[Bug] Local bundle install can advance records without updating existing components

### Spec Kit version

Reproduced with `specify 1.0.4` on Windows.

### Reproduction

1. Install a bundle version whose workflow, two extensions, and preset are already present in an initialized project.
2. Point a clean local release directory at a newer version of the same bundle and components.
3. Run:

```powershell
specify bundle install C:\path\to\new-release\bundle.yml --offline --integration codex
```

The command reports success, for example:

```text
Installed 'program-kit' (0 added, 4 already present).
```

It advances `.specify/bundle-records.json` and its contributed-component versions to the new bundle version, but the installed workflow/registry, extension manifests, and preset/registry can remain at the old version. A subsequent component tool can therefore appear current while executing old code.

When components were installed individually before the bundle, the successful local bundle install can instead create a record without the expected contributed-component entries because every primitive is classified as already present.

### Expected behavior

Bundle installation/update should be transactional across its record and primitive installations:

- update every component to the resolved version before advancing the bundle record;
- validate installed manifests and registries against the resolved bundle before returning success;
- retain the previous coherent record or fail if a primitive update fails; and
- serialize writes when multiple extensions share registry/configuration files.

At minimum, an existing component with a different version must not be treated as satisfied solely because its ID is present.

### Impact

The project records a coherent new bundle version while continuing to execute old extension code. In the observed consumer, managed synchronization misleadingly reported all files unchanged until each workflow, extension, and preset was explicitly reinstalled in sequence.

Start at the bundle install path handling the offline command and reproduce the update with an existing workflow, extensions, and preset. Inspect how .specify/bundle-records.json and primitive manifests or registries are written; done means version-mismatched components are updated before the record advances, failures preserve the prior coherent record, and shared registry writes are serialized.

索引モデルが issue の本文から書いたものです。