fix(sources): handle root skill with metadata dirs

[rudironsoni]

Summary

Fixes #2117.

• allow explicit single-skill declarative sources to install a root-level SKILL.md even when unrelated top-level metadata directories exist
• keep wildcard behavior and real matching skill directories preferred over root fallback
• add git and GitHub transport regression coverage for root SKILL.md plus .claude-plugin metadata
• ignore TokenSave local state through the generated gitignore source registry

Root cause

Root fallback was gated on there being no discovered top-level skill directories. Repositories like blader/humanizer include root SKILL.md plus metadata directories such as .claude-plugin/, so discovery saw a directory, skipped fallback, then filtered out the metadata directory and fetched zero skills.

Validation

• pnpm run check
• pnpm run test
• pnpm run check:supported-tools
• pnpm run check:sync-skill-docs
• pnpm run cspell
• pnpm run secretlint
• pnpm run dev gitignore
• git diff --check

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[dyoshikawa]

@rudironsoni Thank you!