fix(test): stop init-scaffolding from mutating tracked repo files (#1796)

[bradygaster]

Closes #1796.

What was actually mutating the tree

Not the acceptance suite. test/acceptance/acceptance.test.ts run alone leaves git status empty — the worktree guard short-circuits squad init here, so the obvious hypothesis is wrong.

The writer is test/init-scaffolding.test.ts:21:

const TEST_ROOT = join(process.cwd(), `.test-init-scaffold-${randomBytes(4).toString('hex')}`);

The sandbox lives inside the repository. Several cases deliberately exercise init against a sandbox with no .git of its own (initSquad succeeds when git is not initialized at all, and the two monorepo-subfolder cases). Init then walks upward to find the enclosing git root, finds the real repository, and stampVersion() rewrites tracked .github/agents/squad.agent.md from 0.0.0-source to the package version.

Controlled proof

Clean tree, that suite alone:

Tests  24 passed (24)

=== git status after ===
 M .github/agents/squad.agent.md
=== version line ===
<!-- version: 0.13.0 -->

24 tests, all green, silently mutating tracked source. That is the hazard: an agent running a broad git add after a test run commits a spurious version bump.

It was known, and worked around rather than fixed

test/template-sync.test.ts carries two beforeAll re-syncs of scripts/sync-templates.mjs against the real repo. Their comments describe the cause accurately — a race with init-scaffolding running runInit() under the repo root — and then choose to "minimis[e] the window to near-zero".

That is why it survived: the repair ran on every full run, so the damage was intermittent and read as environmental. This is the same shape as #1788 and #1795 — the system reports success while the real outcome is invisible.

The fix

One line: sandbox moves to tmpdir(), so upward git-root resolution can no longer reach the repository.

Plus a two-part guard that is red against the pre-fix state:

FAIL > repository working tree is not mutated by this suite (#1796) > sandbox root is outside the repository working tree
AssertionError: TEST_ROOT (C:\...\bradygaster-fictional-waddle\.test-init-scaffold-99246f71)
  must not live under C:\...\bradygaster-fictional-waddle: expected true to be false

FAIL > repository working tree is not mutated by this suite (#1796) > tracked squad.agent.md files are byte-unchanged after init runs
AssertionError: expected 'M .github/agents/squad.agent.md' to be ''

Test Files  1 failed (1)
     Tests  2 failed | 24 passed (26)

Produced by reverting only the one-line sandbox move and re-running — the rest of the change held constant, so the red isolates the mechanism rather than the diff.

The status guard compares porcelain output against a file-level beforeAll snapshot instead of asserting emptiness, so a developer with a pre-existing local edit to those paths does not get a false red.

The template-sync re-syncs are retained as defence-in-depth: a future suite that reintroduces an in-repo sandbox now fails loudly there rather than leaving a silently mutated tree. Their comments are updated to describe that role instead of the fixed race.

Verification

Check	Result
init-scaffolding post-fix	26 passed, tree clean
template-sync + init + init-scaffolding + init-sdk	327 passed, tree clean
Negative control (pre-fix sandbox restored)	2 failed / 24 passed
npm run build	exit 0
git diff --cached --stat	2 files, +67 / -13
git diff --cached --diff-filter=D --name-only	empty

No changeset: test-only, nothing under packages/*/src.

Deliberately not included

npm test also rewrites test/__snapshots__/parser-contracts.test.ts.snap (reproduced: parser-contracts.test.ts alone, 16 passed, file modified). That diff is pure EOL with zero content lines — the file is i/lf w/crlf and vitest writes LF. It is the #1793 CRLF class, not this one.

Its fix is *.snap text eol=lf, and I checked #1790's diff: it pins *.mjs, *.js, *.cjs, *.ps1 and three .ts paths but does not cover *.snap. So this is a real gap in #1790, not a duplicate. It belongs there rather than here, because per #1793 the attribute repairs nothing on an existing checkout — it only helps after the renormalize #1790 already requires. Flagged for routing; not taken unilaterally, since #1790 is editing that exact region of .gitattributes tonight.

[github-actions]

🟢 Impact Analysis — PR #1798

Risk tier: 🟢 LOW

📊 Summary

Metric	Count
Files changed	2
Files added	0
Files modified	2
Files deleted	0
Modules touched	1

🎯 Risk Factors

• 2 files changed (≤5 → LOW)
• 1 module(s) touched (≤1 → LOW)

📦 Modules Affected

tests (2 files)

• test/init-scaffolding.test.ts
• test/template-sync.test.ts

---

This report is generated automatically for every PR. See #733 for details.

[github-actions]

🛫 PR Readiness Check

ℹ️ This comment updates on each push. Last checked: commit 874214d

PR Scope: 🔧 Infrastructure

⚠️ 2 item(s) to address before review

Status	Check	Details
✅	Single commit	1 commit — clean history
✅	Not in draft	Ready for review
✅	Branch up to date	Up to date with dev
❌	Copilot review	No Copilot review yet — it may still be processing
✅	Changeset present	No source files changed — changeset not required
✅	Scope clean	No .squad/ or docs/proposals/ files
✅	No merge conflicts	No merge conflicts
❌	Copilot threads resolved	1 unresolved Copilot thread(s) — fix and resolve before merging
✅	CI passing	All checks passing

Files Changed (2 files, +67 −13)

File	+/−
test/init-scaffolding.test.ts	+53 −3
test/template-sync.test.ts	+14 −10

Total: +67 −13

---

This check runs automatically on every push. Fix any ❌ items and push again.
See CONTRIBUTING.md and PR Requirements for details.

[Copilot]

Pull request overview

This PR fixes a test isolation issue where the init-scaffolding test suite could accidentally run init against a sandbox located inside the repository, allowing runInit()/initSquad() to walk up to the real git root and mutate tracked files (notably .github/agents/squad.agent.md). It also adds a regression guard and updates template-sync comments to reflect the new defense-in-depth posture.

Changes:

• Move the init-scaffolding sandbox root to os.tmpdir() to prevent git-root “escape” into the real repo.
• Add a working-tree containment / mutation guard to detect future regressions.
• Update template-sync commentary to document the historical cause and the retained defense layers.

Show a summary per file

File	Description
test/init-scaffolding.test.ts	Move sandbox to OS temp dir and add a git-status guard to ensure tracked files aren’t mutated by the suite.
test/template-sync.test.ts	Update comments explaining why template re-syncs remain as defense-in-depth after #1796.

Review details

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• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Lite