skipped: true };
     }
 
-    // Include the YAML file itself, wrapped in XML
+    // Check if web_bundle is explicitly set to false
+    if (workflowConfig.web_bundle === false) {
+      // Mark this workflow as skipped so we can remove the command from agent
+      return { skipped: true, workflowPath };
+    }
+
+    // Create YAML content with only web_bundle section (flattened)
+    let bundleYamlContent;
+    if (workflowConfig.web_bundle && typeof workflowConfig.web_bundle === 'object') {
+      // Only include the web_bundle content, flattened to root level
+      bundleYamlContent = yaml.dump(workflowConfig.web_bundle);
+    } else {
+      // If no web_bundle section, include full YAML
+      bundleYamlContent = yamlContent;
+    }
+
+    // Include the YAML file with only web_bundle content, wrapped in XML
     const yamlId = workflowPath.replace(/^{project-root}\//, '');
-    const wrappedYaml = this.wrapContentInXml(yamlContent, yamlId, 'yaml');
+    const wrappedYaml = this.wrapContentInXml(bundleYamlContent, yamlId, 'yaml');
     dependencies.set(yamlId, wrappedYaml);
 
     // Always include core workflow task when processing workflows
@@ -566,6 +612,8 @@ class WebBundler {
         dependencies.set(bundleFilePath, wrappedContent);
       }
     }
+
+    return { skipped: false };
   }
 
   /**
diff --git a/tools/cli/installers/lib/modules/manager.js b/tools/cli/installers/lib/modules/manager.js
index c8343eeb..61df4a35 100644
--- a/tools/cli/installers/lib/modules/manager.js
+++ b/tools/cli/installers/lib/modules/manager.js
@@ -271,9 +271,15 @@ class ModuleManager {
         }
       }
 
-      // Copy the file
-      await fs.ensureDir(path.dirname(targetFile));
-      await fs.copy(sourceFile, targetFile, { overwrite: true });
+      // Check if this is a workflow.yaml file
+      if (file.endsWith('workflow.yaml')) {
+        await fs.ensureDir(path.dirname(targetFile));
+        await this.copyWorkflowYamlStripped(sourceFile, targetFile);
+      } else {
+        // Copy the file normally
+        await fs.ensureDir(path.dirname(targetFile));
+        await fs.copy(sourceFile, targetFile, { overwrite: true });
+      }
 
       // Track the file if callback provided
       if (fileTrackingCallback) {
@@ -282,6 +288,91 @@ class ModuleManager {
     }
   }
 
+  /**
+   * Copy workflow.yaml file with web_bundle section stripped
+   * Preserves comments, formatting, and line breaks
+   * @param {string} sourceFile - Source workflow.yaml file path
+   * @param {string} targetFile - Target workflow.yaml file path
+   */
+  async copyWorkflowYamlStripped(sourceFile, targetFile) {
+    // Read the source YAML file
+    let yamlContent = await fs.readFile(sourceFile, 'utf8');
+
+    try {
+      // First check if web_bundle exists by parsing
+      const workflowConfig = yaml.load(yamlContent);
+
+      if (workflowConfig.web_bundle === undefined) {
+        // No web_bundle section, just copy as-is
+        await fs.writeFile(targetFile, yamlContent, 'utf8');
+        return;
+      }
+
+      // Remove web_bundle section using regex to preserve formatting
+      // Match the web_bundle key and all its content (including nested items)
+      // This handles both web_bundle: false and web_bundle: {...}
+
+      // Find the line that starts web_bundle
+      const lines = yamlContent.split('\n');
+      let startIdx = -1;
+      let endIdx = -1;
+      let baseIndent = 0;
+
+      // Find the start of web_bundle section
+      for (const [i, line] of lines.entries()) {
+        const match = line.match(/^(\s*)web_bundle:/);
+        if (match) {
+          startIdx = i;
+          baseIndent = match[1].length;
+          break;
+        }
+      }
+
+      if (startIdx === -1) {
+        // web_bundle not found in text (shouldn't happen), copy as-is
+        await fs.writeFile(targetFile, yamlContent, 'utf8');
+        return;
+      }
+
+      // Find the end of web_bundle section
+      // It ends when we find a line with same or less indentation that's not empty/comment
+      endIdx = startIdx;
+      for (let i = startIdx + 1; i < lines.length; i++) {
+        const line = lines[i];
+
+        // Skip empty lines and comments
+        if (line.trim() === '' || line.trim().startsWith('#')) {
+          continue;
+        }
+
+        // Check indentation
+        const indent = line.match(/^(\s*)/)[1].length;
+        if (indent <= baseIndent) {
+          // Found next section at same or lower indentation
+          endIdx = i - 1;
+          break;
+        }
+      }
+
+      // If we didn't find an end, it goes to end of file
+      if (endIdx === startIdx) {
+        endIdx = lines.length - 1;
+      }
+
+      // Remove the web_bundle section (including the line before if it's just a blank line)
+      const newLines = [...lines.slice(0, startIdx), ...lines.slice(endIdx + 1)];
+
+      // Clean up any double blank lines that might result
+      const strippedYaml = newLines.join('\n').replaceAll(/\n\n\n+/g, '\n\n');
+
+      await fs.writeFile(targetFile, strippedYaml, 'utf8');
+    } catch {
+      // If anything fails, just copy the file as-is
+      console.warn(chalk.yellow(`  Warning: Could not process ${path.basename(sourceFile)}, copying as-is`));
+      await fs.copy(sourceFile, targetFile, { overwrite: true });
+    }
+  }
+
   /**
    * Process agent files to inject activation block
    * @param {string} modulePath - Path to installed module