Tommy/tool-specific-config-support

[tommaso-moro]

Overview

This PR adds support for tool-specific MCP configuration via a new --tools flag:

• Users can use the --tools to list which tools they would like to enable
• Users can also use a mix of --tools, --toolsets, --read-only and --dynamic-toolsets and compose them in whatever way they'd like

Example

Default toolset case: no specific config

Behavior: the "default" toolsets are enabled if no preference is expressed (e.g. --toolsets, --tools, --read-only, dynamic)

✅ working as expected (screenshots)

---

Standard case: X-MCP-Tools only

Behavior: the tools are enabled

✅ working as expected (screenshots)

---

Case with both X-MCP-Tools and X-MCP-Toolsets

Behavior: both toolsets and tools are enabled

✅ working as expected (screenshots)

BEFORE (toolsets only)

AFTER (toolsets + tools)

---

Case with both X-MCP-Tools and readonly

Behavior: write tools are not enabled, readonly tools are enabled

✅ working as expected (screenshots)

issue_write is not being enabled (correct behavior)

---

Case with both --tools and --dynamic-toolsets (local MCP only)

Behavior: the MCP starts with the 3 dynamic toolsets (enable_toolset, list_available_toolsets, get_toolset_tools) and the specified tools

✅ working as expected (screenshots)

---

Case with invalid tool name

Behavior: The MCP should throw an error and require the user to use a valid tool

✅ working as expected (screenshots)

[Copilot]

Pull Request Overview

This PR introduces tool-specific configuration support via a new --tools flag, enabling users to specify individual tools instead of (or in addition to) toolsets. Users can now compose their MCP server configuration using --tools, --toolsets, --read-only, and --dynamic-toolsets flags in any combination.

Key changes:

• Added --tools flag for specifying individual tools by name
• Implemented additive composition logic where tools and toolsets can be combined
• Maintained read-only mode enforcement (write tools are skipped even if explicitly requested)

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
pkg/toolsets/toolsets.go	Added ToolDoesNotExistError, FindToolByName method to locate tools across all toolsets, and RegisterSpecificTools method to register individual tools with read-only mode support
pkg/github/tools.go	Added CleanTools utility function to remove duplicates and trim whitespace from tool names
internal/ghmcp/server.go	Added EnabledTools field to both MCPServerConfig and StdioServerConfig, updated NewMCPServer to handle tool registration additively with toolsets
cmd/github-mcp-server/main.go	Added --tools flag, viper binding for the flag, and updated default toolset logic to only apply when neither tools nor toolsets are specified
go.mod	Marked github.com/google/go-querystring as indirect dependency
README.md	Added comprehensive documentation for --tools flag including examples with command line, environment variables, Docker usage, and composition patterns

[JoannaaKL]

Looks good, it would be great if you could add more tests showing different scenarios like toolsets + tools enabled, read only mode + write tools etc. ❤️

[tommaso-moro]

@JoannaaKL good shout, I have added them to the PR description! :)