[Feature] Claude Code desktop app: MCP plugin auto-load + CLI session-flag passthrough at launch

Summary

Two gaps in the Claude Code desktop app that force power users back to CLI for any workflow that depends on launch-time configuration:

1. No CLI flag passthrough at launch — desktop app is a fixed-config GUI; can't accept --channels, --permission-mode, --resume <session-id>, --include-partial-messages, or any other flag the CLI exposes
2. MCP plugins don't auto-attach at session start — connecting Discord plugin (or any MCP server) requires a manual UI flow on every session, vs CLI's --channels plugin:discord@claude-plugins-official flag

Why this matters

Desktop app is currently the only path that gives native terminal-emulator-style scrollback (alt-screen-buffer regression in CLI v2.1.89+ documented in #42670 + family; team-flag-specific scrollback regression in v2.1.119 documented in #53193). Power users who want history-scrolling are forced to desktop app. But desktop app missing flag passthrough + MCP auto-attach means:

• Lose Discord plugin (no way to reach mobile Discord notifications without manual UI dance every session)
• Lose --resume <session-id> for continuing specific sessions (have to use the picker every time)
• Lose --permission-mode auto for non-interactive flow
• Lose any custom env var workflow (e.g., CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1 — though that has its own scrollback regression, see #53193)

CLI gives flag composability + persistent screen sessions but loses native scrollback.
Desktop gives native scrollback but loses CLI's launch-time configuration surface.

There's no path that has both.

Specific asks

A) Flag passthrough at launch — let claude desktop --channels foo --permission-mode auto --resume <id> (or equivalent OS-level launcher flag mechanism) work the same way as CLI. macOS could use URL-scheme handler (claude-desktop://launch?resume=<id>&channels=...); Windows could use registered command-line args; Linux likewise.

B) MCP plugins from settings.json — desktop app should read the same ~/.claude/settings.json as CLI, including enabledPlugins, and auto-attach those plugins at every session start. The current "configure MCP via UI" flow is the gap; the settings file is the source of truth on the CLI side already.

Either A or B alone would close most of the gap. Both would put desktop app at workflow-equivalent to CLI minus the alt-screen-buffer scrollback issue (which is its actual differentiating advantage).

Environment

• Pi-hosted Claude Code via desktop app thin-client (ccd-cli/2.1.119 per the SSH-remote setup), accessed from PC running Windows desktop app
• Use case: long-running scaffold sessions with Discord MCP for mobile-channel notifications, persistent agent teams, session-resume across compaction

Related

• #53193 — CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1 disables TUI scrollback in v2.1.119 (the bug that pushed me to desktop in the first place)
• #42670 — alt-screen-buffer kills scrollback (the broader v2.1.89+ regression family)

Currently I'm working around with a custom cc-scroll helper that reads transcript JSONL into less from a sidecar terminal pane. It works but bypasses the official UX entirely.