[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.

Written by the indexing model from the issue text.