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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CLI Guide
Core Repo Flow
omnigraph init --schema ./schema.pg ./repo.omni
omnigraph load --data ./data.jsonl --mode overwrite ./repo.omni
omnigraph snapshot ./repo.omni --branch main --json
omnigraph read --uri ./repo.omni --query ./queries.gq --name get_person --params '{"name":"Alice"}'
omnigraph change --uri ./repo.omni --query ./queries.gq --name insert_person --params '{"name":"Mina","age":28}'
Branching And Reviewable Data Flows
omnigraph branch create --uri ./repo.omni --from main feature-x
omnigraph branch list --uri ./repo.omni
omnigraph branch merge --uri ./repo.omni feature-x --into main
omnigraph ingest --data ./batch.jsonl --branch review/import-2026-04-09 ./repo.omni
omnigraph export ./repo.omni --branch main --type Person > people.jsonl
omnigraph commit list ./repo.omni --branch main --json
omnigraph commit show --uri ./repo.omni <commit-id> --json
Remote Server Mode
Serve a repo:
omnigraph-server ./repo.omni --bind 127.0.0.1:8080
Read through the HTTP API:
omnigraph read \
--target http://127.0.0.1:8080 \
--query ./queries.gq \
--name get_person \
--params '{"name":"Alice"}'
If the server requires auth, set OMNIGRAPH_SERVER_BEARER_TOKEN on the server
and configure the matching bearer_token_env in omnigraph.yaml.
Runs, Policy, And Diagnostics
omnigraph query lint --query ./queries.gq --schema ./schema.pg --json
omnigraph query check --query ./queries.gq ./repo.omni --json
omnigraph schema plan --schema ./next.pg ./repo.omni --json
omnigraph schema apply --schema ./next.pg ./repo.omni --json
omnigraph policy validate --config ./omnigraph.yaml
omnigraph policy test --config ./omnigraph.yaml
omnigraph policy explain --config ./omnigraph.yaml --actor act-alice --action read --branch main
omnigraph commit list ./repo.omni --json
omnigraph commit show --uri ./repo.omni <commit-id> --json
(The legacy omnigraph run list/show/publish/abort subcommands were removed in MR-771; mutations and loads publish atomically and the commit graph (omnigraph commit list) is the audit surface.)
query lint and query check are the same command surface. In v1, repo-backed
lint uses local or s3:// repo URIs; HTTP targets are only supported when you
also pass --schema.
Config
omnigraph.yaml lets the CLI and server share named graphs, defaults, and
query roots:
graphs:
local:
uri: ./demo.omni
dev:
uri: http://127.0.0.1:8080
bearer_token_env: OMNIGRAPH_BEARER_TOKEN
cli:
graph: local
branch: main
query:
roots:
- queries
- .
The config file can also define:
- server bind defaults
- auth env files
- query aliases for common read and change commands
policy.filefor Cedar authorization rules
When policy is enabled, schema apply is authorized through the
schema_apply action and is typically limited to admins on protected main.