chore: add support for loading config from file MCP-327

[himanshusinghs]

Proposed changes

Adds support for loading configuration from a file. As a drive by:

• have added coverage for Server.tools interface as well
• disabled overriding voyageApiKey from request headers

Checklist

• I have signed the MongoDB CLA

[Copilot]

Pull request overview

This PR adds support for loading server configuration from a JSON file, enabling users to configure the MongoDB MCP Server via --config CLI argument or MDB_MCP_CONFIG environment variable. The implementation includes comprehensive test coverage for the new feature and a drive-by fix for testing the Server.tools interface with custom tools.

Key changes:

• Configuration can now be loaded from JSON files with proper precedence (CLI args > env vars > config file > defaults)
• Documentation updated with security best practices for config file handling
• Test coverage added for valid/invalid config file scenarios and configuration precedence rules
• Integration tests added to verify Server initialization with custom tool sets

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/common/config/createUserConfig.ts	Added config file loading support via parserOptions.config
src/common/config/userConfig.ts	Changed voyageApiKey override behavior from "override" to "not-allowed"
tests/unit/common/config.test.ts	Added comprehensive tests for config file loading and updated precedence tests
tests/integration/server.test.ts	Added test tools and integration tests for Server.tools interface
tests/fixtures/valid-config.json	New fixture with valid configuration
tests/fixtures/config-with-invalid-value.json	New fixture with invalid configuration for error testing
README.md	Added documentation for configuration file usage with security guidance

[coveralls]

Pull Request Test Coverage Report for Build 19933887292

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

• For more information on this, see Tracking coverage changes with pull request builds.
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• For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

• 2 of 2 (100.0%) changed or added relevant lines in 2 files are covered.
• 2 unchanged lines in 1 file lost coverage.
• Overall coverage increased (+0.5%) to 80.313%

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Files with Coverage Reduction	New Missed Lines	%
src/common/config/configOverrides.ts	2	90.91%

Totals
Change from base Build 19928391156:	0.5%
Covered Lines:	6656
Relevant Lines:	8204

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💛 - Coveralls

[gagik]

Let's delete the --config instructions though. If we give instructions then one will do it.