refactor(packages): merge timeout/ into guard/, rename cordis/ to self-modification/
git mv timeout-policy beside repeat-tool-guard (both are loop-hygiene policies on the tool-execution pipeline, and the timeout/ group name collided with util/timeout) and tool-cordis into self-modification/ (naming the role the framework name obscured). Merged/renamed group README triplets, tsconfig globs, generator sources, hierarchy tables, catalogs, and the timeout-policy design note's group references follow. Adds the fifth FIXME marker (dsh-timeout-guard, recorded as a suggestion to settle at resolution time). guard + self-modification suites: 197 passed.
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@@ -34,10 +34,9 @@ Groups hold `packages/<group>/<pkg>/`; names stay `@deepseek-ai/dsh-<pkg>`. **Gr
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| [`spill/`](spill/README.md) | Spill capability family: storage seam, local impl, tool-result spill policy | Product — stable surface |
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| [`todo/`](todo/README.md) | The model-facing `todo_write` tool | Product — stable surface |
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| [`plan/`](plan/README.md) | Plan collaboration state with a direct entry command and reviewed exit | Product — stable surface |
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| [`timeout/`](timeout/README.md) | Tool-call `tools/execute` deadline enforcement | Product — stable surface |
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| [`guard/`](guard/README.md) | Loop-hygiene advisory repeat-call reminders | Product — stable surface |
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| [`guard/`](guard/README.md) | Loop-hygiene guards: advisory repeat-call reminders + the `tools/execute` deadline enforcer | Product — stable surface |
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| [`bundle/`](bundle/README.md) | Installable `dsh --profile` patch layers | Product — stable surface |
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| [`cordis/`](cordis/README.md) | Cordis runtime integration: self-inspection, temporary Plugins, restricted repository Plugin loading | Product — stable surface |
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| [`self-modification/`](self-modification/README.md) | The agent modifies its own runtime: inspect the live runtime's plugins and services, mount/unmount model-written plugins ([design](../.agents/notes/implemented/feature/2026-07-08-self-referential-cordis-toolset.md)) and restricted repository Plugin loading | Product — stable surface |
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| [`hooks/`](hooks/README.md) | Hook bridges + the shared Claude Code / Codex wire-protocol library | Product — stable surface |
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| [`session/`](session/README.md) | Durable session data plane: persistence seam + JSONL/SQLite backends, projection seam, log-backed titles, session reporting | Product — stable surface |
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| [`session-query/`](session-query/README.md) | Session retrieval family: logical corpus, bounded reads, lineage, event relationships, semantic filtering, and SQLite full-text search | Product — stable surface |
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