[Bug]: specify init writes speckit.manifest.json without the speckit-converge skill it just installed

## Version

spec-kit v1.0.1, `specify init --here --integration claude --force`

## Description

After an in-place upgrade, `.specify/integrations/speckit.manifest.json` lists 9 `speckit-*` SKILL.md entries under `files` — but init also installed `.claude/skills/speckit-converge/SKILL.md`, which is absent from the manifest.

Any tooling that uses the manifest to classify vendored files (pristine / modified / missing / untracked — e.g. deciding whether the next `specify init` will clobber local work) sees converge as **untracked**: it cannot be classified at all, which is the worst of the four states for a file the installer itself owns.

Observed identically on two independent upgrades (a template repo and a workflows repo, both 0.5.0 → v1.0.1 in-place).

## Expected behavior

The generated manifest includes every skill file the init run installs, converge included.

Reproduce with `specify init --here --integration claude --force` using spec-kit v1.0.1, then compare `.specify/integrations/speckit.manifest.json` with the installed `.claude/skills/speckit-converge/SKILL.md` and the other listed `speckit-*` files. Trace the init manifest generation path and verify that the generated manifest includes every skill file installed by the command, including converge.

索引モデルが issue の本文から書いたものです。