fix(a2a-server): deep-merge user and workspace settings

[AriaZhao-coder]

Summary

loadSettings() in packages/a2a-server/src/config/settings.ts combined user and workspace settings with a shallow object spread ({ ...userSettings, ...workspaceSettings }).

Any nested section (tools, telemetry, fileFiltering, experimental, ...) defined in workspace settings replaced the entire corresponding section from user settings, silently dropping unrelated user-level configuration.

Example

User settings: { "fileFiltering": { "respectGitIgnore": true, "enableRecursiveFileSearch": true } }
Workspace settings: { "fileFiltering": { "respectGitIgnore": false } }

• Before: enableRecursiveFileSearch is silently lost.
• After: it is preserved; only respectGitIgnore is overridden.

Fix

Replace the shallow spread with a self-contained recursive deep merge:

• nested plain objects are merged key-by-key;
• arrays and primitive values from workspace settings still override the user values;
• __proto__ / constructor / prototype keys are skipped to prevent prototype pollution;
• undefined source values are ignored.

The a2a-server only depends on core, so this intentionally avoids the cli-only customDeepMerge (which is coupled to cli's MergeStrategy/settingsSchema). The policyPaths/adminPolicyPaths security override is unchanged.

Tests

• Updated the existing test that encoded the shallow-merge bug (it previously asserted a nested key becomes undefined).
• Added: multi-section deep merge with array replacement, and prototype-pollution safety.

Verified locally (Node 20):

• The updated/added merge tests fail without the fix and pass with it (red/green).
• a2a-server suite — all 140 tests pass.
• prettier --check, eslint --max-warnings 0, tsc --noEmit — all clean.

Fixes #25747

[github-actions]

📊 PR Size: size/M

• Lines changed: 108
• Additions: +100
• Deletions: -8
• Files changed: 2

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses a configuration merging issue in a2a-server where workspace settings were performing a shallow overwrite of user settings, causing nested configuration blocks to be lost. By implementing a robust deep-merge strategy, the system now correctly preserves nested user-defined keys while allowing workspace-specific overrides. The implementation includes security hardening against prototype pollution and is supported by comprehensive unit tests.

Highlights

• Deep Merge Implementation: Replaced the shallow object spread in loadSettings with a recursive deepMergeSettings function to ensure nested configuration sections are merged rather than overwritten.
• Prototype Pollution Protection: Added explicit checks to skip 'proto', 'constructor', and 'prototype' keys during the merge process to prevent potential prototype pollution vulnerabilities.
• Test Coverage: Updated existing tests to reflect correct deep-merge behavior and added new test cases for multi-section merging and prototype pollution security.

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[gemini-code-assist]

Code Review

This pull request introduces a custom recursive deep merge function (deepMergeSettings) to merge user and workspace settings, along with corresponding unit tests. The review feedback identifies two critical issues in the implementation: a potential server crash if settings are parsed as null, and a reference-sharing issue where nested source objects are assigned directly instead of being deeply cloned.

[gemini-code-assist]

If either target or source is null (which can happen if a settings file is empty or contains null, as JSON.parse("null") returns null), calling Object.entries(source) will throw a TypeError: Cannot convert undefined or null to object and crash the server.

To prevent this, we should safely default target and source to empty objects if they are not plain objects.

Suggested change

	function deepMergeSettings<T extends object>(target: T, source: T): T {
	// eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
	const output = { ...target } as Record<string, unknown>;
	for (const [key, sourceValue] of Object.entries(source)) {
	function deepMergeSettings<T extends object>(target: T, source: T): T {
	const t = isPlainObject(target) ? target : {};
	const s = isPlainObject(source) ? source : {};
	// eslint-disable-next-line @typescript-eslint/no-unsafe-type-assertion
	const output = { ...t } as Record<string, unknown>;
	for (const [key, sourceValue] of Object.entries(s)) {

[gemini-code-assist]

When sourceValue is a plain object but targetValue is not (e.g., it is undefined), the code currently assigns sourceValue directly by reference: output[key] = sourceValue;.

This means the merged settings object will share references with the original source (workspace settings) object. Any subsequent mutations to the merged settings could unintentionally mutate the workspace settings object.

To align with the repository's established deep-merge behavior (as seen in packages/cli/src/utils/deepMerge.ts), we should recursively clone sourceValue when targetValue is not a plain object.

    const targetValue = output[key];
    if (isPlainObject(targetValue) && isPlainObject(sourceValue)) {
      output[key] = deepMergeSettings(targetValue, sourceValue);
    } else if (isPlainObject(sourceValue)) {
      output[key] = deepMergeSettings({}, sourceValue);
    } else {
      output[key] = sourceValue;
    }