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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## Testing
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`packages/ui/app-boot/tests/repository-cache.spec.ts` covers same-process single-flight, cross-instance cache reuse, exact-specifier separation, failed-stage cleanup and retry, and boundary validation. Its real local-Git case invokes the bundled pnpm, runs the fixture repository's `prepare` script, and reads the prepared file from the installed cache entry without network access.
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`packages/boot/app-boot/tests/repository-cache.spec.ts` covers same-process single-flight, cross-instance cache reuse, exact-specifier separation, failed-stage cleanup and retry, and boundary validation. Its real local-Git case invokes the bundled pnpm, runs the fixture repository's `prepare` script, and reads the prepared file from the installed cache entry without network access.
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