refactor: finish state-root migration — all runtime paths now .codewhale
- .gitignore: add deep-swe/ and all_preds.jsonl to prevent accidental commits
- config.rs: home_config_path(), managed_config, requirements, mcp, notes,
memory all prefer ~/.codewhale/config.toml with .deepseek fallback
- commands/config.rs: config_toml_path() prefers .codewhale
- commands/anchor.rs: anchors_path prefers .codewhale/anchors.md
- commands/note.rs: notes_path prefers .codewhale/notes.md
- skills/install.rs: cache defaults to .codewhale/cache/skills
- skills/mod.rs: global skills discovery includes .codewhale/skills
- file_frecency, clipboard, onboarding, audit, task_manager: all .codewhale
- project-local paths (onboarding trust) still .deepseek for compat
Closes #2231.
Hunter Bown
8822e9873a