diff --git a/src/git/__tests__/git-service.test.ts b/src/git/__tests__/git-service.test.ts
index 923a6109..a1c86da7 100644
--- a/src/git/__tests__/git-service.test.ts
+++ b/src/git/__tests__/git-service.test.ts
@@ -1061,6 +1061,73 @@ describe('GitService', () => {
     });
   });
 
+  // Regression coverage for #94: a rebase that conflicts on a submodule
+  // gitlink leaves three mode-160000 entries for one path in the index. The
+  // conflict must be listed (so the UI can stage it) and resolved with
+  // `git add -- <path>` in the superproject, exactly like the manual command.
+  describe('gitlink (submodule) conflicts (#94)', () => {
+    const GITLINK_STAGES =
+      '160000 aaaa000000000000000000000000000000000000 1\tlibs/lib\n' +
+      '160000 bbbb000000000000000000000000000000000000 2\tlibs/lib\n' +
+      '160000 cccc000000000000000000000000000000000000 3\tlibs/lib\n';
+
+    it('lists a conflicted gitlink from the unmerged index entries', async () => {
+      const calls: string[][] = [];
+      mockExec(service, async (args) => { calls.push(args); return GITLINK_STAGES; });
+
+      expect(await service.getConflictFiles()).toEqual(['libs/lib']);
+      expect(calls[0]).toEqual(['ls-files', '--unmerged']);
+    });
+
+    it('lists mixed file and gitlink conflicts once each', async () => {
+      mockExec(service, async () =>
+        '100644 aaaa000000000000000000000000000000000000 1\tsrc/a.ts\n' +
+        '100644 bbbb000000000000000000000000000000000000 3\tsrc/a.ts\n' +
+        GITLINK_STAGES);
+
+      expect(await service.getConflictFiles()).toEqual(['src/a.ts', 'libs/lib']);
+    });
+
+    it('stageFile stages a gitlink path with git add -- <path>', async () => {
+      const calls: string[][] = [];
+      mockExec(service, async (args) => { calls.push(args); return ''; });
+
+      await service.stageFile('libs/lib');
+      expect(calls[0]).toEqual(['add', '--', 'libs/lib']);
+    });
+
+    it('continueOperation stages only the unmerged gitlink path before continuing', async () => {
+      const calls: string[][] = [];
+      mockExec(service, async (args) => {
+        calls.push(args);
+        return args[0] === 'ls-files' ? GITLINK_STAGES : '';
+      });
+      vi.spyOn(service, 'getOperationState').mockResolvedValue({ type: 'rebase' });
+
+      await service.continueOperation();
+
+      expect(calls).toEqual([
+        ['ls-files', '--unmerged'],
+        ['add', '--', 'libs/lib'],
+        ['rebase', '--continue'],
+      ]);
+    });
+
+    it('continueOperation keeps the blanket stage when nothing is unmerged', async () => {
+      const calls: string[][] = [];
+      mockExec(service, async (args) => { calls.push(args); return ''; });
+      vi.spyOn(service, 'getOperationState').mockResolvedValue({ type: 'rebase' });
+
+      await service.continueOperation();
+
+      expect(calls).toEqual([
+        ['ls-files', '--unmerged'],
+        ['add', '-A'],
+        ['rebase', '--continue'],
+      ]);
+    });
+  });
+
   describe('addRemote URL validation', () => {
     it('accepts https URL', async () => {
       const calls: string[][] = [];
diff --git a/src/git/git-service.ts b/src/git/git-service.ts
index 71e65760..50c93a00 100644
--- a/src/git/git-service.ts
+++ b/src/git/git-service.ts
@@ -1762,8 +1762,26 @@ export class GitService {
 
   async getConflictFiles(): Promise<string[]> {
     try {
-      const raw = await this.exec(['diff', '--name-only', '--diff-filter=U']);
-      return raw.trim().split('\n').filter(Boolean);
+      // Read the unmerged entries straight from the index. A gitlink conflict
+      // (submodule pointer) is three mode-160000 stage entries for one path;
+      // `ls-files --unmerged` always reports them, whereas `git diff
+      // --diff-filter=U` is a working-tree diff and can drop entries based on
+      // diff/submodule configuration (#94). Records are
+      // "<mode> <oid> <stage>\t<path>" (paths are literal: exec runs git with
+      // core.quotePath=false), so collapse the stage entries to one path each.
+      const raw = await this.exec(['ls-files', '--unmerged']);
+      const paths: string[] = [];
+      const seen = new Set<string>();
+      for (const line of raw.split('\n')) {
+        const tab = line.indexOf('\t');
+        if (tab < 0) continue;
+        const path = line.slice(tab + 1);
+        if (path && !seen.has(path)) {
+          seen.add(path);
+          paths.push(path);
+        }
+      }
+      return paths;
     } catch (err) {
       console.warn('Git Graph+: failed to get conflict files:', err instanceof Error ? err.message : err);
       return [];
@@ -1791,8 +1809,19 @@ export class GitService {
   }
 
   async continueOperation(): Promise<void> {
-    // Stage all resolved conflict files before continuing
-    await this.exec(['add', '-A']);
+    // Stage the paths that are still unmerged — the ones the user resolved by
+    // hand — with an explicit `git add -- <path>` instead of a blanket
+    // `add -A`. For a conflicted submodule gitlink that is exactly the manual
+    // `git add <submodule>` that works in the superproject (#94), and it keeps
+    // unrelated working-tree edits out of the rebase/cherry-pick commit.
+    // Nothing unmerged (e.g. an `edit` pause or a squash) keeps the previous
+    // blanket staging so edits made during the pause are still included.
+    const unresolved = await this.getConflictFiles();
+    if (unresolved.length > 0) {
+      await this.exec(['add', '--', ...unresolved]);
+    } else {
+      await this.exec(['add', '-A']);
+    }
     const state = await this.getOperationState();
     switch (state.type) {
       case 'merge': await this.exec(['commit', '--no-edit']); break;