Fix watch bugs

[tastelikefeet]

PR type

• Bug Fix
• New Feature
• Document Updates
• Server Enhancement

PR information

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[gemini-code-assist]

Code Review

This pull request replaces the list command with status, updates the format conversion command to use --out-dir, and introduces a new backups command with filtering capabilities. It also refactors workspace conversion to filter out default templates and back up target files, resolves a stale file descriptor issue in the watcher daemon, and filters out stale deletes during incremental pushes. The review feedback highlights a critical test isolation issue where a restore test could overwrite files in the user's home directory, and suggests a more robust, unified parsing logic for filtering backups by framework and agent name.

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