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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# self-modification/ — the agent modifies its own runtime
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English | [中文](README.zh.md)
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Model-facing tools over the live cordis runtime the agent itself runs inside: inspect the loaded plugins and service surface, mount model-written plugins, and dispose them again — plus the restricted repository Plugin runtime. The group is the landing zone for future self-modification packages. Design home: [the toolset Agent Note](../../.agents/notes/implemented/feature/2026-07-08-self-referential-cordis-toolset.md).
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| Package | Role | ctx key |
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|---|---|---|
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| [`tool-cordis/`](tool-cordis/README.md) | Model-facing runtime inspection and temporary-plugin tools | registers on `ctx.tools` |
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| [`repository-plugin/`](repository-plugin/README.md) | Repository skill and MCP composition | registers a Loader builtin |
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