Add per-toolset read-only configuration

[adbcodes]

Summary

Adds --read-only-toolsets and GITHUB_READ_ONLY_TOOLSETS to restrict writes in selected toolsets while keeping other enabled toolsets writable. Supports stdio, self-hosted HTTP, and list-scopes.

Why

Global read-only mode blocks every write tool, preventing mixed configurations such as writable repositories with read-only issues and pull requests.

Fixes #3229

What changed

• Added configuration parsing, toolset validation, and centralized read-only filtering.
• Preserved HTTP request toolset selection while preventing requests from restoring blocked writes.
• Added regression tests and documentation.

MCP impact

• No tool or API changes
• Tool schema or behavior changed

Configured toolsets omit write tools from registration, so those tools cannot be listed or called. Tool schemas and default behavior remain unchanged.

• New tool added

Prompts tested (tool changes only)

Tested in Codex with the locally built server connected as github_3229_local, using --toolsets=repos,issues,pull_requests --read-only-toolsets=issues,pull_requests:

• “Using only github_3229_local, read github/github-mcp-server issue Feature: per-toolset (or per-tool) read-only mode instead of global GITHUB_READ_ONLY #3229 and summarize it.” — Issue read succeeded.
• “Using only github_3229_local, check whether you can post an issue comment or merge a PR. Don’t use shell commands or other connectors.” — Comment and merge tools were unavailable.
• “Check whether push_files is available through github_3229_local, without executing it.” — Repository write tool remained available; no write was performed.

Direct MCP tools/list and blocked tools/call requests were also tested using both CLI and environment configuration.

Security / limits

• No security or limits impact
• Auth / permissions considered

Global read-only remains authoritative. This setting does not alter GitHub token permissions.

• Data exposure, filtering, or token/size limits considered

Explicit tool selection and HTTP request configuration cannot restore restricted writes. Unknown policy names fail validation; tools without read-only annotations are blocked in restricted toolsets.

Tool renaming

• I am renaming tools as part of this PR
  • I have added the new tool aliases in deprecated_tool_aliases.go
• I am not renaming tools as part of this PR

Existing tool names remain unchanged.

Lint & tests

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

Ran the checks directly with Go 1.25.12: golangci-lint run reported zero issues; go test ./... passed. Fresh focused tests and race tests for inventory, HTTP, and CLI packages also passed, as did git diff --check.

Docs

• Not needed
• Updated (README / docs / examples)

Updated README.md and docs/server-configuration.md with configuration examples, precedence rules, validation, and HTTP behavior.