docs: process identity, checkpoint resume hashes, and README repair

[cursor]

Overview

Keep operator and developer docs aligned with the current runtime: process identity, fail-closed checkpoint resume, sealed vs paused artifact layout, and a usable README.

Type of Change

• 📚 Documentation or research notes

Motivation & Context

Recent runtime work (#210 checkpoint manifest integrity, process registry/CLI, final.json sealing) was only partly reflected in docs. The README also mixed verification and resume examples and linked to removed docs/app/... paths. docs.json pointed at a missing reference/llms-txt page.

Docs added/updated

• Updated: README.md, docs/explanation/artifacts.mdx, docs/explanation/core-concepts.mdx, docs/reference/python-api.mdx, docs/reference/cli.mdx, docs/reference/events.mdx, docs/reference/summary.mdx, docs/guides/human-in-the-loop.mdx, docs/guides/configure-shared-storage.mdx, docs/quickstart.mdx, docs/docs.json, llms.txt
• Added: docs/reference/llms-txt.mdx

Codepaths they cover

• Process identity: noesis/domain/process.py, noesis/usecases/process_registry.py, noesis/__init__.py (process=), noesis/cli/__main__.py (--process, processes, runs)
• Resume/checkpoint: noesis/usecases/run_lifecycle.py, noesis/domain/run_lifecycle.py (artifact_manifest_hash, CheckpointConsistencyError)
• Sealing/layout: noesis/core.py _seal_episode, noesis/domain/artifacts/finalization.py, noesis/runtime/paths.py

Key knowledge gaps addressed

• README was not copy-pasteable (broken verification/resume sections, stale docs links)
• Resume docs omitted artifact_manifest_hash and the fail-closed manifest appear/disappear cases from fix(lifecycle): enforce checkpoint artifact integrity during resume #210
• Process identity was a public CLI/API surface with no explanation of how ids are derived or where records live
• Artifact layout still showed nested labels and omitted final.json / checkpoints/ / unsealed paused runs
• Nav referenced reference/llms-txt but the page did not exist; llms.txt listed unpublished guides

Technical Details

Documentation-only. No runtime, schema, or KPI changes.

Validation

Required

• All tests pass locally (uv run pytest) or equivalent targeted suite — docs-only; uv/pytest not used
• Schema validation and export diff clean — no schema edits

Situational

• Docs build successfully — npx --yes mintlify@latest broken-links from docs/ reported no broken links
• Lightweight source checks — PYTHONPATH=. import of derive_process_identity matches documented sha256(workspace|name)[:12]; fenced-code blocks balanced; git diff --check clean

ADR-003 Schema Governance Checklist

Not applicable (no schema/KPI changes).

Observability & Safety

No telemetry or behavior changes. Resume troubleshooting now documents fail-closed artifact hash checks so operators do not hand-edit paused episode files.

Related Issues / References

• fix(lifecycle): enforce checkpoint artifact integrity during resume #210 — checkpoint artifact manifest integrity on resume
• Process registry / CLI noesis processes + ns.run(..., process=...)