refactor(runtime): use OpenAI native ApplyPatch

[Astro-Han]

Summary

• Register the AI SDK native openai.tools.applyPatch() tool only for documented Apply Patch models on native OpenAI Responses; every other model and provider keeps the existing tool surface.
• Use @openai/agents-core.applyDiff() for the official single-file V4A create/update semantics.
• Route create, update, and delete through the existing FilesystemExecutor, its canonical write lock, workspace adapter, permission boundary, and sandbox worker.
• Keep create exclusive with recursive parent creation, and delete the directory entry itself so symlink targets are preserved.
• Remove the prior design entirely: no custom multi-file parser, matcher, planner, editing protocol, provider fallback, second filesystem implementation, version/CAS protocol, or partial/unknown state machine.

Refs #1552

Verification

• npm run format:check
• npm run check:third-party-notices
• npm --workspace @maka/core run build
• npm --workspace @maka/runtime run build
• npm --workspace @maka/runtime-host run build
• 386 affected Runtime tests passed.
• 3 focused Core permission tests passed.
• 20 focused Runtime Host composition tests passed.
• git diff --check

Not run locally: the full repository test suite or a paid OpenAI model call.

Review focus

• Final diff: 30 files, +1,314/-60. Product source is +473/-57, focused tests are +549/-3, and generated dependency lock/notices account for +292.
• Each provider call contains exactly one create_file, update_file, or delete_file operation. There is no multi-file transaction or partial-settlement state machine.
• The AI SDK owns the provider schema, Agents Core owns V4A matching, and Maka owns filesystem authority.
• The runtime uses the provider's canonical apply_patch name so continuation and replay serialize as apply_patch_call_output, including failures.
• The filesystem-worker build resolves only Agents Core's applyDiff.mjs; it does not bundle the unrelated Agents SDK runtime.
• This PR does not add a second Headless executor or expose Apply Patch to non-OpenAI providers.

Checklist

• Tests cover the change and fail without it
• Lint, format, typecheck and the affected suites pass locally

Does this PR entail a change in behavior?

• Yes — described under Summary above
• No