Fix stdio mode panic: inject ToolDependencies into request context

[Copilot]

Summary

Stdio server panics with "ToolDependencies not found in context" on tool calls. After deps were refactored to context-based injection, middleware to inject them was missing.

Why

Tool handlers call MustDepsFromContext(ctx) but no middleware injects deps into the request context.

What changed

• Added middleware in NewMCPServer() that wraps requests with github.ContextWithDeps(ctx, deps)
• Added tests for server creation and toolset resolution logic

// Inject dependencies into context for all tool handlers
ghServer.AddReceivingMiddleware(func(next mcp.MethodHandler) mcp.MethodHandler {
    return func(ctx context.Context, method string, req mcp.Request) (mcp.Result, error) {
        return next(github.ContextWithDeps(ctx, deps), method, req)
    }
})

MCP impact

• No tool or API changes — Fixes runtime panic, no API surface changes

Prompts tested (tool changes only)

• N/A

Security / limits

• No security or limits impact — Middleware only propagates existing deps

Lint & tests

• Linted locally with ./script/lint
• Tested locally with ./script/test

Docs

• Not needed — Internal fix, no user-facing changes

Original prompt

---

This section details on the original issue you should resolve

<issue_title>v0.26.0+ stdio mode panics: ToolDependencies not found in context</issue_title>
<issue_description>## Bug Description

After PR #1640 (inject deps via context instead of closures), the stdio server panics on any tool call:

panic: ToolDependencies not found in context; use ContextWithDeps to inject

Root Cause

In internal/ghmcp/server.go, NewMCPServer() creates deps at line ~196-204 and passes them to inventory.RegisterAll(), but the new context-based tool handlers created by NewServerToolWithContextHandler expect deps to be in context via MustDepsFromContext(ctx).

No middleware injects deps into context before tool handlers execute.

Fix

Add middleware after deps creation (~line 205):

ghServer.AddReceivingMiddleware(func(next mcp.MethodHandler) mcp.MethodHandler {
    return func(ctx context.Context, method string, req mcp.Request) (mcp.Result, error) {
        return next(github.ContextWithDeps(ctx, deps), method, req)
    }
})

Affected Versions

• v0.26.0
• v0.26.1

Reproduction

export GITHUB_PERSONAL_ACCESS_TOKEN=$TOKEN
echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"0.1.0","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}
{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"get_me","arguments":{}}}' | ./github-mcp-server stdio

Workaround

Build from source with the above fix applied.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes v0.26.0+ stdio mode panics: ToolDependencies not found in context #1646

---

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

[Copilot]

Pull request overview

This PR fixes a critical panic in stdio mode that occurs when any tool is called. The panic was introduced after refactoring to context-based dependency injection, where middleware to inject dependencies into the request context was inadvertently omitted.

Key changes:

• Added middleware in NewMCPServer() to inject ToolDependencies into the request context for all tool handlers
• Added comprehensive tests for server creation and toolset resolution logic

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
internal/ghmcp/server.go	Adds middleware after line 205 to inject deps into context via github.ContextWithDeps(ctx, deps) for all tool handlers
internal/ghmcp/server_test.go	Adds new test file with tests for server creation (verifying middleware is configured) and toolset resolution logic