Align NodeBench with frozen NodeKit v1 contracts

[HomenShum]

Outcome

Aligns NodeBenchAI's current post-Phase-2 tree with the frozen NodeKit v1 contracts without moving runtime code or changing production behavior.

What changed

• replaces the planning-only apiVersion/kind/spec manifests with canonical flat nodekit.repo/v1, nodeagent.application/v1, and nodeagent.pack/v1
• keeps repo-local-nodebench explicitly authoritative while recording nodeagent-native as the migration target
• adds the filesystem-authored Entity Intelligence skill
• binds four existing evaluation lanes: conformance, smoke, entity-intelligence benchmark, and production verification
• generates a secret-free .nodeagent/ definition and config hash over the current 1,908-file authored surface
• updates the brownfield/standard-tree documentation and fixes stale policy-path references
• classifies the existing DeepTrace PolicyContext as a domain specialization, not a fork of the runtime policy contract

Validation

Against the latest NodeKit v1 compiler:

• compiled-definition stale check: pass
• config hash: ce762d645646cb409ea3e20e58517608ce921dc9262eae8aa3377847bfc4594f
• inspect: 1,908 files, 93 eval files, 57 integrations, 1 pack, 3 policies, 1 skill, 162 tool files
• repository conformance: pass; 1/1 contract declaration classified
• doctor: pass on Node 22.22.2
• generated-output secret and absolute-user-path scan: pass
• git diff --check: pass
• hot-file diff: empty

Honest boundary

This is contract alignment, not a runtime replacement. It does not edit the live Convex/agent loop, deploy anything, add Pi AI to production, claim a no-key application demo, or promote NodeBenchAI from the registry's untracked command profile. The clean worktree intentionally had no installed application dependencies, so the existing full app typecheck/build were not rerun for this manifest/docs/generated-metadata-only delta.

[vercel]

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Project	Deployment	Actions	Updated (UTC)
nodebench-ai	Ready	Preview, Comment	Jul 20, 2026 2:57am

[github-actions]

PR size advisory

This PR adds 10272 lines of substantive change. CONTRIBUTING.md defines a soft limit of ~400 LOC.

If the PR is genuinely cohesive (e.g. an architecture map, a generated migration, a deletion of a dead module), no action is needed. Otherwise consider:

• splitting into 2-3 PRs along independent concerns
• pre-discussing the architecture change in a GitHub Discussion before merge

This is advisory — it does not block the merge.

[github-actions]

Vercel preflight failed: TypeScript Convex

Detail: convex typecheck failed

error TS5058: The specified path does not exist: 'convex'.

Fix: Run npx tsc -p convex --noEmit --pretty false.

[HomenShum]

Superseded by #592. The replacement preserves this brownfield contract alignment, uses the repository-required chore/<slug> branch and Conventional Commit title, declares the coordinated NodeKit concept dependency, and fixes Vercel preflight to typecheck the backend/convex project declared by convex.json. No force-push or deployment was performed.