Merge development: repo workflow tools, branding sync, OAuth settings

Resolves the registry-count conflict the two branches' descriptions predicted: the repo workflow tools (list_issues, get_issue, create_issue, get_pull_request) and web_search both landed at the same anchor points in the request spec and the MCP spec doc. Both branches now merge into one registry of eleven tools; the doc's frontmatter, tool count callouts, verification section, and key-files list are unioned rather than picking a side.