feat(core): pass agent settings through at the flag tier

[edspencer]

Adds an agent-level settings field: Claude Code settings applied at the flag tier. Needed by edspencer/paddock#955.

What

• Schema: settings: Record<string, unknown>, optional, on AgentConfigSchema. It's agent-level only, with no fleet defaults.settings.
• SDK runtime: toSDKOptions passes it to the Agent SDK's settings option, as a shallow copy so the resolved agent can't be mutated. The key is omitted when unset or empty.
• CLI runtime: emits the same thing as --settings <json>, so a config behaves the same on either runtime.
• Docs: a new settings section in configuration/agent-config.md, plus a changeset (minor).

Why

Flag settings outrank every file source except managed policy, and they apply whatever setting_sources loads. That makes them the only channel for keys a project's checked-in .claude/settings.json isn't trusted to set. The motivating key is autoMemoryDirectory, which Paddock needs to set per agent:

• Claude Code ignores it in projectSettings.
• herdctl never loads userSettings for SDK agents.
• The CLAUDE_COWORK_MEMORY_PATH_OVERRIDE env alternative also switches off the "memory writes are always allowed" exemption, which defeats the purpose.

So there was no working route without this field.

Compatibility: AgentConfigSchema is .strict(), so an older core rejects the key with Unrecognized key: "settings". A consumer that sets it needs this release.

Tests

• addAgent (the real strict schema) → getAgents → toSDKOptions → the options the mocked query() receives.
• No key emitted when unset or empty, and no aliasing.
• The CLI argv: exactly one --settings, whose JSON round-trips.
• A compile-time contract that SDKQueryOptions["settings"] is assignable to the SDK's Options["settings"].
• Mutation-checked: deleting either passthrough line fails 3 tests.
• Runner suite 628/628, tsc --noEmit clean.

End to end with the real binary: a Paddock build overlaid with this branch's dist boots, registers agents with settings, and its memory writes land. The overlay is needed because this isn't released yet. The integration test and a live-instance run are in the Paddock PR.

🤖 Generated with Claude Code

Summary by CodeRabbit

• New Features
  • Agent configuration can pass Claude Code settings through the Agent SDK or CLI. Non-empty settings take precedence over settings files, except managed policy.
  • Settings support keys such as autoMemoryDirectory and effortLevel, and can include ${VAR} or ${VAR:-default} environment variable references.
• Documentation
  • Clarified that settings may appear in process arguments and that unset variables without defaults cause errors.

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📒 Files selected for processing (3)

• docs/src/content/docs/configuration/agent-config.md
• packages/core/src/runner/runtime/__tests__/cli-runtime.test.ts
• packages/core/src/runner/runtime/cli-runtime.ts

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🚧 Files skipped from review as they are similar to previous changes (3)

• packages/core/src/runner/runtime/cli-runtime.ts
• packages/core/src/runner/runtime/tests/cli-runtime.test.ts
• docs/src/content/docs/configuration/agent-config.md

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📝 Walkthrough

Walkthrough

Agent configuration now accepts Claude Code settings and passes non-empty values to the Agent SDK or CLI runtime. Documentation describes the setting’s scope, precedence, and interpolation. Tests cover forwarding, omission, object isolation, CLI log redaction, and SDK option type compatibility.

Changes

Agent settings passthrough

Layer / File(s)	Summary
Agent settings contract and documentation packages/core/src/config/schema.ts, docs/src/content/docs/configuration/agent-config.md, .changeset/agent-settings-passthrough.md	The agent schema accepts an optional settings object. Documentation describes flag-tier application, precedence, scope, and interpolation. The changeset records the passthrough.
SDK settings forwarding packages/core/src/runner/types.ts, packages/core/src/runner/sdk-adapter.ts, packages/core/src/runner/__tests__/mcp-and-plugin-passthrough.test.ts, packages/core/src/runner/__tests__/sdk-type-contract.test.ts	SDKQueryOptions adds a settings property. toSDKOptions shallow-copies non-empty agent settings and omits absent or empty settings. Tests cover forwarding, omission, object isolation, and type compatibility.
CLI settings forwarding and logging packages/core/src/runner/runtime/cli-runtime.ts, packages/core/src/runner/runtime/__tests__/cli-runtime.test.ts	CLIRuntime.execute serializes non-empty settings into a --settings argument and redacts that argument in command logs. Tests cover serialization, redaction, and omission.

Priority: ➖ Normal

Estimated code review effort: 2 (Simple) | ~10 minutes

Change: Feature

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Merge Risk: ⚪ Minimal · up to ca16e

No actionable merge-blocking issue remains in the reviewed changes. Settings values may be visible in process arguments, as documented.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage		Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 2 functions across 7 files. (1 skipped: 1…	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.
Title check		The title clearly and concisely describes the main change: passing agent-level settings through at the flag tier.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

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Full details: Docstring Coverage

Explanation

Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 2 functions across 7 files. (1 skipped: 1 unsupported.)

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Actionable comments posted: 1

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• 🪄 Fix CodeRabbit comments on this PR

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Inline comments:
Review comments at @packages/core/src/runner/runtime/cli-runtime.ts:
- Line 297: Update the handling of options.agent.settings when adding --settings
to args so credentials are not exposed: use a file-backed settings option if the
CLI supports one, and redact the settings value from the command logged by
logger.debug. Preserve the settings passed to the CLI without logging their
contents.

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• Configuration used: defaults
• Review profile: CHILL
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📥 Commits

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📒 Files selected for processing (9)

• .changeset/agent-settings-passthrough.md
• docs/src/content/docs/configuration/agent-config.md
• packages/core/src/config/schema.ts
• packages/core/src/runner/__tests__/mcp-and-plugin-passthrough.test.ts
• packages/core/src/runner/__tests__/sdk-type-contract.test.ts
• packages/core/src/runner/runtime/__tests__/cli-runtime.test.ts
• packages/core/src/runner/runtime/cli-runtime.ts
• packages/core/src/runner/sdk-adapter.ts
• packages/core/src/runner/types.ts

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