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: 237
• Additions: +226
• Deletions: -11
• 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;
    }

[AriaZhao-coder]

Thanks for the review! I've addressed both high-priority points in the latest commit (7b081945d):

• Null-safety: parsed user/workspace settings are now normalized to {} when a file is empty or contains null/a primitive (JSON.parse("null") === null). This guards both the deep merge (Object.entries(null)) and the earlier folderTrust / later policyPaths accesses in loadSettings, so a malformed settings file can no longer crash the server.
• Reference sharing: nested source objects are now deep-cloned during the merge instead of being assigned by reference, so the merged result no longer shares references with the workspace settings object — matching the behavior in packages/cli/src/utils/deepMerge.ts.

Added unit tests covering both (null-safety + reference cloning) plus loadSettings no longer crashing on null settings files. PTAL 🙏

/gemini review

[gemini-code-assist]

Code Review

This pull request replaces the shallow merge of user and workspace settings with a recursive deep merge implementation (deepMergeSettings) to preserve unrelated nested user configurations. It also introduces normalization to safely handle null or empty settings files and adds protection against prototype pollution. Feedback is provided regarding the deep merge implementation, which currently copies array references directly; cloning arrays using structuredClone is recommended to prevent reference sharing and unintended mutations.

[gemini-code-assist]

While the deep merge implementation correctly clones nested plain objects to prevent reference sharing, it currently misses cloning arrays. If a workspace setting contains an array (such as fileFiltering.customIgnoreFilePaths), the array reference is copied directly from the source object to the merged target. Any subsequent mutations to the merged settings will leak back and mutate the original source object, which can cause unexpected side effects or test leakage.

Additionally, security-sensitive settings (such as tools.allowed) must not use a merge strategy that allows less-trusted configuration scopes (like a workspace) to override more-trusted scopes (like global user settings). Ensure that these sensitive settings are protected from being overridden by workspace configurations.

For cloning arrays safely, we can use structuredClone to avoid reference sharing.

    } else if (isPlainObject(sourceValue)) {
      // The source value is a nested object but the target value is not, so
      // recursively clone it. Assigning sourceValue directly would make the
      // merged result share references with the original source object,
      // allowing later mutations to leak back into it.
      output[key] = deepMergeSettings({}, sourceValue);
    } else if (Array.isArray(sourceValue)) {
      // Clone arrays to prevent reference sharing.
      output[key] = structuredClone(sourceValue);
    } else {
      output[key] = sourceValue;
    }

References

1. Security-sensitive settings should not use a merge strategy (e.g., MergeStrategy.REPLACE) that allows less-trusted configuration scopes (like a workspace) to completely override more-trusted scopes (like global user settings).

[AriaZhao-coder]

Thanks for the follow-up review! Addressed in a407905d4:

• Array cloning: arrays are now cloned with structuredClone when they replace the target value, mirroring the nested-object cloning. The merged result no longer shares array references with the source (workspace) settings, so mutations can't leak back. Added a unit test covering reference identity + mutation isolation for customIgnoreFilePaths.

Regarding the note on security-sensitive settings (e.g. tools.allowed): I've intentionally left the merge semantics as "workspace replaces user" for these, for a few reasons:

1. Workspace settings are only merged when the workspace is trusted (isTrusted gate in loadSettings); untrusted workspaces never contribute.
2. The genuinely sensitive policy settings — policyPaths and adminPolicyPaths — are already explicitly protected and can only come from user-level config, even for a trusted workspace.
3. Changing tools.allowed to be non-overridable would be a behavior change beyond this PR's scope (it preserves the pre-existing shallow-merge precedence) and would contradict the existing test that asserts a trusted workspace can override it.

Happy to revisit the trust model for tool settings in a dedicated PR if maintainers feel it's warranted. PTAL 🙏

[AriaZhao-coder]

/gemini review

[gemini-code-assist]

Code Review

This pull request introduces a deep-merge capability for settings in the a2a-server package, replacing the previous shallow merge behavior. It adds a robust deepMergeSettings utility that recursively merges nested configuration objects, prevents prototype pollution by filtering out dangerous keys like __proto__, and avoids shared references by cloning nested objects and arrays. Additionally, it introduces normalizeSettings to safely handle empty or null settings files, preventing server crashes. Comprehensive unit tests have been added to verify these merging behaviors, cloning safety, and security protections. There are no review comments to address, and I have no further feedback to provide as the implementation is solid and well-tested.

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