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docs(user): restructure user docs into topic sections (Phase 1) (#223)

Browse source 
Move the 23 flat docs/user/*.md files into topic subdirectories so the
user guide is organized by area (schema, queries, search, branching, cli,
operations, clusters, concepts, reference) instead of a flat list. This is
a pure structural move — whole files relocated, every cross-doc link
recomputed, no prose rewrites or content splits (those follow in Phase 2).

- 19 `git mv`s (install.md, deployment.md stay top-level); history preserved
  (renames detected at 92–100% similarity).
- All intra-doc links, AGENTS.md's topic table (52 pointers), and the
  docs/dev + docs/releases back-links recomputed via relpath from each
  file's new location.
- docs/user/index.md rewritten as a sectioned nav hub.
- Fixed 5 doc-path references in Rust (comments + two user-facing server
  settings error strings) to point at the new locations.

Verified: zero broken .md links across tracked docs; check-agents-md.sh
green (with the untracked scratch docs set aside); touched crates build.

Note: the public site (omnigraph-web) imports docs/ via a flat-only script;
its import-docs.mjs needs a subdir-aware update before the next re-sync.

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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# CLI Guide
## Core Graph Flow
```bash
omnigraph init --schema schema.pg graph.omni
omnigraph load --data data.jsonl --mode overwrite graph.omni
omnigraph snapshot graph.omni --branch main --json
omnigraph query --uri graph.omni --query queries.gq --name get_person --params '{"name":"Alice"}'
omnigraph mutate --uri graph.omni --query queries.gq --name insert_person --params '{"name":"Mina","age":28}'
```
`omnigraph query` is the canonical read command (pairs with `POST /query`);
`omnigraph mutate` is the canonical write command (pairs with `POST /mutate`).
The previous names `omnigraph read` and `omnigraph change` keep working as
visible aliases — invocations emit a one-line deprecation warning to stderr
and otherwise behave identically. See [Deprecated names](#deprecated-names)
for the migration table.
For ad-hoc reads and mutations (REPLs, AI agents, one-off scripts), pass the
GQ source inline with `-e` / `--query-string` instead of a file path:
```bash
omnigraph query --uri graph.omni \
-e 'query find($name: String) { match { $p: Person { name: $name } } return { $p.name, $p.age } }' \
--params '{"name":"Alice"}'
omnigraph mutate --uri graph.omni \
-e 'query add($name: String, $age: I32) { insert Person { name: $name, age: $age } }' \
--params '{"name":"Inline","age":42}'
```
`-e` is mutually exclusive with `--query <path>` and `--alias <name>`; exactly
one of the three must be provided. The inline source travels through the same
parser, lint, params binding, and commit machinery as a file-based query —
only the source loader changes.
## Branching And Reviewable Data Flows
```bash
omnigraph branch create --uri graph.omni --from main feature-x
omnigraph branch list --uri graph.omni
omnigraph branch merge --uri graph.omni feature-x --into main
omnigraph load --data batch.jsonl --branch review/import-2026-04-09 --from main --mode merge graph.omni
omnigraph export graph.omni --branch main --type Person > people.jsonl
omnigraph commit list graph.omni --branch main --json
omnigraph commit show --uri graph.omni <commit-id> --json
```
## Remote Server Mode
Serve a graph:
```bash
omnigraph-server graph.omni --bind 127.0.0.1:8080
```
Read through the HTTP API:
```bash
omnigraph query \
--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`.
## Multi-graph servers (v0.6.0+)
Against a multi-graph server (started with `--config omnigraph.yaml` referencing a non-empty `graphs:` map), use `omnigraph graphs list` to enumerate the registered graphs. The server must configure bearer tokens and `server.policy.file` with a rule that allows `graph_list`; `/graphs` is closed by default even when the server runs with `--unauthenticated`.
```bash
OMNIGRAPH_BEARER_TOKEN=admin-token \
omnigraph graphs list --uri http://server.example.com --json
```
For config-driven clients, set the remote graph's `bearer_token_env` to an environment variable containing a token whose actor is authorized by `server.policy.file`.
`list` rejects local URI targets — it's for remote multi-graph servers only.
Runtime add/remove is **not** in v0.6.0. To add a graph, stop the server, add a `graphs.<id>` entry to `omnigraph.yaml`, then restart. To remove, stop the server, delete the entry, restart.
Per-graph URLs: hit a graph's cluster route from any subcommand by pointing `--uri` at it:
```bash
omnigraph read --uri http://server.example.com/graphs/beta --query q.gq ...
```
## Runs, Policy, And Diagnostics
```bash
omnigraph lint --query queries.gq --schema schema.pg --json
omnigraph check --query queries.gq graph.omni --json
omnigraph schema plan --schema next.pg graph.omni --json
omnigraph schema apply --schema next.pg graph.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 graph.omni --json
omnigraph commit show --uri graph.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, graph-backed
lint uses local or `s3://` graph 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:
```yaml
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.file` for 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`.
## Deprecated names
The CLI was renamed to align with the HTTP server's canonical endpoint
names (`POST /query`, `POST /mutate`) and the `query` keyword in the GQ
language. The previous spellings keep working forever; invocations emit a
one-line warning to stderr and otherwise behave identically.
| Old (deprecated) | New (canonical) | Migration |
|--------------------------|---------------------|----------------------------------------------------------|
| `omnigraph read` | `omnigraph query` | Same flags and behavior. `read` is a visible clap alias. |
| `omnigraph change` | `omnigraph mutate` | Same flags and behavior. `change` is a visible clap alias. |
| `omnigraph query lint` | `omnigraph lint` | Same flags. The argv-level shim rewrites `query lint` to `lint`. |
| `omnigraph query check` | `omnigraph check` | `check` is a visible alias of `omnigraph lint`. |
The `command:` field in `aliases.<name>` in `omnigraph.yaml` accepts both
`read` / `change` (legacy) and `query` / `mutate` (canonical); the two
spellings are interchangeable on the wire via serde aliases.