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.

.gitignore

@@ -100,6 +100,8 @@ apps/
 # Maintainer-local SWE-bench scratch (instance workspaces, venvs, predictions,
 # Docker harness logs). Never published.
 .swebench/
+deep-swe/
+all_preds.jsonl
 
 # Agent handoffs and version-specific setup plans are working-state notes, not
 # public docs. Keep durable setup guidance in docs/runbooks instead.
@@ -111,3 +113,4 @@ docs/*_PLAN.md
 # direnv
 .envrc
 .direnv
+scripts/run_deep_swe.py