test(cli): stop the skills CLI tests reading the module cache as CLI output

[kojiwakayama]

The flake

cli/commands/skills/handler.test.ts has been failing on coverage shard 7/8 for pull
requests that cannot reach the code it tests — #3648 (proxy WebSocket bridge identity) and
#3651 (a release PR touching three version files), both with the same two steps under
info JSON output, both 412 passed / 1 failed.

Root cause

The failing assertions are handler.test.ts:36 and handler.test.ts:52, both
assertEquals(result.stderr, "") against a child deno run -A cli/main.ts skills info --json. The diff in the CI log (run 31642742785, job coverage shard 7/8) says what
landed there:

    [Diff] Actual / Expected

-   Download https://registry.npmjs.org/yaml\n

That is the Deno runtime narrating its own work, not the CLI writing output. deno.json
sets nodeModulesDir to auto, so a child whose dependencies are not all present first
reconciles node_modules/ against cli/main.ts's graph, and it reports each fetch that
costs on stderr.

Nothing puts yaml where the child would find it. .github/actions/setup-deno warms the
Deno cache from src/index.ts, and npm:yaml@2.9.0 reaches the CLI only through
cli/main.ts — via @opentelemetry/configuration, bash-tool and just-bash — so it is
in neither the warmed blob nor the test process's own graph. actions/cache/restore falls
back through restore-keys, so which packages a shard actually has is decided by which
cache entry the runner happened to restore. That is the whole of the flakiness: the file
was asserting on the machine's module cache alongside the CLI's stderr.

This is a test defect, not a product one. The CLI writes nothing to stderr here; every
environment variable that any file in shard 7 mutates was probed against the command and
none of them change its stdout, stderr or exit code.

The fix

One line: --quiet on the child.

It suppresses the runtime's diagnostics and nothing else. What the CLI writes still
arrives — veryfront skills info with no name and no --json still reports
✗ Usage: veryfront skills info <name> on stderr underneath --quiet — so the assertions
still hold the command to a silent stderr. They just no longer hold the module cache to it
as well. No retry, no tolerance, no skip.

Verification

The failure reproduces deterministically by putting the machine in the state a partially
restored CI cache puts it in — evicting the yaml packument from DENO_DIR before each
run:

rm -rf "$DENO_DIR/npm/registry.npmjs.org/yaml"
deno test --preload=src/testing/preload.ts --no-check --parallel --allow-all \
  --v8-flags=--max-old-space-size=8192 --ignore=tests --ignore=src/workflow/__tests__ \
  --unstable-worker-options --unstable-net <the 232 shard-7 files>

It produces the CI diff byte for byte.

condition	before	after
this file alone, trigger armed each run	0 / 25 passed	25 / 25 passed
full shard-7 file set under --parallel, trigger armed each run	1 / 20 passed (19 skills failures)	55 / 55 passed (0 skills failures, 0 other failures)

Deno 2.7.7 throughout, matching CI.

Noticed while investigating, not fixed here

• src/extensions/factory-loader.test.ts:201 reads const repositoryRoot = Deno.cwd()
  inside a test while cli/commands/schedule/handler.test.ts may hold the process
  directory through withCwd. It failed once in 25 baseline shard-7 runs with
  Module not found "file:///.../vf-schedule-local-timeout-.../src/platform/compat/path/index.ts"
  — a live flake of the class src/testing/cwd.ts exists to prevent, and one that file has
  not opted into. Deriving the root from import.meta.url fixes it.
• With LOG_LEVEL=DEBUG in the environment, veryfront <cmd> --json writes ~35 lines of
  debug logs to stdout ahead of the JSON envelope, which breaks JSON.parse for any
  machine consumer. setJsonMode() (cli/shared/json-output.ts:20) lowers the level only
  after flag parsing, so module-load-time logs escape it. That one is a product bug and
  deserves its own issue.

Summary by CodeRabbit

• Tests
  • Improved CLI test output by suppressing unrelated runtime dependency-resolution diagnostics.
  • Added documentation clarifying expected stderr behavior for CLI assertions.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 88a067ea-1c3a-4361-a094-90864e54e140

📥 Commits

Reviewing files that changed from the base of the PR and between d5a0383 and 2059023.

📒 Files selected for processing (1)

• cli/commands/skills/handler.test.ts

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📝 Walkthrough

Walkthrough

The skills CLI test helper now passes --quiet to Deno. Documentation explains the stderr behavior and dependency-resolution diagnostics. Existing output and error handling remain unchanged.

Changes

Skills CLI test execution

Layer / File(s)	Summary
Quiet Deno subprocess runner cli/commands/skills/handler.test.ts	runSkillsInfo passes --quiet to Deno. A comment documents the stderr behavior and dependency-resolution issue. Output and error handling remain unchanged.

Estimated code review effort: 1 (Trivial) | ~2 minutes

Mergeability Score: ⚪ Minimal · up to 20590

This localized test-only change prevents runtime dependency-fetch diagnostics from being mistaken for CLI stderr output, without changing CLI behavior. No actionable merge-blocking risk remains beyond normal checks and review.

Suggested reviewers: kwakayama

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly identifies the test change that prevents module-cache diagnostics from being treated as CLI output.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/skills-cli-stderr-module-cache

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