feat: compose app server runtime context

[oratis]

Summary

• compose trusted settings, instructions, memory, user/project skills, output style, hooks, and built-in tools inside the app-server
• add a turn-scoped RuntimeHost lease with deterministic cleanup for later MCP/plugin resources
• keep client manifest defaults from overriding shared model/effort/mode settings, and expose Auto mode in Desktop
• document the composition boundary and the remaining hook review/MCP-plugin lifecycle work

Validation

• pnpm format:check
• pnpm lint (one pre-existing unused-import warning)
• pnpm typecheck
• pnpm test (984 passed, 12 skipped)
• pnpm build
• pnpm docs:check
• pnpm --filter @deepcode/desktop test:e2e (4 passed)
• app-server sidecar and VS Code app-server CJS initialize/diagnostics smoke
• VSIX package smoke (8 files, 79.32 KB)

[oratis]

Review: approved ✅

Moves composition (trusted settings, instructions, memory, user/project skills, output style, hooks, built-in tools) inside the app-server, so clients stop assembling context. Same principle as #184 and #197: one assembler, not five.

What I checked

• Turn-scoped RuntimeHost lease with deterministic cleanup. Getting the lease/cleanup boundary in place before MCP clients and plugin subprocesses attach to it (feat: compose MCP and plugin runtime resources #200) is the right order — retrofitting lifecycle onto already-attached resources is how process leaks ship. Deterministic cleanup is the precondition for feat: compose MCP and plugin runtime resources #200's "close on success, interruption, preprocessing failure, and shutdown".
• Client manifest defaults no longer override shared model/effort/mode settings. This was a real bug shape: a client's built-in default silently winning over a user's explicit setting, which reads to the user as "my config is ignored". Settings should beat manifest defaults, and now they do.
• Auto mode exposed in Desktop — parity with the CLI, and it routes through the same trusted executor rather than a client-side reimplementation.
• Composition boundary documented along with the remaining hook-review and MCP/plugin lifecycle work, which feat: compose MCP and plugin runtime resources #200 and feat: require exact project hook review #201 then close. The doc isn't deferring indefinitely; the follow-ups are in this same stack.

Validation: CI green; full suite green locally at the stack tip.