diff --git a/src/core-skills/bmad-module/scripts/install.mjs b/src/core-skills/bmad-module/scripts/install.mjs
index 4d9c2cb26..750c2822e 100644
--- a/src/core-skills/bmad-module/scripts/install.mjs
+++ b/src/core-skills/bmad-module/scripts/install.mjs
@@ -1,11 +1,10 @@
-import fs from 'node:fs/promises';
 import path from 'node:path';
 import { EXIT, BmadModuleError } from './lib/exit.mjs';
 import { findBmadDir, ensureConfigDir } from './lib/bmad-dir.mjs';
 import { parseSource, materializeSource } from './lib/source.mjs';
 import { readAndValidateManifest } from './lib/plugin-json.mjs';
-import { readUserIgnores, buildIgnoreMatcher, buildCopyList, validateDeclaredPaths } from './lib/install-plan.mjs';
-import { copyDir, atomicSwapDir } from './lib/fs-safe.mjs';
+import { readUserIgnores, buildIgnoreMatcher, buildCopyPlan, rewriteManifestPaths, validateDeclaredPaths } from './lib/install-plan.mjs';
+import { stageCopyPlan, atomicSwapDir } from './lib/fs-safe.mjs';
 import { readManifestYaml, addModuleToManifest, appendSkillManifestRows, appendFilesManifestRows } from './lib/manifest-ops.mjs';
 
 // Run the install verb. `opts` shape:
@@ -62,19 +61,25 @@ export async function runInstall(opts) {
     validateDeclaredPaths(materialized.dir, manifest);
     const userIgnores = await readUserIgnores(materialized.dir, manifest);
     const matchIgnore = buildIgnoreMatcher(userIgnores);
-    const copyList = await buildCopyList(materialized.dir, matchIgnore);
+    const { plan, skillDestDirs } = await buildCopyPlan(materialized.dir, manifest, matchIgnore);
+    const rewrittenManifestJson = rewriteManifestPaths(manifest);
 
     if (opts.dryRun) {
       process.stdout.write(`[bmad-module] dry-run: would install ${code} (${manifest.name} ${manifest.version})\n`);
       process.stdout.write(`[bmad-module] target: ${path.join(bmadDir, code)}\n`);
-      process.stdout.write(`[bmad-module] files (${copyList.length}):\n`);
-      for (const rel of copyList) process.stdout.write(`  ${rel}\n`);
+      process.stdout.write(`[bmad-module] files (${plan.length + 1}):\n`);
+      process.stdout.write(`  .claude-plugin/plugin.json (rewritten to canonical paths)\n`);
+      for (const { srcRel, destRel } of plan) {
+        process.stdout.write(srcRel === destRel ? `  ${destRel}\n` : `  ${destRel}  (from ${srcRel})\n`);
+      }
       return;
     }
 
     // §6. Stage to tmp/staged-out, then atomic swap.
     const stagedDir = path.join(path.dirname(materialized.dir), 'staged-out');
-    await copyDir(materialized.dir, stagedDir, (rel) => !copyList.includes(rel) && !isAncestorOfAny(rel, copyList));
+    await stageCopyPlan(materialized.dir, stagedDir, plan, {
+      '.claude-plugin/plugin.json': rewrittenManifestJson,
+    });
     const targetDir = path.join(bmadDir, code);
     try {
       await atomicSwapDir(stagedDir, targetDir);
@@ -93,9 +98,9 @@ export async function runInstall(opts) {
       moduleName: manifest.name,
     });
 
-    const skillDirs = Array.isArray(manifest.skills) ? manifest.skills.map((s) => normalizeSkillDirRelToCode(s)) : [];
-    await appendSkillManifestRows(bmadDir, code, skillDirs);
-    await appendFilesManifestRows(bmadDir, code, copyList);
+    const destPaths = ['.claude-plugin/plugin.json', ...plan.map((p) => p.destRel)];
+    await appendSkillManifestRows(bmadDir, code, skillDestDirs);
+    await appendFilesManifestRows(bmadDir, code, destPaths);
 
     // §8. Warn about Claude-only surfaces.
     const claudeOnly = [];
@@ -108,7 +113,7 @@ export async function runInstall(opts) {
     process.stdout.write(
       `[bmad-module] installed ${code} (${manifest.name} ${manifest.version})${materialized.sha ? ` @ ${materialized.sha.slice(0, 7)}` : ''}\n`,
     );
-    process.stdout.write(`[bmad-module] copied ${copyList.length} file(s) to ${path.relative(projectDir, targetDir)}\n`);
+    process.stdout.write(`[bmad-module] copied ${destPaths.length} file(s) to ${path.relative(projectDir, targetDir)}\n`);
     if (claudeOnly.length) {
       process.stdout.write(
         `[bmad-module] note: ${claudeOnly.join(', ')} were copied but NOT auto-activated. ` +
@@ -122,22 +127,3 @@ export async function runInstall(opts) {
     await materialized.cleanup();
   }
 }
-
-// Strip leading `./` and split the declared skill path. Modules use paths
-// relative to the module root (e.g. `./skills/bmad-devlog-write`). Within
-// `_bmad/<code>/` the same relative layout is preserved, so we just strip
-// the dot-slash.
-function normalizeSkillDirRelToCode(skillPath) {
-  let p = String(skillPath);
-  if (p.startsWith('./')) p = p.slice(2);
-  return p;
-}
-
-// During staging we filter the source tree to just the files we plan to copy.
-// `copyList` is a list of files; we also need to allow their ancestor dirs to
-// be walked. This returns true iff `rel` is a prefix of some path in list.
-function isAncestorOfAny(rel, list) {
-  const prefix = rel + '/';
-  for (const p of list) if (p.startsWith(prefix)) return true;
-  return false;
-}
diff --git a/src/core-skills/bmad-module/scripts/lib/fs-safe.mjs b/src/core-skills/bmad-module/scripts/lib/fs-safe.mjs
index 7f787216d..fe8380844 100644
--- a/src/core-skills/bmad-module/scripts/lib/fs-safe.mjs
+++ b/src/core-skills/bmad-module/scripts/lib/fs-safe.mjs
@@ -64,6 +64,29 @@ export async function copyDir(srcDir, destDir, shouldSkip = () => false) {
   return copied;
 }
 
+// Stage a copy plan into `destDir`: each plan entry copies one file from
+// `srcRoot/srcRel` to `destDir/destRel`. `extras` is an optional map of
+// `destRel → string content` for synthesized files (e.g. a rewritten plugin.json)
+// that have no source-tree counterpart. Returns the union of destRels written.
+export async function stageCopyPlan(srcRoot, destDir, plan, extras = {}) {
+  await fsp.mkdir(destDir, { recursive: true });
+  const written = [];
+  for (const { srcRel, destRel } of plan) {
+    const absSrc = path.join(srcRoot, srcRel);
+    const absDest = path.join(destDir, destRel);
+    await fsp.mkdir(path.dirname(absDest), { recursive: true });
+    await fsp.copyFile(absSrc, absDest);
+    written.push(destRel);
+  }
+  for (const [destRel, content] of Object.entries(extras)) {
+    const absDest = path.join(destDir, destRel);
+    await fsp.mkdir(path.dirname(absDest), { recursive: true });
+    await fsp.writeFile(absDest, content, 'utf8');
+    written.push(destRel);
+  }
+  return written;
+}
+
 // Atomically replace `targetDir` with `stagedDir` contents. Best effort —
 // not truly atomic, but minimizes the inconsistent window.
 //
diff --git a/src/core-skills/bmad-module/scripts/lib/install-plan.mjs b/src/core-skills/bmad-module/scripts/lib/install-plan.mjs
index 69ec7bfc3..66f9a18f4 100644
--- a/src/core-skills/bmad-module/scripts/lib/install-plan.mjs
+++ b/src/core-skills/bmad-module/scripts/lib/install-plan.mjs
@@ -119,3 +119,253 @@ export async function buildCopyList(sourceDir, ignoreMatch) {
   out.sort();
   return out;
 }
+
+// Top-level files we always copy if present (and not ignored). Authors don't
+// have to declare these — they're conventional repo metadata.
+const ALWAYS_TOPLEVEL = new Set([
+  'README.md',
+  'README',
+  'README.rst',
+  'CHANGELOG.md',
+  'CHANGELOG',
+  'LICENSE',
+  'LICENSE.md',
+  'LICENSE.txt',
+  'LICENCE',
+  'LICENCE.md',
+  'NOTICE',
+  'NOTICE.md',
+]);
+
+function stripDotSlash(p) {
+  if (typeof p !== 'string') return p;
+  let s = p.replaceAll('\\', '/');
+  if (s.startsWith('./')) s = s.slice(2);
+  return s;
+}
+
+// Recursively list files under `sourceDir/relDir`, returning POSIX paths
+// relative to `sourceDir`. Skips symlinks and ignore-matched entries.
+async function listFilesUnder(sourceDir, relDir, ignoreMatch) {
+  const out = [];
+  async function walk(rel) {
+    const absDir = path.join(sourceDir, rel);
+    let entries;
+    try {
+      entries = await fs.readdir(absDir, { withFileTypes: true });
+    } catch {
+      return;
+    }
+    for (const entry of entries) {
+      const childRel = rel ? `${rel}/${entry.name}` : entry.name;
+      if (ignoreMatch && ignoreMatch(childRel)) continue;
+      if (entry.isSymbolicLink()) continue;
+      if (entry.isDirectory()) await walk(childRel);
+      else if (entry.isFile()) out.push(childRel);
+    }
+  }
+  await walk(relDir);
+  return out;
+}
+
+// Build a manifest-driven copy plan. Each entry is { srcRel, destRel } in
+// POSIX form, relative to the module's source root / install root respectively.
+//
+// The plan:
+//   - Each declared `skills[]` / `agents[]` / `commands[]` dir is copied
+//     recursively into the canonical slot (`skills/<basename>/...` etc.),
+//     regardless of where the author kept it in source (e.g. under `src/`).
+//   - `bmad.moduleDefinition` → `module.yaml`
+//   - `bmad.moduleHelpCsv` → `module-help.csv`
+//   - `bmad.docs.readme` / `bmad.docs.changelog` / `bmad.docs.homepage`
+//     (relative path) → preserved at module root with their basename.
+//   - `hooks` / `mcpServers` / `lspServers` / `settings` (when string paths) →
+//     canonical root slot (`hooks.json`, `.mcp.json`, etc.).
+//   - `.claude-plugin/plugin.json` is always kept (callers rewrite paths in it
+//     via `rewriteManifestPaths`).
+//   - `.claude-plugin/marketplace.json` is preserved if present.
+//   - Conventional top-level metadata files (README/CHANGELOG/LICENSE/NOTICE)
+//     are copied if present at source root.
+//
+// Anything NOT covered by the above is dropped. This means `tools/`, `website/`,
+// `.github/`, `.trunk/`, etc. don't leak into the install even if the author
+// forgot to list them in `bmad.install.ignore`.
+//
+// Returns: { plan, skillDestDirs } where skillDestDirs is the list of canonical
+// skill paths (`skills/X`) for the skill-manifest writer.
+export async function buildCopyPlan(sourceDir, manifest, ignoreMatch) {
+  const plan = [];
+  const claimedSrc = new Set();
+  const claimedDest = new Set();
+
+  const addFile = (srcRel, destRel) => {
+    if (!srcRel || !destRel) return;
+    if (claimedSrc.has(srcRel)) return;
+    if (claimedDest.has(destRel)) return;
+    claimedSrc.add(srcRel);
+    claimedDest.add(destRel);
+    plan.push({ srcRel, destRel });
+  };
+
+  const addDirRecursive = async (srcRelDir, destRelDir) => {
+    const files = await listFilesUnder(sourceDir, srcRelDir, ignoreMatch);
+    for (const fileSrcRel of files) {
+      const rest = fileSrcRel.slice(srcRelDir.length).replace(/^\//, '');
+      const destRel = rest ? `${destRelDir}/${rest}` : destRelDir;
+      addFile(fileSrcRel, destRel);
+    }
+  };
+
+  // Helper: if `srcRel` exists as a file in source, queue it.
+  const queueFileIfExists = async (srcRel, destRel) => {
+    if (!srcRel) return;
+    if (ignoreMatch && ignoreMatch(srcRel)) return;
+    try {
+      const stat = await fs.stat(path.join(sourceDir, srcRel));
+      if (stat.isFile()) addFile(srcRel, destRel);
+    } catch {
+      /* missing — silently skip; validateDeclaredPaths surfaces declared misses */
+    }
+  };
+
+  // Plugin manifest itself — always kept. Path is rewritten by the caller
+  // before staging; here we just reserve the slot so nothing else claims it.
+  claimedDest.add('.claude-plugin/plugin.json');
+
+  // Optional marketplace.json — copy verbatim if present.
+  await queueFileIfExists('.claude-plugin/marketplace.json', '.claude-plugin/marketplace.json');
+
+  // Skills / agents / commands.
+  const arrCategories = [
+    ['skills', 'skills', manifest.skills],
+    ['agents', 'agents', manifest.agents],
+    ['commands', 'commands', manifest.commands],
+  ];
+  const skillDestDirs = [];
+  for (const [, destPrefix, arr] of arrCategories) {
+    if (!Array.isArray(arr)) continue;
+    for (const declared of arr) {
+      const srcRel = stripDotSlash(declared);
+      if (!srcRel) continue;
+      const destRel = `${destPrefix}/${path.posix.basename(srcRel)}`;
+      await addDirRecursive(srcRel, destRel);
+      if (destPrefix === 'skills') skillDestDirs.push(destRel);
+    }
+  }
+
+  // moduleDefinition / moduleHelpCsv — flatten to canonical names at root.
+  if (typeof manifest.bmad?.moduleDefinition === 'string') {
+    await queueFileIfExists(stripDotSlash(manifest.bmad.moduleDefinition), 'module.yaml');
+  }
+  if (typeof manifest.bmad?.moduleHelpCsv === 'string') {
+    await queueFileIfExists(stripDotSlash(manifest.bmad.moduleHelpCsv), 'module-help.csv');
+  }
+
+  // Top-level docs declared in the manifest — keep at root by basename.
+  const docs = manifest.bmad?.docs;
+  if (docs && typeof docs === 'object') {
+    for (const key of ['readme', 'changelog', 'homepage']) {
+      const v = docs[key];
+      if (typeof v !== 'string') continue;
+      if (/^https?:/i.test(v)) continue;
+      const srcRel = stripDotSlash(v);
+      await queueFileIfExists(srcRel, path.posix.basename(srcRel));
+    }
+  }
+
+  // String-typed Claude-Code surfaces — canonical root slot.
+  const stringSurfaces = [
+    ['hooks', 'hooks.json'],
+    ['mcpServers', '.mcp.json'],
+    ['lspServers', 'lsp-servers.json'],
+    ['settings', 'settings.json'],
+  ];
+  for (const [key, destName] of stringSurfaces) {
+    const v = manifest[key];
+    if (typeof v !== 'string') continue;
+    const srcRel = stripDotSlash(v);
+    if (!srcRel) continue;
+    // If the declared path is a directory, copy it under its basename.
+    try {
+      const stat = await fs.stat(path.join(sourceDir, srcRel));
+      if (stat.isDirectory()) {
+        await addDirRecursive(srcRel, path.posix.basename(srcRel));
+      } else if (stat.isFile()) {
+        addFile(srcRel, destName);
+      }
+    } catch {
+      /* missing — skip */
+    }
+  }
+
+  // Conventional top-level metadata files — copy if present.
+  for (const name of ALWAYS_TOPLEVEL) {
+    await queueFileIfExists(name, name);
+  }
+
+  // Stable order — dest-relative sort makes diffs and dry-run output readable.
+  plan.sort((a, b) => a.destRel.localeCompare(b.destRel));
+  skillDestDirs.sort();
+
+  return { plan, skillDestDirs };
+}
+
+// Produce a rewritten plugin.json where every declared path points at its
+// canonical post-install location (so the on-disk manifest stays self-consistent
+// inside `_bmad/<code>/`). Returns a JSON string.
+export function rewriteManifestPaths(manifest) {
+  const out = structuredClone(manifest);
+
+  const remapArr = (arr, destPrefix) => {
+    if (!Array.isArray(arr)) return arr;
+    return arr.map((entry) => {
+      if (typeof entry !== 'string') return entry;
+      const srcRel = stripDotSlash(entry);
+      return `./${destPrefix}/${path.posix.basename(srcRel)}`;
+    });
+  };
+
+  if (Array.isArray(out.skills)) out.skills = remapArr(out.skills, 'skills');
+  if (Array.isArray(out.agents)) out.agents = remapArr(out.agents, 'agents');
+  if (Array.isArray(out.commands)) out.commands = remapArr(out.commands, 'commands');
+
+  if (typeof out.hooks === 'string') out.hooks = './hooks.json';
+  if (typeof out.mcpServers === 'string') out.mcpServers = './.mcp.json';
+  if (typeof out.lspServers === 'string') out.lspServers = './lsp-servers.json';
+  if (typeof out.settings === 'string') out.settings = './settings.json';
+
+  if (out.bmad && typeof out.bmad === 'object') {
+    if (typeof out.bmad.moduleDefinition === 'string') out.bmad.moduleDefinition = './module.yaml';
+    if (typeof out.bmad.moduleHelpCsv === 'string') out.bmad.moduleHelpCsv = './module-help.csv';
+
+    // customize.schemas — each entry lives inside its skill dir; the skill dir
+    // itself is remapped to `skills/<basename>`, so the schema's new path is
+    // `./skills/<skill-basename>/<file>`.
+    const schemas = out.bmad.customize?.schemas;
+    if (Array.isArray(schemas)) {
+      out.bmad.customize.schemas = schemas.map((entry) => {
+        if (typeof entry !== 'string') return entry;
+        const srcRel = stripDotSlash(entry);
+        const parts = srcRel.split('/');
+        // Heuristic: last two segments are `<skill-name>/<filename>`.
+        if (parts.length >= 2) {
+          const file = parts.at(-1);
+          const skill = parts.at(-2);
+          return `./skills/${skill}/${file}`;
+        }
+        return `./${srcRel}`;
+      });
+    }
+
+    if (out.bmad.docs && typeof out.bmad.docs === 'object') {
+      for (const key of ['readme', 'changelog', 'homepage']) {
+        const v = out.bmad.docs[key];
+        if (typeof v !== 'string') continue;
+        if (/^https?:/i.test(v)) continue;
+        out.bmad.docs[key] = `./${path.posix.basename(stripDotSlash(v))}`;
+      }
+    }
+  }
+
+  return JSON.stringify(out, null, 2) + '\n';
+}
diff --git a/src/core-skills/bmad-module/scripts/update.mjs b/src/core-skills/bmad-module/scripts/update.mjs
index 1eb6cc398..d343767a0 100644
--- a/src/core-skills/bmad-module/scripts/update.mjs
+++ b/src/core-skills/bmad-module/scripts/update.mjs
@@ -1,11 +1,10 @@
-import fs from 'node:fs/promises';
 import path from 'node:path';
 import { EXIT, BmadModuleError } from './lib/exit.mjs';
 import { findBmadDir } from './lib/bmad-dir.mjs';
 import { parseSource, materializeSource } from './lib/source.mjs';
 import { readAndValidateManifest } from './lib/plugin-json.mjs';
-import { readUserIgnores, buildIgnoreMatcher, buildCopyList, validateDeclaredPaths } from './lib/install-plan.mjs';
-import { copyDir, atomicSwapDir, sha256File, pruneEmptyDirs } from './lib/fs-safe.mjs';
+import { readUserIgnores, buildIgnoreMatcher, buildCopyPlan, rewriteManifestPaths, validateDeclaredPaths } from './lib/install-plan.mjs';
+import { stageCopyPlan, atomicSwapDir, sha256File, pruneEmptyDirs } from './lib/fs-safe.mjs';
 import {
   readManifestYaml,
   addModuleToManifest,
@@ -88,14 +87,17 @@ async function updateOne(bmadDir, projectDir, entry, opts) {
       );
     }
 
-    // Build new copy list, stage, swap.
+    // Build new copy plan, stage, swap.
     validateDeclaredPaths(materialized.dir, manifest);
     const userIgnores = await readUserIgnores(materialized.dir, manifest);
     const matchIgnore = buildIgnoreMatcher(userIgnores);
-    const copyList = await buildCopyList(materialized.dir, matchIgnore);
+    const { plan, skillDestDirs } = await buildCopyPlan(materialized.dir, manifest, matchIgnore);
+    const rewrittenManifestJson = rewriteManifestPaths(manifest);
 
     const stagedDir = path.join(path.dirname(materialized.dir), 'staged-out');
-    await copyDir(materialized.dir, stagedDir, (rel) => !copyList.includes(rel) && !isAncestorOfAny(rel, copyList));
+    await stageCopyPlan(materialized.dir, stagedDir, plan, {
+      '.claude-plugin/plugin.json': rewrittenManifestJson,
+    });
     const targetDir = path.join(bmadDir, code);
     try {
       await atomicSwapDir(stagedDir, targetDir);
@@ -115,9 +117,9 @@ async function updateOne(bmadDir, projectDir, entry, opts) {
       rawSource: descriptor.rawInput,
       moduleName: manifest.name,
     });
-    const skillDirs = Array.isArray(manifest.skills) ? manifest.skills.map((s) => (s.startsWith('./') ? s.slice(2) : s)) : [];
-    await appendSkillManifestRows(bmadDir, code, skillDirs);
-    await appendFilesManifestRows(bmadDir, code, copyList);
+    const destPaths = ['.claude-plugin/plugin.json', ...plan.map((p) => p.destRel)];
+    await appendSkillManifestRows(bmadDir, code, skillDestDirs);
+    await appendFilesManifestRows(bmadDir, code, destPaths);
 
     // Prune empty dirs left behind from removed files. (The atomic swap of
     // the module root already replaced everything; this is a no-op guard for
@@ -127,14 +129,8 @@ async function updateOne(bmadDir, projectDir, entry, opts) {
     process.stdout.write(
       `[bmad-module] updated ${code} (${manifest.name} ${manifest.version})${materialized.sha ? ` @ ${materialized.sha.slice(0, 7)}` : ''}\n`,
     );
-    process.stdout.write(`[bmad-module] previous ${oldEntries.length} file(s) → new ${copyList.length} file(s)\n`);
+    process.stdout.write(`[bmad-module] previous ${oldEntries.length} file(s) → new ${destPaths.length} file(s)\n`);
   } finally {
     await materialized.cleanup();
   }
 }
-
-function isAncestorOfAny(rel, list) {
-  const prefix = rel + '/';
-  for (const p of list) if (p.startsWith(prefix)) return true;
-  return false;
-}