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/changes.md

@@ -1,24 +0,0 @@
-# Change Detection / Diff
-
-`changes/mod.rs`. Three-level algorithm:
-
-1. **Manifest diff**: skip sub-tables whose `(table_version, table_branch)` is unchanged.
-2. **Lineage check**:
-   - Same branch lineage → fast path: use the per-row `_row_last_updated_at_version` column to classify Insert/Update/Delete.
-   - Different lineages → ID-based streaming comparison.
-3. **Row-level diff**: streaming, no full materialization.
-
-## Public API
-
-- `diff_between(from: ReadTarget, to: ReadTarget, filter: Option<ChangeFilter>) -> ChangeSet`
-- `diff_commits(from_commit_id, to_commit_id, filter)` — cross-branch safe.
-
-## Types
-
-```
-ChangeOp: Insert | Update | Delete
-EntityKind: Node | Edge
-EntityChange { table_key, kind, type_name, id, op, manifest_version, endpoints?: {src, dst} }
-ChangeFilter { kinds?, type_names?, ops? }
-ChangeSet { from_version, to_version, branch?, changes[], stats }
-```