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MR-794 step 2: docs — runs/invariants/architecture/execution + cleanup
Refresh user-facing and agent-facing docs for the staged-write rewire and clean up stale Run-state-machine references that survived MR-771. MR-794-specific updates: * docs/runs.md — remove "Known limitation: mid-query partial failure" section; document the in-memory accumulator + D₂ rule + the LoadMode::Overwrite residual. * docs/invariants.md §VI.25 — flip from aspirational/open to upheld for inserts/updates. Within-query read-your-writes is now load-bearing for the publisher CAS contract. * docs/architecture.md — add "Mutation atomicity — in-memory accumulator (MR-794)" subsection with per-op flow; refresh the engine + state diagrams to drop RunRegistry and add MutationStaging. * docs/execution.md — rewrite the mutation flow sequence diagram for the staged-write path; updated the LoadMode table to call out per-mode commit semantics; rewrote load vs ingest. * docs/query-language.md — document the D₂ parse-time rule. * docs/errors.md — add the D₂ BadRequest rejection path. * docs/testing.md — extend the runs.rs row to cover the new MR-794 contract tests; add the staged_writes.rs row. * docs/releases/v0.4.1.md (new) — release note covering the rewire, test additions, residuals, and files changed. * AGENTS.md (CLAUDE.md symlink) — update the atomic-per-query description and the L2 capability matrix row. Stale-reference cleanup (MR-771 leftovers): * docs/storage.md — drop live _graph_runs.lance / _graph_run_actors.lance from the layout diagram and prose; mark legacy. * docs/branches-commits.md — move __run__<id> to a legacy note; remove publish_run from the publish-trigger list. * docs/audit.md — refresh _as API list (drop begin_run_as / publish_run_as); legacy RunRecord.actor_id moved to a historical note. * docs/constants.md — mark run registry / branch-prefix rows as legacy. * docs/cli.md — replace the legacy omnigraph run * quickstart block with omnigraph commit list/show. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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| `MANIFEST_DIR` | `__manifest` | `db/manifest/layout.rs` |
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| Commit graph dir | `_graph_commits.lance` | `db/commit_graph.rs` |
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| Run registry dir | `_graph_runs.lance` | `db/run_registry.rs` |
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| Run branch prefix | `__run__` | `db/run_registry.rs` |
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| Run registry dir (legacy, removed MR-771) | `_graph_runs.lance` | inert post-v0.4.0; reclaimed by MR-770 |
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| Run branch prefix (legacy, removed MR-771) | `__run__` | filtered by `is_internal_run_branch` defense-in-depth |
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| Schema apply lock | `__schema_apply_lock__` | `db/mod.rs` |
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| Manifest publisher retry budget | `PUBLISHER_RETRY_BUDGET = 5` | `db/manifest/publisher.rs` |
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| Internal manifest schema version | `INTERNAL_MANIFEST_SCHEMA_VERSION = 2` | `db/manifest/migrations.rs` |
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