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.

scripts/gen-tool-catalog.ts

@@ -226,7 +226,7 @@ const TOOL_PACKAGES: ToolPackage[] = [
   {
     pkg: '@deepseek-ai/dsh-tool-cordis',
     dir: 'tool-cordis',
-    source: 'packages/cordis/tool-cordis/src/index.ts',
+    source: 'packages/self-modification/tool-cordis/src/index.ts',
     requires: ['ctx.tools'],
     writes: ['tool/call', 'tool/result', 'process-local temporary Plugin lifecycle'],
     async mount(ctx) {