diff --git a/src/bmm-skills/2-plan-workflows/bmad-create-prd/bmad-skill-manifest.yaml b/src/bmm-skills/2-plan-workflows/bmad-create-prd/bmad-skill-manifest.yaml
new file mode 100644
index 000000000..cdf2e1ac2
--- /dev/null
+++ b/src/bmm-skills/2-plan-workflows/bmad-create-prd/bmad-skill-manifest.yaml
@@ -0,0 +1,3 @@
+# Cross-referenced by bmad-edit-prd for prd-purpose.md and data files.
+# Must remain in _bmad/ until those references are refactored.
+install_to_bmad: true
diff --git a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-01-discovery.md b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-01-discovery.md
index ed9381338..f8d84ecb3 100644
--- a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-01-discovery.md
+++ b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-01-discovery.md
@@ -1,6 +1,6 @@
 ---
 # File references (ONLY variables used in this step)
-prdPurpose: '{project-root}/_bmad/bmm-skills/2-plan-workflows/bmad-create-prd/data/prd-purpose.md'
+prdPurpose: '{project-root}/_bmad/bmm/2-plan-workflows/bmad-create-prd/data/prd-purpose.md'
 ---
 
 # Step E-1: Discovery & Understanding
diff --git a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-01b-legacy-conversion.md b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-01b-legacy-conversion.md
index 55948f378..8ce979f10 100644
--- a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-01b-legacy-conversion.md
+++ b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-01b-legacy-conversion.md
@@ -1,7 +1,7 @@
 ---
 # File references (ONLY variables used in this step)
 prdFile: '{prd_file_path}'
-prdPurpose: '{project-root}/_bmad/bmm-skills/2-plan-workflows/bmad-create-prd/data/prd-purpose.md'
+prdPurpose: '{project-root}/_bmad/bmm/2-plan-workflows/bmad-create-prd/data/prd-purpose.md'
 ---
 
 # Step E-1B: Legacy PRD Conversion Assessment
diff --git a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-02-review.md b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-02-review.md
index 22706b4c7..6eaac3c25 100644
--- a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-02-review.md
+++ b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-02-review.md
@@ -2,7 +2,7 @@
 # File references (ONLY variables used in this step)
 prdFile: '{prd_file_path}'
 validationReport: '{validation_report_path}'  # If provided
-prdPurpose: '{project-root}/_bmad/bmm-skills/2-plan-workflows/bmad-create-prd/data/prd-purpose.md'
+prdPurpose: '{project-root}/_bmad/bmm/2-plan-workflows/bmad-create-prd/data/prd-purpose.md'
 ---
 
 # Step E-2: Deep Review & Analysis
diff --git a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-03-edit.md b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-03-edit.md
index 1f7e595a0..99d942495 100644
--- a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-03-edit.md
+++ b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-03-edit.md
@@ -1,7 +1,7 @@
 ---
 # File references (ONLY variables used in this step)
 prdFile: '{prd_file_path}'
-prdPurpose: '{project-root}/_bmad/bmm-skills/2-plan-workflows/bmad-create-prd/data/prd-purpose.md'
+prdPurpose: '{project-root}/_bmad/bmm/2-plan-workflows/bmad-create-prd/data/prd-purpose.md'
 ---
 
 # Step E-3: Edit & Update
diff --git a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-04-complete.md b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-04-complete.md
index 4ab9d05ea..bba9385de 100644
--- a/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-04-complete.md
+++ b/src/bmm-skills/2-plan-workflows/bmad-edit-prd/steps-e/step-e-04-complete.md
@@ -1,7 +1,7 @@
 ---
 # File references (ONLY variables used in this step)
 prdFile: '{prd_file_path}'
-validationWorkflow: '{project-root}/_bmad/bmm-skills/2-plan-workflows/bmad-validate-prd/steps-v/step-v-01-discovery.md'
+validationWorkflow: '{project-root}/_bmad/bmm/2-plan-workflows/bmad-validate-prd/steps-v/step-v-01-discovery.md'
 ---
 
 # Step E-4: Complete & Validate
diff --git a/src/bmm-skills/2-plan-workflows/bmad-validate-prd/bmad-skill-manifest.yaml b/src/bmm-skills/2-plan-workflows/bmad-validate-prd/bmad-skill-manifest.yaml
new file mode 100644
index 000000000..86714441d
--- /dev/null
+++ b/src/bmm-skills/2-plan-workflows/bmad-validate-prd/bmad-skill-manifest.yaml
@@ -0,0 +1,3 @@
+# Cross-referenced by bmad-edit-prd for validation workflow steps.
+# Must remain in _bmad/ until those references are refactored.
+install_to_bmad: true
diff --git a/test/test-install-to-bmad.js b/test/test-install-to-bmad.js
index d33218eb8..f5df68d6c 100644
--- a/test/test-install-to-bmad.js
+++ b/test/test-install-to-bmad.js
@@ -4,8 +4,9 @@
  * Unit tests against the functions that implement the install_to_bmad flag.
  * These nail down the 4 core design decisions:
  *
- * 1. true/omitted → skill stays in _bmad/ (default behavior)
- * 2. false → skill removed from _bmad/ after IDE install
+ * 1. omitted → skill removed from _bmad/ (default behavior)
+ * 2. true → skill stays in _bmad/ (explicit opt-in)
+ * 2b. false → skill removed from _bmad/ after IDE install
  * 3. No platform → no cleanup runs (cleanup lives in installVerbatimSkills)
  * 4. Mixed flags → each skill evaluated independently
  *
@@ -49,20 +50,22 @@ async function runTests() {
   console.log(`========================================${colors.reset}\n`);
 
   // ============================================================
-  // 1. true/omitted → getInstallToBmad returns true (keep in _bmad/)
+  // 1. omitted → getInstallToBmad returns false (remove from _bmad/)
+  //    Skills are self-contained in IDE directories, so the default
+  //    is to clean up from _bmad/ after IDE install.
   // ============================================================
-  console.log(`${colors.yellow}Design decision 1: true or omitted → skill stays in _bmad/${colors.reset}\n`);
+  console.log(`${colors.yellow}Design decision 1: omitted → skill removed from _bmad/ (default)${colors.reset}\n`);
 
-  // Null manifest (no bmad-skill-manifest.yaml) → true
-  assert(getInstallToBmad(null, 'workflow.md') === true, 'null manifest defaults to true');
+  // Null manifest (no bmad-skill-manifest.yaml) → false
+  assert(getInstallToBmad(null, 'workflow.md') === false, 'null manifest defaults to false');
 
-  // Single-entry, flag omitted → true
+  // Single-entry, flag omitted → false
   assert(
-    getInstallToBmad({ __single: { type: 'skill' } }, 'workflow.md') === true,
-    'single-entry manifest with flag omitted defaults to true',
+    getInstallToBmad({ __single: { type: 'skill' } }, 'workflow.md') === false,
+    'single-entry manifest with flag omitted defaults to false',
   );
 
-  // Single-entry, explicit true → true
+  // Single-entry, explicit true → true (opt-in to keep in _bmad/)
   assert(
     getInstallToBmad({ __single: { type: 'skill', install_to_bmad: true } }, 'workflow.md') === true,
     'single-entry manifest with explicit true returns true',
@@ -124,7 +127,7 @@ async function runTests() {
     };
     assert(getInstallToBmad(manifest, 'workflow.md') === false, 'multi-entry: workflow.md with false returns false');
     assert(getInstallToBmad(manifest, 'other.md') === true, 'multi-entry: other.md with true returns true');
-    assert(getInstallToBmad(manifest, 'unknown.md') === true, 'multi-entry: unknown file defaults to true');
+    assert(getInstallToBmad(manifest, 'unknown.md') === false, 'multi-entry: unknown file defaults to false');
   }
 
   console.log('');
diff --git a/tools/installer/ide/shared/skill-manifest.js b/tools/installer/ide/shared/skill-manifest.js
index c5ae4aed8..c5caa0cc8 100644
--- a/tools/installer/ide/shared/skill-manifest.js
+++ b/tools/installer/ide/shared/skill-manifest.js
@@ -56,17 +56,20 @@ function getArtifactType(manifest, filename) {
 
 /**
  * Get the install_to_bmad flag for a specific file from a loaded skill manifest.
+ * Skills are self-contained in their IDE skill directories (.claude/skills/, etc.),
+ * so the default is false — skill content is removed from _bmad/ after IDE install.
+ * Set install_to_bmad: true in bmad-skill-manifest.yaml to opt a skill back in.
  * @param {Object|null} manifest - Loaded manifest (from loadSkillManifest)
  * @param {string} filename - Source filename to look up
- * @returns {boolean} install_to_bmad value (defaults to true)
+ * @returns {boolean} install_to_bmad value (defaults to false)
  */
 function getInstallToBmad(manifest, filename) {
-  if (!manifest) return true;
+  if (!manifest) return false;
   // Single-entry manifest applies to all files in the directory
-  if (manifest.__single) return manifest.__single.install_to_bmad !== false;
+  if (manifest.__single) return manifest.__single.install_to_bmad === true;
   // Multi-entry: look up by filename directly
-  if (manifest[filename]) return manifest[filename].install_to_bmad !== false;
-  return true;
+  if (manifest[filename]) return manifest[filename].install_to_bmad === true;
+  return false;
 }
 
 module.exports = { loadSkillManifest, getCanonicalId, getArtifactType, getInstallToBmad };
diff --git a/tools/validate-file-refs.js b/tools/validate-file-refs.js
index 5f412eb88..75a802967 100644
--- a/tools/validate-file-refs.js
+++ b/tools/validate-file-refs.js
@@ -156,8 +156,15 @@ function mapInstalledToSource(refPath) {
   // Skip install-only paths (generated at install time, not in source)
   if (isInstallOnly(cleaned)) return null;
 
-  // core/, bmm/, and utility/ are directly under src/
-  if (cleaned.startsWith('core/') || cleaned.startsWith('bmm/') || cleaned.startsWith('utility/')) {
+  // Map installed module names to their source directory names
+  // _bmad/core/ → src/core-skills/, _bmad/bmm/ → src/bmm-skills/
+  if (cleaned.startsWith('core/')) {
+    return path.join(SRC_DIR, 'core-skills', cleaned.slice('core/'.length));
+  }
+  if (cleaned.startsWith('bmm/')) {
+    return path.join(SRC_DIR, 'bmm-skills', cleaned.slice('bmm/'.length));
+  }
+  if (cleaned.startsWith('utility/')) {
     return path.join(SRC_DIR, cleaned);
   }