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

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>

docs/user/deployment.md

@@ -17,7 +17,7 @@ The server also has two **boot sources**: `omnigraph.yaml` (graph targets
 declared in the per-operator config) or a **cluster directory**
 (`omnigraph-server --cluster <dir>`), which serves the cluster control
 plane's applied revision — see
-[cluster-config.md](cluster-config.md#serving-from-the-cluster-the-mode-switch).
+[cluster-config.md](clusters/config.md#serving-from-the-cluster-the-mode-switch).
 The two are exclusive per deployment; switching is a restart with a different
 flag.