feat(cli): add dub modify --into stack branch workflow

QUICKSTART.md

@@ -166,6 +166,10 @@ dub repo        # current repository GitHub page
 When feedback lands on a middle branch:
 
 ```bash
+# from anywhere in the same stack, target that branch directly
+dub m --into feat/auth-login -a -m "fix: address review feedback"
+
+# or switch first, then modify in-place
 dub co feat/auth-login
 
 # amend current commit

README.md

@@ -205,6 +205,9 @@ dub modify -vv
 
 # interactive rebase of this branch's commits
 dub modify --interactive-rebase
+
+# apply changes to an older branch in the current stack
+dub modify --into feat/auth-login -a -m "fix: address feedback"
 ```
 
 Flags:
@@ -216,6 +219,7 @@ Flags:
 - `-m, --message <message>` (repeatable)
 - `-v, --verbose` (repeatable)
 - `--interactive-rebase`
+- `--into <branch>` (modify another branch in current stack and restack descendants)
 
 ### `dub checkout` / `dub co`
 

apps/docs/content/docs/commands/modify.mdx

@@ -26,6 +26,9 @@ dub modify -vv
 
 # Interactive rebase of this branch's commits
 dub modify --interactive-rebase
+
+# Apply changes to an older branch in the current stack
+dub modify --into feat/auth-login -a -m "fix: address feedback"
 ```
 
 ## Flags
@@ -40,6 +43,7 @@ dub modify --interactive-rebase
 | `-m, --message <msg>` | Commit message (repeatable) |
 | `-v, --verbose` | Show diff before modify (repeatable: `-vv` for staged+unstaged) |
 | `--interactive-rebase` | Interactive rebase of branch commits |
+| `--into <branch>` | Modify another branch in the current stack, then restack descendants |
 
 **Aliases:** `dub m`
 

docs/reports/2026-03-13-ds-3wn-autoship-report.md

@@ -0,0 +1,128 @@
+# Autonomous Ship Report
+
+## 1. Overview
+
+- Date: 2026-03-13
+- Bead ID: ds-3wn
+- Bead title: Fix dub modify workflow for editing an older PR in a stack
+- Assignee: Daniel Wise
+- PR link: https://github.com/wiseiodev/dubstack/pull/32
+
+## 2. Scope Completed
+
+- Primary objective:
+  - Add `dub modify --into <branch>` support to target an older stack branch and restack descendants.
+  - Keep users anchored with clear validation and conflict recovery messaging.
+  - Update docs and tests for happy path and error behavior.
+
+- Acceptance criteria completed:
+  - Users can apply modify to an older stack branch in the current stack.
+  - Descendant branches are restacked when possible, conflicts are surfaced.
+  - Invalid targets fail with explicit `DubError` messages.
+  - Docs and tests cover new behavior.
+
+- Out-of-scope items intentionally deferred:
+  - Additional proactive dirty working-tree staging-risk heuristics for unstaged file carry-over.
+  - Conflict message refactor beyond current branch-aware log line behavior.
+
+## 3. Assumptions Made (No User Questions Mode)
+
+- Assumption 1: `ds-3wn` remained the active issue to complete and should continue through PR flow.
+- Assumption 2: using `dub`-style stack semantics as-is was preferred over introducing new flow abstractions.
+
+## 4. Plan Review Council (Architect, Prefer Claude)
+
+- Major feedback:
+  - Earlier review required stronger conflict-restack semantics and validation guardrails.
+- Plan changes applied:
+  - Added explicit `--into` flow design, branch validation, restack conflict handling, and test coverage plan.
+- Risks mitigated after revision:
+  - Reduced risk of restacking the wrong stack by validating target branch from current stack only.
+
+## 5. Implementation Summary
+
+- Files changed:
+  - `README.md`
+  - `QUICKSTART.md`
+  - `apps/docs/content/docs/commands/modify.mdx`
+  - `packages/cli/src/commands/modify.ts`
+  - `packages/cli/src/commands/modify.test.ts`
+  - `packages/cli/src/commands/modify-into.test.ts`
+  - `packages/cli/src/index.ts`
+
+- Core logic updates:
+  - Added `--into` command option and branching validation in `modify`.
+  - Implemented target branch checkout and post-modify restack flow with conflict-aware branch restoration.
+  - Integrated `printVerboseDiff` with existing `runModifyFlow` behavior.
+  - Added explicit root-branch and cross-stack safeguards.
+
+- Pattern/standards alignment notes:
+  - Kept edits within existing CLI and command helper style.
+  - Preserved explicit `DubError` UX wording and existing restack semantics.
+
+## 6. Quality Gates - Pass 1 (Sequential)
+
+- `pnpm checks`: success, no warnings
+- `pnpm typecheck`: success, no warnings
+- `pnpm test`: success, all tests passing (499/499)
+- `pnpm evals` (only if AI metadata/prompt outputs changed): not run (not changed)
+- Warnings observed: 0
+
+## 7. Code Review Council (Staff Engineer, Prefer Claude+Codex+Gemini)
+
+- Critical issues found:
+  - Review initially flagged stale concerns in docs/option coverage and missing test-file diff listing; both were already addressed in current working tree.
+
+- Minor issues found:
+  - Suggestion to broaden conflict guidance for `--into` remains optional and was intentionally deferred.
+
+- Fixes applied:
+  - Reconciled command docs and option wiring.
+  - Ensured tests include unit + integration-style coverage for `--into` path and invalid targets.
+
+- Feedback rejected and why:
+  - No outstanding required feedback blocking merge.
+
+## 8. Quality Gates - Pass 2 (Sequential)
+
+- `pnpm checks`: success, no warnings
+- `pnpm typecheck`: success, no warnings
+- `pnpm test`: success, all tests passing (499/499)
+- `pnpm evals` (only if AI metadata/prompt outputs changed): not run (not changed)
+- Warnings observed: 0
+
+## 9. Follow-up Beads
+
+- Created issues (`discovered-from:<current-id>`): none
+- Deferred items:
+  - Optional unstaged-work detection in `--into` workflows (non-blocking)
+
+## 10. PR Checks Watch Loop
+
+- First `gh pr checks --watch` result: initially Vercel deploy checks showed cancellation, then re-ran.
+- Issues found: Vercel preview cancellation noise during first run.
+- Fixes applied: re-ran `gh pr checks --watch` after deployment progressed.
+- Number of watch/fix cycles: 2
+- Final checks status: pass
+  - autofix: pass
+  - check: pass
+  - merge-order: pass
+  - Vercel Preview Comments: pass
+  - Vercel: pass
+
+## 11. Copilot PR Review Resolution
+
+- Copilot review present: no
+- Total Copilot comments: 0
+- Comments resolved: 0
+- Rejected comments and rationale: none
+- Additional code/test changes required: none
+
+## 12. Final Status
+
+- Ready for merge: yes
+- Remaining blockers: none
+- Handoff notes:
+  - Changes are committed on branch `codex/ds-3wn-modify-into`.
+  - PR: https://github.com/wiseiodev/dubstack/pull/32
+  - Issue `ds-3wn` is closed in bd.

packages/cli/src/commands/modify-into.test.ts

@@ -0,0 +1,58 @@
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import { createTestRepo, gitInRepo } from '../../test/helpers';
+import { getCurrentBranch } from '../lib/git';
+import { create } from './create';
+import { init } from './init';
+import { modify } from './modify';
+
+let dir: string;
+let cleanup: () => Promise<void>;
+
+beforeEach(async () => {
+  const repo = await createTestRepo();
+  dir = repo.dir;
+  cleanup = repo.cleanup;
+
+  await init(dir);
+  await gitInRepo(dir, ['add', '.']);
+  await gitInRepo(dir, ['commit', '-m', 'init dubstack']);
+});
+
+afterEach(async () => {
+  await cleanup();
+});
+
+describe('modify --into', () => {
+  it('updates an older branch and restores the original branch', async () => {
+    await create('feat/a', dir);
+    fs.writeFileSync(path.join(dir, 'a.txt'), 'feature a\n');
+    await gitInRepo(dir, ['add', '.']);
+    await gitInRepo(dir, ['commit', '-m', 'feat(a): initial']);
+
+    await create('feat/b', dir);
+    fs.writeFileSync(path.join(dir, 'b.txt'), 'feature b\n');
+    await gitInRepo(dir, ['add', '.']);
+    await gitInRepo(dir, ['commit', '-m', 'feat(b): initial']);
+
+    fs.appendFileSync(path.join(dir, 'a.txt'), 'hotfix\n');
+
+    await modify(dir, {
+      into: 'feat/a',
+      all: true,
+      commit: true,
+      message: 'fix(a): apply targeted fix',
+    });
+
+    expect(await getCurrentBranch(dir)).toBe('feat/b');
+
+    const targetLastCommit = (
+      await gitInRepo(dir, ['log', '-1', '--format=%s', 'feat/a'])
+    ).stdout.trim();
+    expect(targetLastCommit).toBe('fix(a): apply targeted fix');
+
+    const fileContent = fs.readFileSync(path.join(dir, 'a.txt'), 'utf8');
+    expect(fileContent).toContain('hotfix');
+  });
+});