test(#1973): consolidate 48 workflow regression tests into workflow-aspect suites

Fold 48 issue-named workflow-markdown regression files into the canonical test
that owns each workflow aspect (execute-phase-*, plan-phase-*, quick-*, discuss-*,
worktree-cleanup, secure-phase, verify, update, settings, etc.), across 32 existing
suites. Verbatim block-scoped describe wrappers; 281 subtests conserved 1:1. No new
test files. Host-env pre-check: only gsd-settings-advanced spawns CLI and it sets no
GSD_WORKSTREAM/GSD_PROJECT value — no leak risk.

Regenerates regression-name allowlist (222->181), ratchets file-count allowlist
(verify 11->10), makes 30 relocated allow-test-rule exemptions issue-ref-compliant
(ADR-456; prunes 30 stale ids). lint:ci green.

Part of epic #1969. Closes #1973.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

tests/git-base-branch.test.cjs

@@ -338,3 +338,101 @@ describe('#1406: setGsdConfig prototype-pollution guard', () => {
     assert.strictEqual(cfg.git.base_branch, 'develop');
   });
 });
+
+
+// ────────────────────────────────────────────────────────────────────────
+// Folded from tests/bug-2004-pr-branch-milestone.test.cjs — consolidation epic #1969 (B4 #1973)
+// ────────────────────────────────────────────────────────────────────────
+{
+  const { describe: __foldDescribe } = require('node:test');
+  __foldDescribe("folded:bug-2004-pr-branch-milestone (consolidation epic #1969 B4 #1973)", () => {
+/**
+ * Regression tests for bug #2004
+ *
+ * /gsd-pr-branch must not exclude milestone archive and structural planning
+ * commits. The previous implementation filtered ALL .planning/-only commits,
+ * including STATE.md, ROADMAP.md, MILESTONES.md, and milestones/** updates
+ * that are needed to preserve repository planning state after a merge.
+ *
+ * Fixed: pr-branch.md now distinguishes:
+ *   - Transient planning commits (phase plans, summaries, research, context) → EXCLUDE
+ *   - Structural planning commits (STATE.md, ROADMAP.md, MILESTONES.md,
+ *     PROJECT.md, milestones/**) → INCLUDE
+ *   - Code commits (any non-.planning/ file) → INCLUDE
+ *   - Mixed commits (code + planning) → INCLUDE
+ */
+
+'use strict';
+
+const { describe, test } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const path = require('node:path');
+
+const workflowPath = path.resolve(
+  __dirname, '..', 'gsd-core', 'workflows', 'pr-branch.md'
+);
+
+describe('bug #2004: pr-branch preserves structural planning commits', () => {
+  let content;
+
+  test('setup: pr-branch workflow is readable', () => {
+    content = fs.readFileSync(workflowPath, 'utf-8');
+    assert.ok(content.length > 0, 'pr-branch.md must not be empty');
+  });
+
+  test('workflow distinguishes structural vs transient planning commits', () => {
+    content = content || fs.readFileSync(workflowPath, 'utf-8');
+    // Must contain language distinguishing structural from transient/phase planning files
+    assert.ok(
+      /structural|milestone.*archive|STATE\.md.*INCLUDE|preserve.*milestone|milestone.*preserve/i.test(content),
+      'pr-branch.md must distinguish structural planning commits from transient ones'
+    );
+  });
+
+  test('workflow lists STATE.md and ROADMAP.md as structural files to preserve', () => {
+    content = content || fs.readFileSync(workflowPath, 'utf-8');
+    assert.ok(
+      content.includes('STATE.md'),
+      'pr-branch.md must reference STATE.md as a structural file to preserve'
+    );
+    assert.ok(
+      content.includes('ROADMAP.md'),
+      'pr-branch.md must reference ROADMAP.md as a structural file to preserve'
+    );
+  });
+
+  test('workflow lists MILESTONES.md or milestones/ as structural files to preserve', () => {
+    content = content || fs.readFileSync(workflowPath, 'utf-8');
+    assert.ok(
+      content.includes('MILESTONES.md') || content.includes('milestones/'),
+      'pr-branch.md must reference MILESTONES.md or milestones/ as structural files to preserve'
+    );
+  });
+
+  test('workflow has four commit categories (code, planning-only, mixed, structural)', () => {
+    content = content || fs.readFileSync(workflowPath, 'utf-8');
+    // Must have at least a "structural" or "milestone" category beyond the original three
+    assert.ok(
+      /structural.*commit|milestone.*commit|commit.*structural|commit.*milestone/i.test(content) ||
+      /INCLUDE.*STATE\.md|STATE\.md.*INCLUDE/i.test(content),
+      'pr-branch.md must classify structural planning commits as INCLUDE'
+    );
+  });
+
+  test('create_pr_branch step does not rm -r --cached all of .planning/', () => {
+    content = content || fs.readFileSync(workflowPath, 'utf-8');
+    // The original bug: `git rm -r --cached .planning/` nuked structural files.
+    // The fix must either remove this wholesale rm or scope it to transient dirs.
+    // Acceptable: narrowed rm targeting only phase/, quick/, research/, etc.
+    // Not acceptable: `git rm -r --cached .planning/` with no scoping.
+    const hasUnscoped = /git rm -r --cached \.planning\/(?!\*)?(?!phases|quick|research|threads|todos|debug|seeds|ui-reviews|codebase)/
+      .test(content);
+    assert.ok(
+      !hasUnscoped,
+      'create_pr_branch must not use unscoped "git rm -r --cached .planning/" — scope to transient subdirectories only'
+    );
+  });
+});
+  });
+}