diff --git a/tools/cli/commands/build.js b/tools/cli/commands/build.js
index ec5c6dec..54d24c9a 100644
--- a/tools/cli/commands/build.js
+++ b/tools/cli/commands/build.js
@@ -166,8 +166,66 @@ async function buildAllAgents(projectDir, force = false) {
   let builtCount = 0;
   let skippedCount = 0;
 
-  // First, build standalone agents in bmad/agents/
-  const standaloneAgentsDir = path.join(projectDir, 'bmad', 'agents');
+  // Detect .bmad folder name (could be .bmad or bmad)
+  const bmadFolder = (await fs.pathExists(path.join(projectDir, '.bmad'))) ? '.bmad' : 'bmad';
+  const bmadDir = path.join(projectDir, bmadFolder);
+
+  // Build agents from ALL module directories in .bmad/ (including custom, hde, etc.)
+  if (await fs.pathExists(bmadDir)) {
+    console.log(chalk.cyan('\nScanning all modules in .bmad/...'));
+    const moduleEntries = await fs.readdir(bmadDir, { withFileTypes: true });
+
+    for (const moduleEntry of moduleEntries) {
+      // Skip special directories
+      if (!moduleEntry.isDirectory() || moduleEntry.name === '_cfg' || moduleEntry.name === 'docs') {
+        continue;
+      }
+
+      const modulePath = path.join(bmadDir, moduleEntry.name);
+      const agentsPath = path.join(modulePath, 'agents');
+
+      // Check if this module has an agents/ directory
+      if (!(await fs.pathExists(agentsPath))) {
+        continue;
+      }
+
+      console.log(chalk.cyan(`\nBuilding agents in ${moduleEntry.name} module...`));
+      const agentFiles = await fs.readdir(agentsPath);
+
+      for (const file of agentFiles) {
+        if (!file.endsWith('.agent.yaml')) {
+          continue;
+        }
+
+        const agentName = file.replace('.agent.yaml', '');
+        const agentYamlPath = path.join(agentsPath, file);
+        const outputPath = path.join(agentsPath, `${agentName}.md`);
+
+        // Check if rebuild needed
+        if (!force && (await fs.pathExists(outputPath))) {
+          const needsRebuild = await checkIfNeedsRebuild(agentYamlPath, outputPath, projectDir, agentName);
+          if (!needsRebuild) {
+            console.log(chalk.dim(`  ${agentName}: up to date`));
+            skippedCount++;
+            continue;
+          }
+        }
+
+        console.log(chalk.cyan(`  Building ${agentName}...`));
+
+        const customizePath = path.join(bmadDir, '_cfg', 'agents', `${moduleEntry.name}-${agentName}.customize.yaml`);
+        const customizeExists = await fs.pathExists(customizePath);
+
+        await builder.buildAgent(agentYamlPath, customizeExists ? customizePath : null, outputPath, { includeMetadata: true });
+
+        console.log(chalk.green(`  ✓ ${agentName} (${moduleEntry.name})`));
+        builtCount++;
+      }
+    }
+  }
+
+  // Also build standalone agents in bmad/agents/ (top-level, for backward compatibility)
+  const standaloneAgentsDir = path.join(projectDir, bmadFolder, 'agents');
   if (await fs.pathExists(standaloneAgentsDir)) {
     console.log(chalk.cyan('\nBuilding standalone agents...'));
     const agentDirs = await fs.readdir(standaloneAgentsDir);
@@ -205,7 +263,7 @@ async function buildAllAgents(projectDir, force = false) {
 
       console.log(chalk.cyan(`  Building standalone agent ${agentName}...`));
 
-      const customizePath = path.join(projectDir, 'bmad', '_cfg', 'agents', `${agentName}.customize.yaml`);
+      const customizePath = path.join(projectDir, bmadFolder, '_cfg', 'agents', `${agentName}.customize.yaml`);
       const customizeExists = await fs.pathExists(customizePath);
 
       await builder.buildAgent(agentYamlPath, customizeExists ? customizePath : null, outputPath, { includeMetadata: true });
@@ -275,8 +333,52 @@ async function checkBuildStatus(projectDir) {
   const needsRebuild = [];
   const upToDate = [];
 
-  // Check standalone agents in bmad/agents/
-  const standaloneAgentsDir = path.join(projectDir, 'bmad', 'agents');
+  // Detect .bmad folder name (could be .bmad or bmad)
+  const bmadFolder = (await fs.pathExists(path.join(projectDir, '.bmad'))) ? '.bmad' : 'bmad';
+  const bmadDir = path.join(projectDir, bmadFolder);
+
+  // Check agents in ALL module directories in .bmad/
+  if (await fs.pathExists(bmadDir)) {
+    const moduleEntries = await fs.readdir(bmadDir, { withFileTypes: true });
+
+    for (const moduleEntry of moduleEntries) {
+      // Skip special directories
+      if (!moduleEntry.isDirectory() || moduleEntry.name === '_cfg' || moduleEntry.name === 'docs') {
+        continue;
+      }
+
+      const modulePath = path.join(bmadDir, moduleEntry.name);
+      const agentsPath = path.join(modulePath, 'agents');
+
+      // Check if this module has an agents/ directory
+      if (!(await fs.pathExists(agentsPath))) {
+        continue;
+      }
+
+      const agentFiles = await fs.readdir(agentsPath);
+
+      for (const file of agentFiles) {
+        if (!file.endsWith('.agent.yaml')) {
+          continue;
+        }
+
+        const agentName = file.replace('.agent.yaml', '');
+        const agentYamlPath = path.join(agentsPath, file);
+        const outputPath = path.join(agentsPath, `${agentName}.md`);
+
+        if (!(await fs.pathExists(outputPath))) {
+          needsRebuild.push(`${agentName} (${moduleEntry.name})`);
+        } else if (await checkIfNeedsRebuild(agentYamlPath, outputPath, projectDir, agentName)) {
+          needsRebuild.push(`${agentName} (${moduleEntry.name})`);
+        } else {
+          upToDate.push(`${agentName} (${moduleEntry.name})`);
+        }
+      }
+    }
+  }
+
+  // Check standalone agents in bmad/agents/ (top-level)
+  const standaloneAgentsDir = path.join(projectDir, bmadFolder, 'agents');
   if (await fs.pathExists(standaloneAgentsDir)) {
     const agentDirs = await fs.readdir(standaloneAgentsDir);
 
@@ -406,8 +508,42 @@ async function checkIfNeedsRebuild(yamlPath, outputPath, projectDir, agentName)
  * List available agents
  */
 async function listAvailableAgents(projectDir) {
-  // List standalone agents first
-  const standaloneAgentsDir = path.join(projectDir, 'bmad', 'agents');
+  // Detect .bmad folder name (could be .bmad or bmad)
+  const bmadFolder = (await fs.pathExists(path.join(projectDir, '.bmad'))) ? '.bmad' : 'bmad';
+  const bmadDir = path.join(projectDir, bmadFolder);
+
+  // List agents from ALL module directories in .bmad/
+  if (await fs.pathExists(bmadDir)) {
+    console.log(chalk.dim('     Module agents:'));
+    const moduleEntries = await fs.readdir(bmadDir, { withFileTypes: true });
+
+    for (const moduleEntry of moduleEntries) {
+      // Skip special directories
+      if (!moduleEntry.isDirectory() || moduleEntry.name === '_cfg' || moduleEntry.name === 'docs') {
+        continue;
+      }
+
+      const modulePath = path.join(bmadDir, moduleEntry.name);
+      const agentsPath = path.join(modulePath, 'agents');
+
+      // Check if this module has an agents/ directory
+      if (!(await fs.pathExists(agentsPath))) {
+        continue;
+      }
+
+      const agentFiles = await fs.readdir(agentsPath);
+
+      for (const file of agentFiles) {
+        if (file.endsWith('.agent.yaml')) {
+          const agentName = file.replace('.agent.yaml', '');
+          console.log(chalk.dim(`       - ${agentName} (${moduleEntry.name})`));
+        }
+      }
+    }
+  }
+
+  // List standalone agents
+  const standaloneAgentsDir = path.join(projectDir, bmadFolder, 'agents');
   if (await fs.pathExists(standaloneAgentsDir)) {
     console.log(chalk.dim('     Standalone agents:'));
     const agentDirs = await fs.readdir(standaloneAgentsDir);
diff --git a/tools/cli/installers/lib/core/installer.js b/tools/cli/installers/lib/core/installer.js
index c43a197b..db5ee46e 100644
--- a/tools/cli/installers/lib/core/installer.js
+++ b/tools/cli/installers/lib/core/installer.js
@@ -1792,7 +1792,17 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
             // Rebuild module agents from installer source
             const agentsPath = path.join(modulePath, 'agents');
             if (await fs.pathExists(agentsPath)) {
-              await this.rebuildAgentFiles(modulePath, entry.name);
+              // Check if this module has source in the installer
+              const sourceAgentsPath =
+                entry.name === 'core'
+                  ? path.join(getModulePath('core'), 'agents')
+                  : path.join(getSourcePath(`modules/${entry.name}`), 'agents');
+
+              // Only rebuild if source exists in installer, otherwise skip (for custom modules)
+              if (await fs.pathExists(sourceAgentsPath)) {
+                await this.rebuildAgentFiles(modulePath, entry.name);
+              }
+
               const agentFiles = await fs.readdir(agentsPath);
               agentCount += agentFiles.filter((f) => f.endsWith('.md')).length;
             }
@@ -1817,9 +1827,16 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         spinner.succeed('No custom agents found to rebuild');
       }
 
-      // Skip full manifest regeneration during compileAgents to preserve custom agents
-      // Custom agents are already added to manifests during individual installation
-      // Only regenerate YAML manifest for IDE updates if needed
+      // Detect installed modules for manifest regeneration and IDE configuration
+      spinner.start('Regenerating manifests...');
+      const existingInstall = await this.detector.detect(bmadDir);
+      const installedModules = existingInstall.modules.map((m) => m.id);
+
+      // Regenerate manifests to include all discovered content (including custom)
+      const { ManifestGenerator } = require('./manifest-generator');
+      const manifestGen = new ManifestGenerator();
+
+      // Get existing IDE list from current manifest
       const existingManifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
       let existingIdes = [];
       if (await fs.pathExists(existingManifestPath)) {
@@ -1829,6 +1846,12 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         existingIdes = manifest.ides || [];
       }
 
+      await manifestGen.generateManifests(bmadDir, installedModules, [], {
+        ides: existingIdes,
+        preservedModules: [],
+      });
+      spinner.succeed('Manifests regenerated');
+
       // Update IDE configurations using the existing IDE list from manifest
       if (existingIdes && existingIdes.length > 0) {
         spinner.start('Updating IDE configurations...');
diff --git a/tools/cli/installers/lib/core/manifest-generator.js b/tools/cli/installers/lib/core/manifest-generator.js
index 644fd494..1020bea6 100644
--- a/tools/cli/installers/lib/core/manifest-generator.js
+++ b/tools/cli/installers/lib/core/manifest-generator.js
@@ -87,20 +87,24 @@ class ManifestGenerator {
   }
 
   /**
-   * Collect all workflows from core and selected modules
+   * Collect all workflows from ALL directories in bmad installation
    * Scans the INSTALLED bmad directory, not the source
    */
   async collectWorkflows(selectedModules) {
     this.workflows = [];
 
-    // Use updatedModules which already includes deduplicated 'core' + selectedModules
-    for (const moduleName of this.updatedModules) {
-      const modulePath = path.join(this.bmadDir, moduleName);
+    // Scan all directories under bmad installation
+    const entries = await fs.readdir(this.bmadDir, { withFileTypes: true });
 
-      if (await fs.pathExists(modulePath)) {
-        const moduleWorkflows = await this.getWorkflowsFromPath(modulePath, moduleName);
-        this.workflows.push(...moduleWorkflows);
+    for (const entry of entries) {
+      // Skip special directories that don't contain modules
+      if (!entry.isDirectory() || entry.name === '_cfg' || entry.name === 'docs') {
+        continue;
       }
+
+      const modulePath = path.join(this.bmadDir, entry.name);
+      const moduleWorkflows = await this.getWorkflowsFromPath(modulePath, entry.name);
+      this.workflows.push(...moduleWorkflows);
     }
   }
 
@@ -184,23 +188,32 @@ class ManifestGenerator {
   }
 
   /**
-   * Collect all agents from core and selected modules
+   * Collect all agents from ALL directories in bmad installation
    * Scans the INSTALLED bmad directory, not the source
    */
   async collectAgents(selectedModules) {
     this.agents = [];
 
-    // Use updatedModules which already includes deduplicated 'core' + selectedModules
-    for (const moduleName of this.updatedModules) {
-      const agentsPath = path.join(this.bmadDir, moduleName, 'agents');
+    // Scan all directories under bmad installation
+    const entries = await fs.readdir(this.bmadDir, { withFileTypes: true });
 
+    for (const entry of entries) {
+      // Skip special directories that don't contain modules
+      if (!entry.isDirectory() || entry.name === '_cfg' || entry.name === 'docs') {
+        continue;
+      }
+
+      const modulePath = path.join(this.bmadDir, entry.name);
+
+      // Check for agents/ subdirectory in this module
+      const agentsPath = path.join(modulePath, 'agents');
       if (await fs.pathExists(agentsPath)) {
-        const moduleAgents = await this.getAgentsFromDir(agentsPath, moduleName);
+        const moduleAgents = await this.getAgentsFromDir(agentsPath, entry.name);
         this.agents.push(...moduleAgents);
       }
     }
 
-    // Get standalone agents from bmad/agents/ directory
+    // Also check for standalone agents in bmad/agents/ directory (top-level)
     const standaloneAgentsDir = path.join(this.bmadDir, 'agents');
     if (await fs.pathExists(standaloneAgentsDir)) {
       const agentDirs = await fs.readdir(standaloneAgentsDir, { withFileTypes: true });
@@ -292,18 +305,27 @@ class ManifestGenerator {
   }
 
   /**
-   * Collect all tasks from core and selected modules
+   * Collect all tasks from ALL directories in bmad installation
    * Scans the INSTALLED bmad directory, not the source
    */
   async collectTasks(selectedModules) {
     this.tasks = [];
 
-    // Use updatedModules which already includes deduplicated 'core' + selectedModules
-    for (const moduleName of this.updatedModules) {
-      const tasksPath = path.join(this.bmadDir, moduleName, 'tasks');
+    // Scan all directories under bmad installation
+    const entries = await fs.readdir(this.bmadDir, { withFileTypes: true });
 
+    for (const entry of entries) {
+      // Skip special directories that don't contain modules
+      if (!entry.isDirectory() || entry.name === '_cfg' || entry.name === 'docs') {
+        continue;
+      }
+
+      const modulePath = path.join(this.bmadDir, entry.name);
+
+      // Check for tasks/ subdirectory in this module
+      const tasksPath = path.join(modulePath, 'tasks');
       if (await fs.pathExists(tasksPath)) {
-        const moduleTasks = await this.getTasksFromDir(tasksPath, moduleName);
+        const moduleTasks = await this.getTasksFromDir(tasksPath, entry.name);
         this.tasks.push(...moduleTasks);
       }
     }