feat: add host-local catalog initialization

[myobie]

Summary

• add an idempotent st2 init that creates only agents/<host>/config.kdl with the portable $CATALOG/pty declaration and never overwrites existing content
• resolve PTY roots as non-empty ambient override → matching host config → shared root config → native default, with lower malformed layers isolated until needed
• reserve host config from agent discovery, validate every host config, and apply host selection consistently across runtime/native-tool flows
• document the portable shared root versus deliberate host-local override boundary

Verification

• cargo test (all targets exercised; the known concurrent nomad_survival executable-replacement race hit Linux ETXTBSY, then both affected tests passed as isolated exact reruns)
• cargo test --doc
• focused init, precedence, discovery, runtime, native-tool, validation, and clean-PATH regressions pass

Nathan completed hand review and the PR is ready. No rollout or merge is requested by this PR.