diff --git a/.gitignore b/.gitignore
index 331672b..3e82476 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,4 +11,5 @@ coverage/
 .bun.lockb
 .memory/
 opencode-plugin-template/
-opencode-docs-*/
\ No newline at end of file
+opencode-docs-*/
+.worktrees/
diff --git a/README.md b/README.md
index e296e79..67a22b5 100644
--- a/README.md
+++ b/README.md
@@ -89,9 +89,12 @@ Create `~/.config/opencode/opencode-synced.jsonc`:
 - `~/.config/opencode/opencode.json` and `opencode.jsonc`
 - `~/.config/opencode/AGENTS.md`
 - `~/.config/opencode/agent/`, `command/`, `mode/`, `tool/`, `themes/`, `plugin/`
+- `~/.config/opencode/agents/`, `instructions/`, `plugins/`, `skills/`, `superpowers/`
 - `~/.local/state/opencode/model.json` (model favorites)
 - Any extra paths in `extraConfigPaths` (allowlist, files or folders)
 
+Extra path manifests store home-relative `~` paths when possible to avoid Linux/macOS/WSL path churn.
+
 ### Secrets (private repos only)
 
 Enable secrets with `/sync-enable-secrets` or set `"includeSecrets": true`:
diff --git a/src/sync/apply.test.ts b/src/sync/apply.test.ts
new file mode 100644
index 0000000..9492893
--- /dev/null
+++ b/src/sync/apply.test.ts
@@ -0,0 +1,166 @@
+import { mkdir, mkdtemp, readFile, rm, writeFile } from 'node:fs/promises';
+import os from 'node:os';
+import path from 'node:path';
+import { describe, expect, it } from 'vitest';
+
+import { syncRepoToLocal } from './apply.js';
+import type { SyncPlan } from './paths.js';
+import { normalizePath } from './paths.js';
+
+describe('syncRepoToLocal extra manifest repoPath validation', () => {
+  it('rejects absolute repoPath values from manifest', async () => {
+    const root = await mkdtemp(path.join(os.tmpdir(), 'opencode-sync-apply-'));
+    try {
+      const homeDir = path.join(root, 'home');
+      const repoRoot = path.join(root, 'repo');
+      const localPath = path.join(homeDir, 'target.txt');
+      const manifestPath = path.join(repoRoot, 'config', 'extra-manifest.json');
+
+      await mkdir(path.dirname(manifestPath), { recursive: true });
+      await writeFile(
+        manifestPath,
+        JSON.stringify(
+          {
+            entries: [
+              {
+                sourcePath: localPath,
+                repoPath: '/etc/passwd',
+                type: 'file',
+              },
+            ],
+          },
+          null,
+          2
+        ),
+        'utf8'
+      );
+
+      const plan: SyncPlan = {
+        items: [],
+        extraConfigs: {
+          allowlist: [normalizePath(localPath, homeDir, 'linux')],
+          manifestPath,
+          entries: [],
+        },
+        extraSecrets: {
+          allowlist: [],
+          manifestPath: path.join(repoRoot, 'secrets', 'extra-manifest.json'),
+          entries: [],
+        },
+        repoRoot,
+        homeDir,
+        platform: 'linux',
+      };
+
+      await expect(syncRepoToLocal(plan, null)).rejects.toThrow(/absolute paths are not allowed/);
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  it('rejects traversal repoPath values from manifest', async () => {
+    const root = await mkdtemp(path.join(os.tmpdir(), 'opencode-sync-apply-'));
+    try {
+      const homeDir = path.join(root, 'home');
+      const repoRoot = path.join(root, 'repo');
+      const localPath = path.join(homeDir, 'target.txt');
+      const manifestPath = path.join(repoRoot, 'config', 'extra-manifest.json');
+
+      await mkdir(path.dirname(manifestPath), { recursive: true });
+      await writeFile(
+        manifestPath,
+        JSON.stringify(
+          {
+            entries: [
+              {
+                sourcePath: localPath,
+                repoPath: '../../etc/passwd',
+                type: 'file',
+              },
+            ],
+          },
+          null,
+          2
+        ),
+        'utf8'
+      );
+
+      const plan: SyncPlan = {
+        items: [],
+        extraConfigs: {
+          allowlist: [normalizePath(localPath, homeDir, 'linux')],
+          manifestPath,
+          entries: [],
+        },
+        extraSecrets: {
+          allowlist: [],
+          manifestPath: path.join(repoRoot, 'secrets', 'extra-manifest.json'),
+          entries: [],
+        },
+        repoRoot,
+        homeDir,
+        platform: 'linux',
+      };
+
+      await expect(syncRepoToLocal(plan, null)).rejects.toThrow(/path escapes repository root/);
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  it('accepts safe relative repoPath values from manifest', async () => {
+    const root = await mkdtemp(path.join(os.tmpdir(), 'opencode-sync-apply-'));
+    try {
+      const homeDir = path.join(root, 'home');
+      const repoRoot = path.join(root, 'repo');
+      const localPath = path.join(homeDir, 'target.txt');
+      const manifestPath = path.join(repoRoot, 'config', 'extra-manifest.json');
+      const repoSourcePath = path.join(repoRoot, 'config', 'extra', 'safe.txt');
+
+      await mkdir(path.dirname(manifestPath), { recursive: true });
+      await mkdir(path.dirname(repoSourcePath), { recursive: true });
+      await writeFile(repoSourcePath, 'safe-data\n', 'utf8');
+      await writeFile(
+        manifestPath,
+        JSON.stringify(
+          {
+            entries: [
+              {
+                sourcePath: localPath,
+                repoPath: 'config/extra/safe.txt',
+                type: 'file',
+              },
+            ],
+          },
+          null,
+          2
+        ),
+        'utf8'
+      );
+
+      const plan: SyncPlan = {
+        items: [],
+        extraConfigs: {
+          allowlist: [normalizePath(localPath, homeDir, 'linux')],
+          manifestPath,
+          entries: [],
+        },
+        extraSecrets: {
+          allowlist: [],
+          manifestPath: path.join(repoRoot, 'secrets', 'extra-manifest.json'),
+          entries: [],
+        },
+        repoRoot,
+        homeDir,
+        platform: 'linux',
+      };
+
+      await syncRepoToLocal(plan, null);
+
+      const output = await readFile(localPath, 'utf8');
+      expect(output).toBe('safe-data\n');
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+});
diff --git a/src/sync/apply.ts b/src/sync/apply.ts
index 98bc65e..e4f1df2 100644
--- a/src/sync/apply.ts
+++ b/src/sync/apply.ts
@@ -17,7 +17,7 @@ import {
   stripOverrideKeys,
 } from './mcp-secrets.js';
 import type { ExtraPathPlan, SyncItem, SyncPlan } from './paths.js';
-import { normalizePath } from './paths.js';
+import { expandHome, normalizePath } from './paths.js';
 
 type ExtraPathType = 'file' | 'dir';
 
@@ -238,10 +238,8 @@ async function applyExtraPaths(plan: SyncPlan, extra: ExtraPathPlan): Promise<vo
     const isAllowed = allowlist.includes(normalized);
     if (!isAllowed) continue;
 
-    const repoPath = path.isAbsolute(entry.repoPath)
-      ? entry.repoPath
-      : path.join(plan.repoRoot, entry.repoPath);
-    const localPath = entry.sourcePath;
+    const repoPath = resolveManifestRepoPath(plan.repoRoot, entry.repoPath);
+    const localPath = expandHome(entry.sourcePath, plan.homeDir);
     const entryType: ExtraPathType = entry.type ?? 'file';
 
     if (!(await pathExists(repoPath))) continue;
@@ -374,6 +372,25 @@ function resolveExtraPathItem(basePath: string, relativePath: string): string |
   return resolvedPath;
 }
 
+function resolveManifestRepoPath(repoRoot: string, manifestRepoPath: string): string {
+  if (path.isAbsolute(manifestRepoPath)) {
+    throw new Error('Invalid extra manifest repoPath: absolute paths are not allowed');
+  }
+
+  const resolvedRepoRoot = path.resolve(repoRoot);
+  const resolvedRepoPath = path.resolve(repoRoot, manifestRepoPath);
+  const relativePath = path.relative(resolvedRepoRoot, resolvedRepoPath);
+  const outsideRepo =
+    relativePath === '..' ||
+    relativePath.startsWith(`..${path.sep}`) ||
+    path.isAbsolute(relativePath);
+  if (outsideRepo) {
+    throw new Error('Invalid extra manifest repoPath: path escapes repository root');
+  }
+
+  return resolvedRepoPath;
+}
+
 function isDeepEqual(left: unknown, right: unknown): boolean {
   if (left === right) return true;
   if (typeof left !== typeof right) return false;
diff --git a/src/sync/paths.test.ts b/src/sync/paths.test.ts
index 9ede236..16beeb2 100644
--- a/src/sync/paths.test.ts
+++ b/src/sync/paths.test.ts
@@ -41,6 +41,24 @@ describe('resolveSyncLocations', () => {
 });
 
 describe('buildSyncPlan', () => {
+  it('includes modern opencode config directories by default', () => {
+    const env = { HOME: '/home/test' } as NodeJS.ProcessEnv;
+    const locations = resolveSyncLocations(env, 'linux');
+    const config: SyncConfig = {
+      repo: { owner: 'acme', name: 'config' },
+      includeSecrets: false,
+    };
+
+    const plan = buildSyncPlan(normalizeSyncConfig(config), locations, '/repo', 'linux');
+    const localPaths = new Set(plan.items.map((item) => item.localPath));
+
+    expect(localPaths.has('/home/test/.config/opencode/agents')).toBe(true);
+    expect(localPaths.has('/home/test/.config/opencode/instructions')).toBe(true);
+    expect(localPaths.has('/home/test/.config/opencode/plugins')).toBe(true);
+    expect(localPaths.has('/home/test/.config/opencode/skills')).toBe(true);
+    expect(localPaths.has('/home/test/.config/opencode/superpowers')).toBe(true);
+  });
+
   it('excludes secrets when includeSecrets is false', () => {
     const env = { HOME: '/home/test' } as NodeJS.ProcessEnv;
     const locations = resolveSyncLocations(env, 'linux');
@@ -87,6 +105,49 @@ describe('buildSyncPlan', () => {
     expect(plan.extraConfigs.allowlist.length).toBe(0);
   });
 
+  it('stores extra config paths as portable home-relative source paths', () => {
+    const env = { HOME: '/home/test' } as NodeJS.ProcessEnv;
+    const locations = resolveSyncLocations(env, 'linux');
+    const config: SyncConfig = {
+      repo: { owner: 'acme', name: 'config' },
+      includeSecrets: false,
+      extraConfigPaths: ['/home/test/.config/opencode/skills'],
+    };
+
+    const plan = buildSyncPlan(normalizeSyncConfig(config), locations, '/repo', 'linux');
+
+    expect(plan.extraConfigs.entries[0]?.sourcePath).toBe('~/.config/opencode/skills');
+  });
+
+  it('uses stable repo paths for home-relative extras across platforms', () => {
+    const linuxEnv = { HOME: '/home/test' } as NodeJS.ProcessEnv;
+    const macEnv = { HOME: '/Users/test' } as NodeJS.ProcessEnv;
+    const linuxLocations = resolveSyncLocations(linuxEnv, 'linux');
+    const macLocations = resolveSyncLocations(macEnv, 'darwin');
+    const linuxConfig: SyncConfig = {
+      repo: { owner: 'acme', name: 'config' },
+      includeSecrets: false,
+      extraConfigPaths: ['/home/test/.config/opencode/skills'],
+    };
+    const macConfig: SyncConfig = {
+      repo: { owner: 'acme', name: 'config' },
+      includeSecrets: false,
+      extraConfigPaths: ['/Users/test/.config/opencode/skills'],
+    };
+
+    const linuxPlan = buildSyncPlan(
+      normalizeSyncConfig(linuxConfig),
+      linuxLocations,
+      '/repo',
+      'linux'
+    );
+    const macPlan = buildSyncPlan(normalizeSyncConfig(macConfig), macLocations, '/repo', 'darwin');
+
+    expect(linuxPlan.extraConfigs.entries[0]?.repoPath).toBe(
+      macPlan.extraConfigs.entries[0]?.repoPath
+    );
+  });
+
   it('includes secrets when includeSecrets is true', () => {
     const env = { HOME: '/home/test' } as NodeJS.ProcessEnv;
     const locations = resolveSyncLocations(env, 'linux');
diff --git a/src/sync/paths.ts b/src/sync/paths.ts
index 995118d..1f6285d 100644
--- a/src/sync/paths.ts
+++ b/src/sync/paths.ts
@@ -51,7 +51,19 @@ const DEFAULT_SYNC_CONFIG_NAME = 'opencode-synced.jsonc';
 const DEFAULT_OVERRIDES_NAME = 'opencode-synced.overrides.jsonc';
 const DEFAULT_STATE_NAME = 'sync-state.json';
 
-const CONFIG_DIRS = ['agent', 'command', 'mode', 'tool', 'themes', 'plugin'];
+const CONFIG_DIRS = [
+  'agent',
+  'command',
+  'mode',
+  'tool',
+  'themes',
+  'plugin',
+  'agents',
+  'instructions',
+  'plugins',
+  'skills',
+  'superpowers',
+];
 const SESSION_DIRS = ['storage/session', 'storage/message', 'storage/part', 'storage/session_diff'];
 const PROMPT_STASH_FILES = ['prompt-stash.jsonl', 'prompt-history.jsonl'];
 const MODEL_FAVORITES_FILE = 'model.json';
@@ -156,6 +168,30 @@ export function encodeExtraPath(inputPath: string): string {
   return `${base}-${hash}`;
 }
 
+export function toPortableSourcePath(
+  inputPath: string,
+  homeDir: string,
+  platform: NodeJS.Platform = process.platform
+): string {
+  if (!homeDir) {
+    return inputPath;
+  }
+
+  const normalizedInput = normalizePath(inputPath, homeDir, platform);
+  const normalizedHome = normalizePath(homeDir, homeDir, platform);
+  if (normalizedInput === normalizedHome) {
+    return '~';
+  }
+
+  const relativeToHome = path.relative(normalizedHome, normalizedInput);
+  const outsideHome = relativeToHome === '..' || relativeToHome.startsWith(`..${path.sep}`);
+  if (outsideHome || path.isAbsolute(relativeToHome)) {
+    return normalizedInput;
+  }
+
+  return `~/${relativeToHome.split(path.sep).join('/')}`;
+}
+
 export const encodeSecretPath = encodeExtraPath;
 
 export function resolveRepoRoot(config: SyncConfig | null, locations: SyncLocations): string {
@@ -319,10 +355,13 @@ function buildExtraPathPlan(
     normalizePath(entry, locations.xdg.homeDir, platform)
   );
 
-  const entries = allowlist.map((sourcePath) => ({
-    sourcePath,
-    repoPath: path.join(repoExtraDir, encodeExtraPath(sourcePath)),
-  }));
+  const entries = allowlist.map((sourcePath) => {
+    const portableSourcePath = toPortableSourcePath(sourcePath, locations.xdg.homeDir, platform);
+    return {
+      sourcePath: portableSourcePath,
+      repoPath: path.join(repoExtraDir, encodeExtraPath(portableSourcePath)),
+    };
+  });
 
   return {
     allowlist,