Add user-scoped setup for Claude Code and Codex

Problem

zenith init currently stages MCP configuration, prompts, agents, and skills inside one target workspace. Users who want Zenith across many workspaces must repeat initialization and restart each host for every workspace.

Proposal

Add an explicit user-scoped setup mode:

uv run zenith init --scope user --agent claude
uv run zenith init --scope user --agent codex

The existing project-scoped behavior remains the default for compatibility.

User scope registers the host's user-level MCP server and managed Zenith assets, honors CLAUDE_CONFIG_DIR and CODEX_HOME, preserves unrelated user configuration, and never selects or overwrites model/reasoning/sandbox/feature preferences or persists ambient API/model environment variables. It is idempotent and supports installing both hosts in either order.

Hermes retains project scope until its authoritative user-scope paths are established.

Start at the existing zenith init entry point and trace how project-scoped MCP configuration, prompts, agents, and skills are staged for Claude and Codex. Add an explicit user scope while retaining project scope as the default, honoring the named environment paths and preserving unrelated settings. Done means both hosts can be installed in either order, repeated setup is idempotent, and Hermes remains project-scoped.