fix(input-json): only read stdin with explicit --input-json -

[rafa-thayto]

Summary

In agent mode the program-level --input-json expander consumed any non-TTY stdin and parsed it as the options payload, even when --input-json was never passed. That broke two common patterns:

# shell loops — the clerk process swallows the rest of the worklist
while read -r app ins; do clerk config patch --app "$app" --instance "$ins" --json '…' --yes; done < worklist.tsv

# commands that read their own stdin
cat payload.json | clerk api /users   # body was pre-empted and parsed as --input-json

Non-JSON stdin then failed with invalid_json before the command ran. This makes stdin read only with an explicit --input-json -; piped stdin is otherwise left untouched.

Test plan

• bun test src/lib/input-json.test.ts and src/test/integration/input-json.test.ts pass
• Updated unit tests assert piped stdin is ignored without --input-json -

Fixes #333

[changeset-bot]

🦋 Changeset detected

Latest commit: 9662f59

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 1 package

Name	Type
clerk	Patch

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

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Run ID: a20d8b61-8e1c-4bd2-969c-af86a03ac4a2

📥 Commits

Reviewing files that changed from the base of the PR and between e8a1e1b and 9662f59.

📒 Files selected for processing (4)

• .changeset/input-json-explicit-stdin.md
• packages/cli-core/src/commands/users/README.md
• packages/cli-core/src/lib/input-json.test.ts
• packages/cli-core/src/lib/input-json.ts

✅ Files skipped from review due to trivial changes (2)

• packages/cli-core/src/commands/users/README.md
• .changeset/input-json-explicit-stdin.md

🚧 Files skipped from review as they are similar to previous changes (2)

• packages/cli-core/src/lib/input-json.test.ts
• packages/cli-core/src/lib/input-json.ts

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📝 Walkthrough

Walkthrough

expandInputJson now returns the original argv unchanged when --input-json is absent, and stdin is only read when --input-json - is explicitly provided. The helper that previously read optional piped stdin is removed. Tests now assert that piped JSON object, array, and non-JSON input are ignored without the flag, while the README and changeset document the updated behavior.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 66.67% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly states the stdin behavior fix for --input-json -.
Description check	✅ Passed	Description matches the stdin parsing fix and test updates.
Linked Issues check	✅ Passed	Changes satisfy #333 by only reading stdin with explicit --input-json - and updating docs and tests accordingly.
Out of Scope Changes check	✅ Passed	No obvious out-of-scope changes; edits are limited to the stdin fix, related docs, and tests.

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_{Comment @coderabbitai help to get the list of available commands.}

[wyattjoh]

One minor test-cleanup note inline. The fix itself is correct: stopping expandInputJson from implicitly draining stdin is the right call, since that stdin is shared with commands that read their own body (clerk api, clerk config push).