enhance(reapply-patches): post-merge verification to catch dropped hunks (#1775)

* feat(reapply-patches): post-merge verification to catch dropped hunks

Add a post-merge verification step to the reapply-patches workflow that
detects when user-modified content hunks are silently lost during
three-way merge. The verification performs line-count sanity checks and
hunk-presence verification against signature lines from each user
addition.

Warnings are advisory — the merge result is kept and the backup remains
available for manual recovery. This strengthens the never-skip invariant
from PR #1474 by ensuring not just that files are processed, but that
their content survives the merge intact.

Closes #1758

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* enhance(reapply-patches): add structural ordering test and refactor test setup (#1758)

- Add ordering test: verification section appears between merge-write
  and status-report steps (positional constraint, not just substring)
- Move file reads into before() hook per project test conventions
- Update commit prefix from feat: to enhance: per contribution taxonomy
  (addition to existing workflow, not new concept)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

commands/gsd/reapply-patches.md

@@ -217,6 +217,21 @@ git -C "$CONFIG_DIR" log --oneline --no-merges -- "{file_path}" | grep -v "gsd:u
 Each matching commit represents an intentional user modification. Use the commit messages and diffs to understand what was changed and why.
 
 4. **Write merged result** to the installed location
+
+### Post-merge verification
+
+After writing each merged file, verify that user modifications survived the merge:
+
+1. **Line-count check:** Count lines in the backup and the merged result. If the merged result has fewer lines than the backup minus the expected upstream removals, flag for review.
+2. **Hunk presence check:** For each user-added section identified during diff analysis, search the merged output for at least the first significant line (non-blank, non-comment) of each addition. Missing signature lines indicate a dropped hunk.
+3. **Report warnings inline** (do not block):
+   ```
+   ⚠ Potential dropped content in {file_path}:
+     - Missing hunk near line {N}: "{first_line_preview}..." ({line_count} lines)
+     - Backup available: {patches_dir}/{file_path}
+   ```
+4. **Track verification status** — add to per-file report: `Merged (verified)` vs `Merged (⚠ {N} hunks may be missing)`
+
 5. **Report status per file:**
    - `Merged` — user modifications applied cleanly (show summary of what was preserved)
    - `Conflict` — user reviewed and chose resolution
@@ -253,4 +268,5 @@ Ask user:
 - [ ] User modifications identified and merged into new version
 - [ ] Conflicts surfaced to user with both versions shown
 - [ ] Status reported for each file with summary of what was preserved
+- [ ] Post-merge verification checks each file for dropped hunks and warns if content appears missing
 </success_criteria>

tests/reapply-verify-hunks.test.cjs

@@ -0,0 +1,102 @@
+/**
+ * GSD Tools Tests - reapply-patches post-merge verification
+ *
+ * Validates that the reapply-patches workflow includes post-merge
+ * verification to detect dropped hunks during three-way merge.
+ *
+ * Closes: #1758
+ */
+
+const { describe, test, before } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('fs');
+const path = require('path');
+
+const WORKFLOW_PATH = path.join(
+  __dirname, '..', 'commands', 'gsd', 'reapply-patches.md'
+);
+
+describe('reapply-patches post-merge verification (#1758)', () => {
+  let content;
+
+  before(() => {
+    content = fs.readFileSync(WORKFLOW_PATH, 'utf8');
+  });
+
+  test('workflow file contains "Post-merge verification" section', () => {
+    assert.ok(
+      content.includes('Post-merge verification'),
+      'workflow must contain a "Post-merge verification" section'
+    );
+  });
+
+  test('workflow mentions "Hunk presence check"', () => {
+
+    assert.ok(
+      content.includes('Hunk presence check'),
+      'workflow must describe hunk presence checking'
+    );
+  });
+
+  test('workflow mentions "Line-count check"', () => {
+
+    assert.ok(
+      content.includes('Line-count check'),
+      'workflow must describe line-count sanity checking'
+    );
+  });
+
+  test('success criteria includes verification', () => {
+
+    const criteria = content.split('<success_criteria>')[1] || '';
+    assert.ok(
+      criteria.includes('Post-merge verification') ||
+      criteria.includes('dropped hunks'),
+      'success_criteria must reference post-merge verification or dropped hunks'
+    );
+  });
+
+  test('verification warns but never auto-reverts', () => {
+
+    assert.ok(
+      content.includes('do not block'),
+      'verification must be advisory (do not block)'
+    );
+  });
+
+  test('verification references backup availability for recovery', () => {
+
+    assert.ok(
+      content.includes('Backup available'),
+      'verification warning must reference backup path for manual recovery'
+    );
+  });
+
+  test('verification tracks per-file status', () => {
+
+    assert.ok(
+      content.includes('Merged (verified)') &&
+      content.includes('hunks may be missing'),
+      'verification must distinguish "Merged (verified)" from "hunks may be missing" status'
+    );
+  });
+
+  test('verification section appears between merge-write and status-report steps', () => {
+    const mergeWritePos = content.indexOf('Write merged result');
+    const verificationPos = content.indexOf('Post-merge verification');
+    const statusReportPos = content.indexOf('Report status per file');
+
+    assert.ok(mergeWritePos > -1, 'workflow must contain "Write merged result" step');
+    assert.ok(verificationPos > -1, 'workflow must contain "Post-merge verification" section');
+    assert.ok(statusReportPos > -1, 'workflow must contain "Report status per file" step');
+
+    assert.ok(
+      mergeWritePos < verificationPos,
+      'Post-merge verification must appear after "Write merged result"'
+    );
+    assert.ok(
+      verificationPos < statusReportPos,
+      'Post-merge verification must appear before "Report status per file"'
+    );
+  });
+});