Merge d5e5796ba3 into c24821b6ed

Adds Step 5 to quick-dev that automatically runs adversarial code review
after implementation completes. Captures baseline commit at workflow start
and reviews all changes (tracked + newly created files) using a cynical
reviewer persona via subagent, CLI fallback, or inline self-review.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

src/modules/bmm/workflows/4-implementation/code-review/instructions.xml

@@ -104,52 +104,104 @@
       </action>
       <action>Find at least 3 more specific, actionable issues</action>
     </check>
+
+    <!-- Store context-aware findings for later consolidation -->
+    <action>Set {{context_aware_findings}} = all issues found in this step (numbered list with file:line locations)</action>
   </step>
 
-  <step n="4" goal="Present findings and fix them">
-    <action>Categorize findings: HIGH (must fix), MEDIUM (should fix), LOW (nice to fix)</action>
+  <step n="4" goal="Run information-asymmetric adversarial review">
+    <critical>Reviewer has FULL repo access but NO knowledge of WHY changes were made</critical>
+    <critical>DO NOT include story file in prompt - asymmetry is about intent, not visibility</critical>
+    <critical>Reviewer can explore codebase to understand impact, but judges changes on merit alone</critical>
+
+    <!-- Construct diff of story-related changes -->
+    <action>Construct the diff of story-related changes:
+      - Uncommitted changes: `git diff` + `git diff --cached`
+      - Committed changes (if story spans commits): `git log --oneline` to find relevant commits, then `git diff base..HEAD`
+      - Exclude story file from diff: `git diff -- . ':!{{story_path}}'`
+    </action>
+    <action>Set {{asymmetric_target}} = the diff output (reviewer can explore repo but is prompted to review this diff)</action>
+
+    <!-- Execution hierarchy: cleanest context first -->
+    <check if="Task tool available (can spawn subagent)">
+      <action>Launch general-purpose subagent with adversarial prompt:
+        "You are a cynical, jaded code reviewer with zero patience for sloppy work.
+        A clueless weasel submitted the following changes and you expect to find problems.
+        Find at least ten findings to fix or improve. Look for what's missing, not just what's wrong.
+        Number each finding (1., 2., 3., ...). Be skeptical of everything.
+
+        Changes to review:
+        {{asymmetric_target}}"
+      </action>
+      <action>Collect numbered findings into {{asymmetric_findings}}</action>
+    </check>
+
+    <check if="no Task tool BUT can use Bash to invoke CLI for fresh context">
+      <action>Execute adversarial review via CLI (e.g., claude --print) in fresh context with same prompt</action>
+      <action>Collect numbered findings into {{asymmetric_findings}}</action>
+    </check>
+
+    <check if="cannot create clean slate agent by any means (fallback)">
+      <action>Execute adversarial prompt inline in main context</action>
+      <action>Note: Has context pollution but cynical reviewer persona still adds significant value</action>
+      <action>Collect numbered findings into {{asymmetric_findings}}</action>
+    </check>
+  </step>
+
+  <step n="5" goal="Consolidate findings and present to user">
+    <critical>Merge findings from BOTH context-aware review (step 3) AND asymmetric review (step 4)</critical>
+
+    <action>Combine {{context_aware_findings}} from step 3 with {{asymmetric_findings}} from step 4</action>
+
+    <action>Deduplicate findings:
+      - Identify findings that describe the same underlying issue
+      - Keep the more detailed/actionable version
+      - Note when both reviews caught the same issue (validates severity)
+    </action>
+
+    <action>Assess each finding:
+      - Is this a real issue or noise/false positive?
+      - Assign severity: 🔴 CRITICAL, 🟠 HIGH, 🟡 MEDIUM, 🟢 LOW
+    </action>
+
+    <action>Filter out non-issues:
+      - Remove false positives
+      - Remove nitpicks that do not warrant action
+      - Keep anything that could cause problems in production
+    </action>
+
+    <action>Sort by severity (CRITICAL → HIGH → MEDIUM → LOW)</action>
+
     <action>Set {{fixed_count}} = 0</action>
     <action>Set {{action_count}} = 0</action>
 
     <output>**🔥 CODE REVIEW FINDINGS, {user_name}!**
 
-      **Story:** {{story_file}}
+      **Story:** {{story_path}}
       **Git vs Story Discrepancies:** {{git_discrepancy_count}} found
-      **Issues Found:** {{high_count}} High, {{medium_count}} Medium, {{low_count}} Low
+      **Issues Found:** {{critical_count}} Critical, {{high_count}} High, {{medium_count}} Medium, {{low_count}} Low
 
-      ## 🔴 CRITICAL ISSUES
-      - Tasks marked [x] but not actually implemented
-      - Acceptance Criteria not implemented
-      - Story claims files changed but no git evidence
-      - Security vulnerabilities
+      | # | Severity | Summary | Location |
+      |---|----------|---------|----------|
+      {{findings_table}}
 
-      ## 🟡 MEDIUM ISSUES
-      - Files changed but not documented in story File List
-      - Uncommitted changes not tracked
-      - Performance problems
-      - Poor test coverage/quality
-      - Code maintainability issues
-
-      ## 🟢 LOW ISSUES
-      - Code style improvements
-      - Documentation gaps
-      - Git commit message quality
+      **{{total_count}} issues found** ({{critical_count}} critical, {{high_count}} high, {{medium_count}} medium, {{low_count}} low)
     </output>
 
     <ask>What should I do with these issues?
 
-      1. **Fix them automatically** - I'll update the code and tests
+      1. **Fix them automatically** - I'll fix all HIGH and CRITICAL, you approve each
       2. **Create action items** - Add to story Tasks/Subtasks for later
-      3. **Show me details** - Deep dive into specific issues
+      3. **Details on #N** - Explain specific issue
 
       Choose [1], [2], or specify which issue to examine:</ask>
 
     <check if="user chooses 1">
-      <action>Fix all HIGH and MEDIUM issues in the code</action>
+      <action>Fix all CRITICAL and HIGH issues in the code</action>
       <action>Add/update tests as needed</action>
       <action>Update File List in story if files changed</action>
       <action>Update story Dev Agent Record with fixes applied</action>
-      <action>Set {{fixed_count}} = number of HIGH and MEDIUM issues fixed</action>
+      <action>Set {{fixed_count}} = number of CRITICAL and HIGH issues fixed</action>
       <action>Set {{action_count}} = 0</action>
     </check>
 
@@ -166,13 +218,13 @@
     </check>
   </step>
 
-  <step n="5" goal="Update story status and sync sprint tracking">
+  <step n="6" goal="Update story status and sync sprint tracking">
     <!-- Determine new status based on review outcome -->
-    <check if="all HIGH and MEDIUM issues fixed AND all ACs implemented">
+    <check if="all CRITICAL and HIGH issues fixed AND all ACs implemented">
       <action>Set {{new_status}} = "done"</action>
       <action>Update story Status field to "done"</action>
     </check>
-    <check if="HIGH or MEDIUM issues remain OR ACs not fully implemented">
+    <check if="CRITICAL or HIGH issues remain OR ACs not fully implemented">
       <action>Set {{new_status}} = "in-progress"</action>
       <action>Update story Status field to "in-progress"</action>
     </check>

src/modules/bmm/workflows/bmad-quick-flow/quick-dev/checklist.md

@@ -23,3 +23,11 @@
 - [ ] Acceptance criteria satisfied
 - [ ] Tech-spec updated (if applicable)
 - [ ] Summary provided to user
+
+## Adversarial Review
+
+- [ ] Diff constructed (tracked changes from {baseline_commit} + new untracked files)
+- [ ] Adversarial review executed (subagent preferred)
+- [ ] Findings presented with severity and classification
+- [ ] User chose handling approach (walk through / auto-fix / skip)
+- [ ] Findings resolved or acknowledged

src/modules/bmm/workflows/bmad-quick-flow/quick-dev/instructions.md

@@ -15,6 +15,8 @@
 
 <step n="1" goal="Load project context and determine execution mode">
 
+<action>Record current HEAD as baseline for later review. Run `git rev-parse HEAD` and store the result as {baseline_commit}.</action>
+
 <action>Check if {project_context} exists. If yes, load it - this is your foundational reference for ALL implementation decisions (patterns, conventions, architecture).</action>
 
 <action>Parse user input:
@@ -170,7 +172,7 @@ Use holistic judgment, not mechanical keyword matching.</action>
 
 </step>
 
-<step n="4" goal="Verify and complete">
+<step n="4" goal="Verify and transition to review">
 
 <action>Verify: all tasks [x], tests passing, AC satisfied, patterns followed</action>
 
@@ -185,17 +187,89 @@ Use holistic judgment, not mechanical keyword matching.</action>
 **Tests:** {{test_summary}}
 **AC Status:** {{ac_status}}
 
----
+Running adversarial code review...
+</output>
 
-**Before committing (Recommended): Copy this code review prompt to a different LLM**
+<action>Proceed immediately to step 5</action>
 
+</step>
+
+<step n="5" goal="Adversarial code review (automatic)">
+
+<action>Construct diff of all changes since workflow started and capture as {diff_output}:
+
+**Tracked file changes:**
+
+```bash
+git diff {baseline_commit}
 ```
-You are a cynical, jaded code reviewer with zero patience for sloppy work. These uncommitted changes were submitted by a clueless weasel and you expect to find problems. Find at least five issues to fix or improve in it. Number them. Be skeptical of everything.
-```
+
+**New files created by this workflow:**
+Only include untracked files that YOU actually created during steps 2-4. Do not include pre-existing untracked files. For each new file you created, include its full content as a "new file" addition.
+
+Combine both into {diff_output} for review. Do NOT `git add` anything - this is read-only inspection.</action>
+
+<action>Execute adversarial review using this hierarchy (try in order until one succeeds):
+
+1. **Spawn subagent** (preferred) - pass the diff output along with this prompt:
+
+   ```
+   You are a cynical, jaded code reviewer with zero patience for sloppy work. This diff was submitted by a clueless weasel and you expect to find problems. Find at least five issues to fix or improve. Number them. Be skeptical of everything.
+
+   <diff>
+   {diff_output}
+   </diff>
+   ```
+
+2. **CLI fallback** - pipe diff to `claude --print` with same prompt
+
+3. **Inline self-review** - Review the diff output yourself using the cynical reviewer persona above
+   </action>
+
+<check if="zero findings returned">
+  <action>HALT - Zero findings is suspicious. Adversarial review should always find something. Request user guidance.</action>
+</check>
+
+<action>Process findings:
+
+- Assign IDs: F1, F2, F3...
+- Assign severity: 🔴 Critical | 🟠 High | 🟡 Medium | 🟢 Low
+- Classify each: **real** (confirmed issue) | **noise** (false positive) | **uncertain** (needs discussion)
+  </action>
+
+<output>**Adversarial Review Findings**
+
+| ID  | Severity | Classification | Finding |
+| --- | -------- | -------------- | ------- |
+| F1  | 🟠       | real           | ...     |
+| F2  | 🟡       | noise          | ...     |
+| ... |
 
 </output>
 
-<action>You must explain what was implemented based on {user_skill_level}</action>
+<ask>How would you like to handle these findings?
+
+**[1] Walk through** - Discuss each finding individually
+**[2] Auto-fix** - Automatically fix issues classified as "real"
+**[3] Skip** - Acknowledge and proceed to commit</ask>
+
+<check if="1">
+  <action>Present each finding one by one. For each, ask: fix now / skip / discuss</action>
+  <action>Apply fixes as approved</action>
+</check>
+
+<check if="2">
+  <action>Automatically fix all findings classified as "real"</action>
+  <action>Report what was fixed</action>
+</check>
+
+<check if="3">
+  <action>Acknowledge findings were reviewed and user chose to skip</action>
+</check>
+
+<output>**Review complete. Ready to commit.**</output>
+
+<action>Explain what was implemented based on {user_skill_level}</action>
 
 </step>
 

tools/cli/commands/install.js

@@ -21,15 +21,6 @@ module.exports = {
         return;
       }
 
-      // Handle agent compilation separately
-      if (config.actionType === 'compile') {
-        const result = await installer.compileAgents(config);
-        console.log(chalk.green('\n✨ Agent compilation complete!'));
-        console.log(chalk.cyan(`Rebuilt ${result.agentCount} agents and ${result.taskCount} tasks`));
-        process.exit(0);
-        return;
-      }
-
       // Handle quick update separately
       if (config.actionType === 'quick-update') {
         const result = await installer.quickUpdate(config);

tools/cli/installers/lib/core/installer.js

@@ -439,6 +439,33 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         }
       }
     } else {
+      // For regular updates (modify flow), check manifest for custom module sources
+      if (config._isUpdate && config._existingInstall && config._existingInstall.customModules) {
+        for (const customModule of config._existingInstall.customModules) {
+          // Ensure we have an absolute sourcePath
+          let absoluteSourcePath = customModule.sourcePath;
+
+          // Check if sourcePath is a cache-relative path (starts with _config)
+          if (absoluteSourcePath && absoluteSourcePath.startsWith('_config')) {
+            // Convert cache-relative path to absolute path
+            absoluteSourcePath = path.join(bmadDir, absoluteSourcePath);
+          }
+          // If no sourcePath but we have relativePath, convert it
+          else if (!absoluteSourcePath && customModule.relativePath) {
+            // relativePath is relative to the project root (parent of bmad dir)
+            absoluteSourcePath = path.resolve(projectDir, customModule.relativePath);
+          }
+          // Ensure sourcePath is absolute for anything else
+          else if (absoluteSourcePath && !path.isAbsolute(absoluteSourcePath)) {
+            absoluteSourcePath = path.resolve(absoluteSourcePath);
+          }
+
+          if (absoluteSourcePath) {
+            customModulePaths.set(customModule.id, absoluteSourcePath);
+          }
+        }
+      }
+
       // Build custom module paths map from customContent
 
       // Handle selectedFiles (from existing install path or manual directory input)
@@ -589,20 +616,39 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
 
           // Detect custom and modified files BEFORE updating (compare current files vs files-manifest.csv)
           const existingFilesManifest = await this.readFilesManifest(bmadDir);
-          console.log(chalk.dim(`DEBUG: Read ${existingFilesManifest.length} files from manifest`));
-          console.log(chalk.dim(`DEBUG: Manifest has hashes: ${existingFilesManifest.some((f) => f.hash)}`));
-
           const { customFiles, modifiedFiles } = await this.detectCustomFiles(bmadDir, existingFilesManifest);
 
-          console.log(chalk.dim(`DEBUG: Found ${customFiles.length} custom files, ${modifiedFiles.length} modified files`));
-          if (modifiedFiles.length > 0) {
-            console.log(chalk.yellow('DEBUG: Modified files:'));
-            for (const f of modifiedFiles) console.log(chalk.dim(`  - ${f.path}`));
-          }
-
           config._customFiles = customFiles;
           config._modifiedFiles = modifiedFiles;
 
+          // Also check cache directory for custom modules (like quick update does)
+          const cacheDir = path.join(bmadDir, '_config', 'custom');
+          if (await fs.pathExists(cacheDir)) {
+            const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
+
+            for (const cachedModule of cachedModules) {
+              if (cachedModule.isDirectory()) {
+                const moduleId = cachedModule.name;
+
+                // Skip if we already have this module from manifest
+                if (customModulePaths.has(moduleId)) {
+                  continue;
+                }
+
+                const cachedPath = path.join(cacheDir, moduleId);
+
+                // Check if this is actually a custom module (has module.yaml)
+                const moduleYamlPath = path.join(cachedPath, 'module.yaml');
+                if (await fs.pathExists(moduleYamlPath)) {
+                  customModulePaths.set(moduleId, cachedPath);
+                }
+              }
+            }
+
+            // Update module manager with the new custom module paths from cache
+            this.moduleManager.setCustomModulePaths(customModulePaths);
+          }
+
           // If there are custom files, back them up temporarily
           if (customFiles.length > 0) {
             const tempBackupDir = path.join(projectDir, '_bmad-custom-backup-temp');
@@ -625,20 +671,16 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
             const tempModifiedBackupDir = path.join(projectDir, '_bmad-modified-backup-temp');
             await fs.ensureDir(tempModifiedBackupDir);
 
-            console.log(chalk.yellow(`\nDEBUG: Backing up ${modifiedFiles.length} modified files to temp location`));
             spinner.start(`Backing up ${modifiedFiles.length} modified files...`);
             for (const modifiedFile of modifiedFiles) {
               const relativePath = path.relative(bmadDir, modifiedFile.path);
               const tempBackupPath = path.join(tempModifiedBackupDir, relativePath);
-              console.log(chalk.dim(`DEBUG: Backing up ${relativePath} to temp`));
               await fs.ensureDir(path.dirname(tempBackupPath));
               await fs.copy(modifiedFile.path, tempBackupPath, { overwrite: true });
             }
             spinner.succeed(`Backed up ${modifiedFiles.length} modified files`);
 
             config._tempModifiedBackupDir = tempModifiedBackupDir;
-          } else {
-            console.log(chalk.dim('DEBUG: No modified files detected'));
           }
         }
       } else if (existingInstall.installed && config._quickUpdate) {
@@ -654,6 +696,34 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         config._customFiles = customFiles;
         config._modifiedFiles = modifiedFiles;
 
+        // Also check cache directory for custom modules (like quick update does)
+        const cacheDir = path.join(bmadDir, '_config', 'custom');
+        if (await fs.pathExists(cacheDir)) {
+          const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
+
+          for (const cachedModule of cachedModules) {
+            if (cachedModule.isDirectory()) {
+              const moduleId = cachedModule.name;
+
+              // Skip if we already have this module from manifest
+              if (customModulePaths.has(moduleId)) {
+                continue;
+              }
+
+              const cachedPath = path.join(cacheDir, moduleId);
+
+              // Check if this is actually a custom module (has module.yaml)
+              const moduleYamlPath = path.join(cachedPath, 'module.yaml');
+              if (await fs.pathExists(moduleYamlPath)) {
+                customModulePaths.set(moduleId, cachedPath);
+              }
+            }
+          }
+
+          // Update module manager with the new custom module paths from cache
+          this.moduleManager.setCustomModulePaths(customModulePaths);
+        }
+
         // Back up custom files
         if (customFiles.length > 0) {
           const tempBackupDir = path.join(projectDir, '_bmad-custom-backup-temp');
@@ -832,7 +902,6 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
       // For dependency resolution, we need to pass the project root
       // Create a temporary module manager that knows about custom content locations
       const tempModuleManager = new ModuleManager({
-        scanProjectForModules: true,
         bmadDir: bmadDir, // Pass bmadDir so we can check cache
       });
 
@@ -1057,7 +1126,7 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
 
             // Pass pre-collected configuration to avoid re-prompting
             await this.ideManager.setup(ide, projectDir, bmadDir, {
-              selectedModules: config.modules || [],
+              selectedModules: allModules || [],
               preCollectedConfig: ideConfigurations[ide] || null,
               verbose: config.verbose,
             });
@@ -1184,11 +1253,6 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
       // Report custom and modified files if any were found
       if (customFiles.length > 0) {
         console.log(chalk.cyan(`\n📁 Custom files preserved: ${customFiles.length}`));
-        console.log(chalk.dim('The following custom files were found and restored:\n'));
-        for (const customFile of customFiles) {
-          const relativePath = path.relative(projectDir, customFile);
-          console.log(chalk.dim(`  • ${relativePath}`));
-        }
       }
 
       if (modifiedFiles.length > 0) {
@@ -2184,41 +2248,8 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
       const configuredIdes = existingInstall.ides || [];
       const projectRoot = path.dirname(bmadDir);
 
-      // Get custom module sources from manifest and cache
+      // Get custom module sources from cache
       const customModuleSources = new Map();
-
-      // First check manifest for backward compatibility
-      if (existingInstall.customModules) {
-        for (const customModule of existingInstall.customModules) {
-          // Ensure we have an absolute sourcePath
-          let absoluteSourcePath = customModule.sourcePath;
-
-          // Check if sourcePath is a cache-relative path (starts with _config/)
-          if (absoluteSourcePath && absoluteSourcePath.startsWith('_config')) {
-            // Convert cache-relative path to absolute path
-            absoluteSourcePath = path.join(bmadDir, absoluteSourcePath);
-          }
-          // If no sourcePath but we have relativePath, convert it
-          else if (!absoluteSourcePath && customModule.relativePath) {
-            // relativePath is relative to the project root (parent of bmad dir)
-            absoluteSourcePath = path.resolve(projectRoot, customModule.relativePath);
-          }
-          // Ensure sourcePath is absolute for anything else
-          else if (absoluteSourcePath && !path.isAbsolute(absoluteSourcePath)) {
-            absoluteSourcePath = path.resolve(absoluteSourcePath);
-          }
-
-          // Update the custom module object with the absolute path
-          const updatedModule = {
-            ...customModule,
-            sourcePath: absoluteSourcePath,
-          };
-
-          customModuleSources.set(customModule.id, updatedModule);
-        }
-      }
-
-      // Also check cache directory for any modules not in manifest
       const cacheDir = path.join(bmadDir, '_config', 'custom');
       if (await fs.pathExists(cacheDir)) {
         const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
@@ -2277,126 +2308,6 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         }
       }
 
-      // Check for untracked custom modules (installed but not in manifest)
-      const untrackedCustomModules = [];
-      for (const installedModule of installedModules) {
-        // Skip standard modules and core
-        const standardModuleIds = ['bmb', 'bmgd', 'bmm', 'cis', 'core'];
-        if (standardModuleIds.includes(installedModule)) {
-          continue;
-        }
-
-        // Check if this installed module is not tracked in customModules
-        if (!customModuleSources.has(installedModule)) {
-          const modulePath = path.join(bmadDir, installedModule);
-          if (await fs.pathExists(modulePath)) {
-            untrackedCustomModules.push({
-              id: installedModule,
-              name: installedModule, // We don't have the original name
-              path: modulePath,
-              untracked: true,
-            });
-          }
-        }
-      }
-
-      // If we found untracked custom modules, offer to track them
-      if (untrackedCustomModules.length > 0) {
-        spinner.stop();
-        console.log(chalk.yellow(`\n⚠️  Found ${untrackedCustomModules.length} custom module(s) not tracked in manifest:`));
-
-        for (const untracked of untrackedCustomModules) {
-          console.log(chalk.dim(`  • ${untracked.id} (installed at ${path.relative(projectRoot, untracked.path)})`));
-        }
-
-        const { trackModules } = await inquirer.prompt([
-          {
-            type: 'confirm',
-            name: 'trackModules',
-            message: chalk.cyan('Would you like to scan for their source locations?'),
-            default: true,
-          },
-        ]);
-
-        if (trackModules) {
-          const { scanDirectory } = await inquirer.prompt([
-            {
-              type: 'input',
-              name: 'scanDirectory',
-              message: 'Enter directory to scan for custom module sources (or leave blank to skip):',
-              default: projectRoot,
-              validate: async (input) => {
-                if (input && input.trim() !== '') {
-                  const expandedPath = path.resolve(input.trim());
-                  if (!(await fs.pathExists(expandedPath))) {
-                    return 'Directory does not exist';
-                  }
-                  const stats = await fs.stat(expandedPath);
-                  if (!stats.isDirectory()) {
-                    return 'Path must be a directory';
-                  }
-                }
-                return true;
-              },
-            },
-          ]);
-
-          if (scanDirectory && scanDirectory.trim() !== '') {
-            console.log(chalk.dim('\nScanning for custom module sources...'));
-
-            // Scan for all module.yaml files
-            const allModulePaths = await this.moduleManager.findModulesInProject(scanDirectory);
-            const { ModuleManager } = require('../modules/manager');
-            const mm = new ModuleManager({ scanProjectForModules: true });
-
-            for (const untracked of untrackedCustomModules) {
-              let foundSource = null;
-
-              // Try to find by module ID
-              for (const modulePath of allModulePaths) {
-                try {
-                  const moduleInfo = await mm.getModuleInfo(modulePath);
-                  if (moduleInfo && moduleInfo.id === untracked.id) {
-                    foundSource = {
-                      path: modulePath,
-                      info: moduleInfo,
-                    };
-                    break;
-                  }
-                } catch {
-                  // Continue searching
-                }
-              }
-
-              if (foundSource) {
-                console.log(chalk.green(`  ✓ Found source for ${untracked.id}: ${path.relative(projectRoot, foundSource.path)}`));
-
-                // Add to manifest
-                await this.manifest.addCustomModule(bmadDir, {
-                  id: untracked.id,
-                  name: foundSource.info.name || untracked.name,
-                  sourcePath: path.resolve(foundSource.path),
-                  installDate: new Date().toISOString(),
-                  tracked: true,
-                });
-
-                // Add to customModuleSources for processing
-                customModuleSources.set(untracked.id, {
-                  id: untracked.id,
-                  name: foundSource.info.name || untracked.name,
-                  sourcePath: path.resolve(foundSource.path),
-                });
-              } else {
-                console.log(chalk.yellow(`  ⚠ Could not find source for ${untracked.id}`));
-              }
-            }
-          }
-        }
-
-        console.log(chalk.dim('\nUntracked custom modules will remain installed but cannot be updated without their source.'));
-        spinner.start('Preparing update...');
-      }
-
       // Handle missing custom module sources using shared method
       const customModuleResult = await this.handleMissingCustomSources(
         customModuleSources,
@@ -2414,18 +2325,6 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         hasUpdate: true,
       }));
 
-      // Add untracked modules to the update list but mark them as untrackable
-      for (const untracked of untrackedCustomModules) {
-        if (!customModuleSources.has(untracked.id)) {
-          customModulesFromManifest.push({
-            ...untracked,
-            isCustom: true,
-            hasUpdate: false, // Can't update without source
-            untracked: true,
-          });
-        }
-      }
-
       const allAvailableModules = [...availableModules, ...customModulesFromManifest];
       const availableModuleIds = new Set(allAvailableModules.map((m) => m.id));
 

tools/cli/installers/lib/modules/manager.js

@@ -28,7 +28,6 @@ class ModuleManager {
     this.modulesSourcePath = getSourcePath('modules');
     this.xmlHandler = new XmlHandler();
     this.bmadFolderName = 'bmad'; // Default, can be overridden
-    this.scanProjectForModules = options.scanProjectForModules !== false; // Default to true for backward compatibility
     this.customModulePaths = new Map(); // Initialize custom module paths
   }
 
@@ -116,76 +115,6 @@ class ModuleManager {
     }
   }
 
-  /**
-   * Find all modules in the project by searching for module.yaml files
-   * @returns {Array} List of module paths
-   */
-  async findModulesInProject() {
-    const projectRoot = getProjectRoot();
-    const modulePaths = new Set();
-
-    // Helper function to recursively scan directories
-    async function scanDirectory(dir, excludePaths = []) {
-      try {
-        const entries = await fs.readdir(dir, { withFileTypes: true });
-
-        for (const entry of entries) {
-          const fullPath = path.join(dir, entry.name);
-
-          // Skip hidden directories, node_modules, and literal placeholder directories
-          if (
-            entry.name.startsWith('.') ||
-            entry.name === 'node_modules' ||
-            entry.name === 'dist' ||
-            entry.name === 'build' ||
-            entry.name === '{project-root}'
-          ) {
-            continue;
-          }
-
-          // Skip excluded paths
-          if (excludePaths.some((exclude) => fullPath.startsWith(exclude))) {
-            continue;
-          }
-
-          if (entry.isDirectory()) {
-            // Skip core module - it's always installed first and not selectable
-            if (entry.name === 'core') {
-              continue;
-            }
-
-            // Check if this directory contains a module (module.yaml OR custom.yaml)
-            const moduleConfigPath = path.join(fullPath, 'module.yaml');
-            const installerConfigPath = path.join(fullPath, '_module-installer', 'module.yaml');
-            const customConfigPath = path.join(fullPath, '_module-installer', 'custom.yaml');
-            const rootCustomConfigPath = path.join(fullPath, 'custom.yaml');
-
-            if (
-              (await fs.pathExists(moduleConfigPath)) ||
-              (await fs.pathExists(installerConfigPath)) ||
-              (await fs.pathExists(customConfigPath)) ||
-              (await fs.pathExists(rootCustomConfigPath))
-            ) {
-              modulePaths.add(fullPath);
-              // Don't scan inside modules - they might have their own nested structures
-              continue;
-            }
-
-            // Recursively scan subdirectories
-            await scanDirectory(fullPath, excludePaths);
-          }
-        }
-      } catch {
-        // Ignore errors (e.g., permission denied)
-      }
-    }
-
-    // Scan the entire project, but exclude src/modules since we handle it separately
-    await scanDirectory(projectRoot, [this.modulesSourcePath]);
-
-    return [...modulePaths];
-  }
-
   /**
    * List all available modules (excluding core which is always installed)
    * @returns {Object} Object with modules array and customModules array
@@ -228,43 +157,19 @@ class ModuleManager {
       }
     }
 
-    // Then, find all other modules in the project (only if scanning is enabled)
-    if (this.scanProjectForModules) {
-      const otherModulePaths = await this.findModulesInProject();
-      for (const modulePath of otherModulePaths) {
-        const moduleName = path.basename(modulePath);
-        const relativePath = path.relative(getProjectRoot(), modulePath);
-
-        // Skip core module - it's always installed first and not selectable
-        if (moduleName === 'core') {
-          continue;
-        }
-
-        const moduleInfo = await this.getModuleInfo(modulePath, moduleName, relativePath);
-        if (moduleInfo && !modules.some((m) => m.id === moduleInfo.id) && !customModules.some((m) => m.id === moduleInfo.id)) {
-          // Avoid duplicates - skip if we already have this module ID
-          if (moduleInfo.isCustom) {
-            customModules.push(moduleInfo);
-          } else {
-            modules.push(moduleInfo);
-          }
-        }
-      }
-
-      // Also check for cached custom modules in _config/custom/
-      if (this.bmadDir) {
-        const customCacheDir = path.join(this.bmadDir, '_config', 'custom');
-        if (await fs.pathExists(customCacheDir)) {
-          const cacheEntries = await fs.readdir(customCacheDir, { withFileTypes: true });
-          for (const entry of cacheEntries) {
-            if (entry.isDirectory()) {
-              const cachePath = path.join(customCacheDir, entry.name);
-              const moduleInfo = await this.getModuleInfo(cachePath, entry.name, '_config/custom');
-              if (moduleInfo && !modules.some((m) => m.id === moduleInfo.id) && !customModules.some((m) => m.id === moduleInfo.id)) {
-                moduleInfo.isCustom = true;
-                moduleInfo.fromCache = true;
-                customModules.push(moduleInfo);
-              }
+    // Check for cached custom modules in _config/custom/
+    if (this.bmadDir) {
+      const customCacheDir = path.join(this.bmadDir, '_config', 'custom');
+      if (await fs.pathExists(customCacheDir)) {
+        const cacheEntries = await fs.readdir(customCacheDir, { withFileTypes: true });
+        for (const entry of cacheEntries) {
+          if (entry.isDirectory()) {
+            const cachePath = path.join(customCacheDir, entry.name);
+            const moduleInfo = await this.getModuleInfo(cachePath, entry.name, '_config/custom');
+            if (moduleInfo && !modules.some((m) => m.id === moduleInfo.id) && !customModules.some((m) => m.id === moduleInfo.id)) {
+              moduleInfo.isCustom = true;
+              moduleInfo.fromCache = true;
+              customModules.push(moduleInfo);
             }
           }
         }

tools/cli/lib/ui.js

@@ -195,11 +195,7 @@ class UI {
       }
 
       // Common actions
-      choices.push(
-        { name: 'Modify BMAD Installation', value: 'update' },
-        { name: 'Add / Update Custom Content', value: 'add-custom' },
-        { name: 'Rebuild Agents', value: 'compile' },
-      );
+      choices.push({ name: 'Modify BMAD Installation', value: 'update' });
 
       const promptResult = await inquirer.prompt([
         {
@@ -224,64 +220,6 @@ class UI {
         };
       }
 
-      // Handle add custom content separately
-      if (actionType === 'add-custom') {
-        customContentConfig = await this.promptCustomContentSource();
-        // After adding custom content, continue to select additional modules
-        const { installedModuleIds } = await this.getExistingInstallation(confirmedDirectory);
-
-        // Ask if user wants to add additional modules
-        const { wantsMoreModules } = await inquirer.prompt([
-          {
-            type: 'confirm',
-            name: 'wantsMoreModules',
-            message: 'Do you want to add any additional modules?',
-            default: false,
-          },
-        ]);
-
-        let selectedModules = [];
-        if (wantsMoreModules) {
-          const moduleChoices = await this.getModuleChoices(installedModuleIds, customContentConfig);
-          selectedModules = await this.selectModules(moduleChoices);
-
-          // Process custom content selection
-          const selectedCustomContent = selectedModules.filter((mod) => mod.startsWith('__CUSTOM_CONTENT__'));
-
-          if (selectedCustomContent.length > 0) {
-            customContentConfig.selected = true;
-            customContentConfig.selectedFiles = selectedCustomContent.map((mod) => mod.replace('__CUSTOM_CONTENT__', ''));
-
-            // Convert to module IDs
-            const customContentModuleIds = [];
-            const customHandler = new CustomHandler();
-            for (const customFile of customContentConfig.selectedFiles) {
-              const customInfo = await customHandler.getCustomInfo(customFile);
-              if (customInfo) {
-                customContentModuleIds.push(customInfo.id);
-              }
-            }
-            selectedModules = [...selectedModules.filter((mod) => !mod.startsWith('__CUSTOM_CONTENT__')), ...customContentModuleIds];
-          }
-        }
-
-        return {
-          actionType: 'update',
-          directory: confirmedDirectory,
-          installCore: false, // Don't reinstall core
-          modules: selectedModules,
-          customContent: customContentConfig,
-        };
-      }
-
-      // Handle agent compilation separately
-      if (actionType === 'compile') {
-        return {
-          actionType: 'compile',
-          directory: confirmedDirectory,
-        };
-      }
-
       // If actionType === 'update', handle it with the new flow
       // Return early with modify configuration
       if (actionType === 'update') {
@@ -293,7 +231,7 @@ class UI {
           {
             type: 'confirm',
             name: 'changeModuleSelection',
-            message: 'Change which modules are installed?',
+            message: 'Modify official module selection (BMad Method, BMad Builder, Creative Innovation Suite)?',
             default: false,
           },
         ]);
@@ -307,6 +245,14 @@ class UI {
           selectedModules = [...installedModuleIds];
         }
 
+        // After module selection, ask about custom modules
+        const customModuleResult = await this.handleCustomModulesInModifyFlow(confirmedDirectory, selectedModules);
+
+        // Merge any selected custom modules
+        if (customModuleResult.selectedCustomModules.length > 0) {
+          selectedModules.push(...customModuleResult.selectedCustomModules);
+        }
+
         // Get tool selection
         const toolSelection = await this.promptToolSelection(confirmedDirectory, selectedModules);
 
@@ -337,7 +283,7 @@ class UI {
           ides: toolSelection.ides,
           skipIde: toolSelection.skipIde,
           coreConfig: coreConfig,
-          customContent: { hasCustomContent: false },
+          customContent: customModuleResult.customContentConfig,
           enableAgentVibes: enableTts,
           agentVibesInstalled: false,
         };
@@ -352,7 +298,7 @@ class UI {
       {
         type: 'confirm',
         name: 'wantsOfficialModules',
-        message: 'Will you be installing any official modules (BMad Method, BMad Builder, Creative Innovation Suite)?',
+        message: 'Will you be installing any official BMad modules (BMad Method, BMad Builder, Creative Innovation Suite)?',
         default: true,
       },
     ]);
@@ -368,7 +314,7 @@ class UI {
       {
         type: 'confirm',
         name: 'wantsCustomContent',
-        message: 'Will you be installing any locally stored custom content?',
+        message: 'Would you like to install a local custom module (this includes custom agents and workflows also)?',
         default: false,
       },
     ]);
@@ -734,14 +680,8 @@ class UI {
 
     // Add official modules
     const { ModuleManager } = require('../installers/lib/modules/manager');
-    // For new installations, don't scan project yet (will do after custom content is discovered)
-    // For existing installations, scan if user selected custom content
-    const shouldScanProject =
-      !isNewInstallation && customContentConfig && customContentConfig.hasCustomContent && customContentConfig.selected;
-    const moduleManager = new ModuleManager({
-      scanProjectForModules: shouldScanProject,
-    });
-    const { modules: availableModules, customModules: customModulesFromProject } = await moduleManager.listAvailable();
+    const moduleManager = new ModuleManager();
+    const { modules: availableModules, customModules: customModulesFromCache } = await moduleManager.listAvailable();
 
     // First, add all items to appropriate sections
     const allCustomModules = [];
@@ -749,14 +689,14 @@ class UI {
     // Add custom content items from directory
     allCustomModules.push(...customContentItems);
 
-    // Add custom modules from project scan (if scanning is enabled)
-    for (const mod of customModulesFromProject) {
+    // Add custom modules from cache
+    for (const mod of customModulesFromCache) {
       // Skip if this module is already in customContentItems (by path)
       const isDuplicate = allCustomModules.some((item) => item.path && mod.path && path.resolve(item.path) === path.resolve(mod.path));
 
       if (!isDuplicate) {
         allCustomModules.push({
-          name: `${chalk.cyan('✓')} ${mod.name} ${chalk.gray(`(${mod.source})`)}`,
+          name: `${chalk.cyan('✓')} ${mod.name} ${chalk.gray(`(cached)`)}`,
           value: mod.id,
           checked: isNewInstallation ? mod.defaultSelected || false : installedModuleIds.has(mod.id),
         });
@@ -803,7 +743,9 @@ class UI {
       },
     ]);
 
-    return moduleAnswer.modules || [];
+    const selected = moduleAnswer.modules || [];
+
+    return selected;
   }
 
   /**
@@ -1472,6 +1414,136 @@ class UI {
 
     return customContentConfig;
   }
+
+  /**
+   * Handle custom modules in the modify flow
+   * @param {string} directory - Installation directory
+   * @param {Array} selectedModules - Currently selected modules
+   * @returns {Object} Result with selected custom modules and custom content config
+   */
+  async handleCustomModulesInModifyFlow(directory, selectedModules) {
+    // Get existing installation to find custom modules
+    const { existingInstall } = await this.getExistingInstallation(directory);
+
+    // Check if there are any custom modules in cache
+    const { Installer } = require('../installers/lib/core/installer');
+    const installer = new Installer();
+    const { bmadDir } = await installer.findBmadDir(directory);
+
+    const cacheDir = path.join(bmadDir, '_config', 'custom');
+    const cachedCustomModules = [];
+
+    if (await fs.pathExists(cacheDir)) {
+      const entries = await fs.readdir(cacheDir, { withFileTypes: true });
+      for (const entry of entries) {
+        if (entry.isDirectory()) {
+          const moduleYamlPath = path.join(cacheDir, entry.name, 'module.yaml');
+          if (await fs.pathExists(moduleYamlPath)) {
+            const yaml = require('yaml');
+            const content = await fs.readFile(moduleYamlPath, 'utf8');
+            const moduleData = yaml.parse(content);
+
+            cachedCustomModules.push({
+              id: entry.name,
+              name: moduleData.name || entry.name,
+              description: moduleData.description || 'Custom module from cache',
+              checked: selectedModules.includes(entry.name),
+              fromCache: true,
+            });
+          }
+        }
+      }
+    }
+
+    const result = {
+      selectedCustomModules: [],
+      customContentConfig: { hasCustomContent: false },
+    };
+
+    if (cachedCustomModules.length === 0) {
+      return result;
+    }
+
+    // Ask user about custom modules
+    console.log(chalk.cyan('\n⚙️  Custom Modules'));
+    console.log(chalk.dim('Found custom modules in your installation:'));
+
+    const { customAction } = await inquirer.prompt([
+      {
+        type: 'list',
+        name: 'customAction',
+        message: 'What would you like to do with custom modules?',
+        choices: [
+          { name: 'Keep all existing custom modules', value: 'keep' },
+          { name: 'Select which custom modules to keep', value: 'select' },
+          { name: 'Add new custom modules', value: 'add' },
+          { name: 'Remove all custom modules', value: 'remove' },
+        ],
+        default: 'keep',
+      },
+    ]);
+
+    switch (customAction) {
+      case 'keep': {
+        // Keep all existing custom modules
+        result.selectedCustomModules = cachedCustomModules.map((m) => m.id);
+        console.log(chalk.dim(`Keeping ${result.selectedCustomModules.length} custom module(s)`));
+        break;
+      }
+
+      case 'select': {
+        // Let user choose which to keep
+        const choices = cachedCustomModules.map((m) => ({
+          name: `${m.name} ${chalk.gray(`(${m.id})`)}`,
+          value: m.id,
+        }));
+
+        const { keepModules } = await inquirer.prompt([
+          {
+            type: 'checkbox',
+            name: 'keepModules',
+            message: 'Select custom modules to keep:',
+            choices: choices,
+            default: cachedCustomModules.filter((m) => m.checked).map((m) => m.id),
+          },
+        ]);
+        result.selectedCustomModules = keepModules;
+        break;
+      }
+
+      case 'add': {
+        // First ask to keep existing ones
+        const { keepExisting } = await inquirer.prompt([
+          {
+            type: 'confirm',
+            name: 'keepExisting',
+            message: 'Keep existing custom modules?',
+            default: true,
+          },
+        ]);
+
+        if (keepExisting) {
+          result.selectedCustomModules = cachedCustomModules.map((m) => m.id);
+        }
+
+        // Then prompt for new ones (reuse existing method)
+        const newCustomContent = await this.promptCustomContentSource();
+        if (newCustomContent.hasCustomContent && newCustomContent.selected) {
+          result.selectedCustomModules.push(...newCustomContent.selectedModuleIds);
+          result.customContentConfig = newCustomContent;
+        }
+        break;
+      }
+
+      case 'remove': {
+        // Remove all custom modules
+        console.log(chalk.yellow('All custom modules will be removed from the installation'));
+        break;
+      }
+    }
+
+    return result;
+  }
 }
 
 module.exports = { UI };