feat: mcp subcommand for managing MCP servers independently

[christso]

Summary

Add an `allagents mcp` subcommand surface for managing MCP servers independently of full plugin installs, mirroring the `claude mcp` command surface.

Motivation

Currently, MCP servers are synced as part of plugin install/update. Users may want to:

• Install only MCP servers from a plugin without syncing skills/agents/hooks
• List which MCP servers AllAgents has synced across clients
• Remove specific MCP servers
• Update MCP configs without running a full workspace update

AllAgents already syncs MCP servers during `plugin install` — this issue adds a dedicated subcommand for MCP-only workflows.

Proposed Commands

Command	Description
`allagents mcp add [args...]`	Add an MCP server across configured clients
`allagents mcp list`	List MCP servers managed by AllAgents (with per-client status)
`allagents mcp remove `	Remove a synced MCP server from all clients
`allagents mcp update`	Sync MCP servers from plugins without syncing other artifacts
`allagents mcp get `	Show details of a specific MCP server (config, which clients have it)

Consistency Notes

• `mcp update` is consistent with `workspace update` (which supersedes the old sync command)
• Command surface mirrors `claude mcp` (`add`, `list`, `remove`, `get`) for familiarity
• Respects existing ownership tracking — only manages servers AllAgents added, never touches user-managed servers

Implementation Notes

Key source files

• MCP sync per client:
  • `src/core/claude-mcp.ts` — syncs to `.mcp.json`, tracks owned servers via `trackedServers`
  • `src/core/vscode-mcp.ts` — syncs to `.vscode/settings.json` MCP section
  • `src/core/codex-mcp.ts` — project-scoped MCP config
• Sync state: `src/core/sync-state.ts` — `getPreviouslySyncedMcpServers()` returns what AllAgents owns
• CLI commands: `src/cli/commands/` — add new `mcp.ts` command file
• Sync output formatting: `src/cli/format-sync.ts` — reuse for `mcp list` display

Ownership model

AllAgents tracks which MCP servers it installed via `trackedServers` in sync state. This is critical:

• `mcp add` must add the server to `trackedServers` so AllAgents owns it
• `mcp remove` must only remove servers in `trackedServers`, never user-managed ones
• `mcp list` should show ownership status (AllAgents-managed vs user-managed)
• See CLAUDE.md "MCP Server Sync" section for the ownership rule

`mcp add` behavior

Should mirror `claude mcp add` flags where applicable:

• `--transport http|stdio` (default: infer from URL vs command)
• `-e KEY=VALUE` for environment variables
• `--client claude,copilot` to target specific clients (default: all configured)
• Writes to each client's MCP config file using existing per-client sync logic

`mcp update` behavior

Runs only the MCP portion of the sync pipeline:

1. Collect `.mcp.json` configs from all plugins in workspace
2. Sync to each client's MCP config (using existing `claude-mcp.ts`, `vscode-mcp.ts`, etc.)
3. Purge servers no longer provided by plugins
4. Skip skill/agent/hook/command sync entirely

Acceptance Criteria

• `allagents mcp add ` adds an MCP server to all configured clients
• `allagents mcp add --client claude,copilot` targets specific clients
• `allagents mcp list` shows all AllAgents-managed MCP servers with per-client sync status
• `allagents mcp remove ` removes server from all clients and sync state
• `allagents mcp update` syncs MCP servers from plugins without touching other artifacts
• `allagents mcp get ` shows server config and which clients have it
• Respects ownership model — never modifies user-managed servers
• New servers added via `mcp add` are tracked in sync state

Context

From analysis of enterprise adoption — some teams primarily need MCP server distribution (e.g., connecting AI assistants to internal APIs) and don't need full plugin artifact sync. An MCP-focused entry point lowers the barrier.

[christso]

Reopening — this was closed shortly after PR #347 ("docs: MCP proxy design spec") merged, but that PR only added a design document for the MCP proxy feature (rewriting plugin-provided HTTP servers to stdio via mcp-remote). It did not implement any of the originally-requested scope:

• allagents mcp add <name> <commandOrUrl> — add an MCP server without going through a plugin
• allagents mcp list / remove / get / update
• Any inline way to declare MCP servers directly in workspace.yaml (no top-level mcpServers: field exists in WorkspaceConfigSchema)

Verified on current main:

• allagents mcp --help → no such subcommand (only update, workspace, plugin, self, skills)
• No src/cli/commands/mcp.ts exists
• MCP servers still must come from a plugin's .mcp.json

The MCP proxy feature solves the OAuth-fragmentation motivation, but users still have no way to add an ad-hoc MCP server without authoring or installing a plugin. Leaving this open to track that gap.