fix: separate host and skill write targets before locking

[ScriptedAlchemy]

Summary

• Merged feat: TraceDecay V2 delivery (PR8–PR13) + daemon performance, memory, and reliability overhaul #707 tip 3e6167b265 into this branch. No conflicts.
• Host-bundle journals and writer locks stay per host. Skill usage stays per skill file.
• Publication pointer memo no longer treats same size and mtime as the same file. A same-length rewrite in one timestamp tick was failing the undecoded compare-and-swap after the tip's multi-term CAS test.

Motivation

Principle: separate-before-serializing-shared-state.

This PR stays on the #707 tip (codex/tracedecay-total-redesign-plan-reopened). It does not merge #707 or this PR to master.

Merge

• Tip SHA merged: 3e6167b265639c17b7d1c174cd3b7baa3116adae
• Conflicts: none
• Tip already absorbed NotApplicable admission and the removed changes.reused list. Terminal publication park tests still pass.

Changes

• HostBundleWriterV1 no longer takes lifecycle-root writer.v1.lock or host-blind journal.v1.json. Journals are journal.{slug}.v1.json; locks are writer.{slug}.v1.lock. Legacy names are still read and retired only for the host that wrote them.
• Skill usage writers update one skill file under agent_managed/skill_usage/<hex>.json.
• read_publication_pointer identifies a cached pointer by content digest, not size and mtime.

Test plan

• cargo test -p tracedecay-code-index-runtime --lib publication_store (27 passed, including the undecoded CAS refusal)
• cargo test -p tracedecay-code-index-runtime --lib branch_publication (10 passed, including terminal publication park)
• cargo test -p tracedecay-code-index-runtime --lib park_convergence
• cargo test -p tracedecay-agent-hosts --lib host_bundle::tests (33 passed)
• cargo test -p tracedecay-automation-runtime --lib recording_one_skill_does_not_rewrite_another_skills_file
• cargo nextest run --workspace --no-fail-fast not run

Checklist

• CHANGELOG.md updated
• No secrets, credentials, or .env files included
• Breaking changes documented (if any)

  

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[ScriptedAlchemy]

Integrated or superseded directly on the #707 branch at ff36c4f; follow-up compile/typecheck regressions were fixed on that branch.