Implement check and update commands

[sjquant]

Why

skul needed real update flows for remote-backed bundles instead of a planning-only foundation. This change makes remote bundles inspectable and refreshable in place, while preserving the repo/worktree state model and fixing legacy migration and partial-tool update edge cases found in review.

Changes

• add skul check and skul update command parsing and runtime handling
• extend remote source fetching to inspect cached revisions, resolve remote refs, and refresh cached sources
• persist resolved source commit/ref metadata during add/apply and use it during check/update
• update repeated add --agent behavior to merge desired tool selection instead of overwriting it
• add black-box integration coverage for remote update flows, including legacy registries without resolved commit metadata
• remove the temporary planning document from this branch