diff --git a/src/sync/apply.ts b/src/sync/apply.ts
index 98bc65e..4af440b 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';
 
@@ -241,7 +241,7 @@ async function applyExtraPaths(plan: SyncPlan, extra: ExtraPathPlan): Promise<vo
     const repoPath = path.isAbsolute(entry.repoPath)
       ? entry.repoPath
       : path.join(plan.repoRoot, entry.repoPath);
-    const localPath = entry.sourcePath;
+    const localPath = path.resolve(expandHome(entry.sourcePath, plan.homeDir));
     const entryType: ExtraPathType = entry.type ?? 'file';
 
     if (!(await pathExists(repoPath))) continue;
@@ -266,13 +266,15 @@ async function writeExtraPathManifest(plan: SyncPlan, extra: ExtraPathPlan): Pro
 
   for (const entry of extra.entries) {
     const sourcePath = entry.sourcePath;
-    if (!(await pathExists(sourcePath))) {
+    const actualSourcePath = path.resolve(expandHome(sourcePath, plan.homeDir));
+
+    if (!(await pathExists(actualSourcePath))) {
       continue;
     }
-    const stat = await fs.stat(sourcePath);
+    const stat = await fs.stat(actualSourcePath);
     if (stat.isDirectory()) {
-      await copyDirRecursive(sourcePath, entry.repoPath);
-      const items = await collectExtraPathItems(sourcePath, sourcePath);
+      await copyDirRecursive(actualSourcePath, entry.repoPath);
+      const items = await collectExtraPathItems(actualSourcePath, actualSourcePath);
       entries.push({
         sourcePath,
         repoPath: path.relative(plan.repoRoot, entry.repoPath),
@@ -283,7 +285,7 @@ async function writeExtraPathManifest(plan: SyncPlan, extra: ExtraPathPlan): Pro
       continue;
     }
     if (stat.isFile()) {
-      await copyFileWithMode(sourcePath, entry.repoPath);
+      await copyFileWithMode(actualSourcePath, entry.repoPath);
       entries.push({
         sourcePath,
         repoPath: path.relative(plan.repoRoot, entry.repoPath),
diff --git a/src/sync/paths.test.ts b/src/sync/paths.test.ts
index 9ede236..002c9e9 100644
--- a/src/sync/paths.test.ts
+++ b/src/sync/paths.test.ts
@@ -105,6 +105,44 @@ describe('buildSyncPlan', () => {
     expect(plan.extraConfigs.allowlist.length).toBe(1);
   });
 
+  it('stores extra manifest sourcePath using portable home paths', () => {
+    const env = { HOME: '/home/test' } as NodeJS.ProcessEnv;
+    const locations = resolveSyncLocations(env, 'linux');
+    const config: SyncConfig = {
+      repo: { owner: 'acme', name: 'config' },
+      includeSecrets: true,
+      extraSecretPaths: ['/home/test/.ssh/id_rsa'],
+      extraConfigPaths: [
+        '/home/test/.config/opencode/custom.json',
+        '~/.config/opencode/other.json',
+      ],
+    };
+
+    const plan = buildSyncPlan(normalizeSyncConfig(config), locations, '/repo', 'linux');
+    const sources = plan.extraConfigs.entries.map((e) => e.sourcePath).sort();
+
+    expect(sources).toEqual(['~/.config/opencode/custom.json', '~/.config/opencode/other.json']);
+    expect(sources.some((p) => p.includes('/home/test'))).toBe(false);
+
+    // Allowlist remains normalized for matching.
+    expect(plan.extraConfigs.allowlist).toContain('/home/test/.config/opencode/custom.json');
+    expect(plan.extraConfigs.allowlist).toContain('/home/test/.config/opencode/other.json');
+  });
+
+  it('keeps extra manifest sourcePath absolute when outside home dir', () => {
+    const env = { HOME: '/home/test' } as NodeJS.ProcessEnv;
+    const locations = resolveSyncLocations(env, 'linux');
+    const config: SyncConfig = {
+      repo: { owner: 'acme', name: 'config' },
+      includeSecrets: false,
+      extraConfigPaths: ['/etc/hosts'],
+    };
+
+    const plan = buildSyncPlan(normalizeSyncConfig(config), locations, '/repo', 'linux');
+
+    expect(plan.extraConfigs.entries.map((e) => e.sourcePath)).toEqual(['/etc/hosts']);
+  });
+
   it('excludes auth files when using 1password backend', () => {
     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..8a19577 100644
--- a/src/sync/paths.ts
+++ b/src/sync/paths.ts
@@ -126,6 +126,32 @@ export function expandHome(inputPath: string, homeDir: string): string {
   return inputPath;
 }
 
+function collapseHome(
+  inputPath: string,
+  homeDir: string,
+  platform: NodeJS.Platform = process.platform
+): string {
+  if (!inputPath) return inputPath;
+  if (!homeDir) return inputPath;
+
+  if (inputPath === '~' || inputPath.startsWith('~/')) return inputPath;
+
+  // Best-effort on POSIX platforms.
+  if (platform === 'win32') return inputPath;
+
+  const resolvedHome = path.resolve(homeDir);
+  const resolvedPath = path.resolve(inputPath);
+
+  if (resolvedPath === resolvedHome) return '~';
+
+  const prefix = `${resolvedHome}${path.sep}`;
+  if (resolvedPath.startsWith(prefix)) {
+    return `~/${resolvedPath.slice(prefix.length)}`;
+  }
+
+  return inputPath;
+}
+
 export function normalizePath(
   inputPath: string,
   homeDir: string,
@@ -315,11 +341,20 @@ function buildExtraPathPlan(
   manifestPath: string,
   platform: NodeJS.Platform
 ): ExtraPathPlan {
-  const allowlist = (inputPaths ?? []).map((entry) =>
+  // Keep sourcePath portable ("~/...") so the manifest and hashed filenames
+  // are stable across machines/OSes. Use a normalized allowlist for matching.
+  const rawPaths = (inputPaths ?? []).filter(
+    (entry) => typeof entry === 'string' && entry.length > 0
+  );
+  const portablePaths = rawPaths.map((entry) =>
+    collapseHome(entry, locations.xdg.homeDir, platform)
+  );
+
+  const allowlist = portablePaths.map((entry) =>
     normalizePath(entry, locations.xdg.homeDir, platform)
   );
 
-  const entries = allowlist.map((sourcePath) => ({
+  const entries = portablePaths.map((sourcePath) => ({
     sourcePath,
     repoPath: path.join(repoExtraDir, encodeExtraPath(sourcePath)),
   }));