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/reference/constants.md

@@ -0,0 +1,40 @@
+# Constants & Tunables (cheat sheet)
+
+| Name | Value | Where |
+|---|---|---|
+| `MANIFEST_DIR` | `__manifest` | `db/manifest/layout.rs` |
+| Commit graph dir | `_graph_commits.lance` | `db/commit_graph.rs` |
+| Run registry dir (legacy, removed MR-771) | `_graph_runs.lance` | inert post-v0.4.0; bytes remain until a `delete_prefix` primitive lands |
+| Run branch prefix (legacy, removed MR-771/MR-770) | `__run__` | swept off `__manifest` by the v2→v3 migration; no longer a reserved name |
+| Schema apply lock | `__schema_apply_lock__` | `db/mod.rs` |
+| Manifest publisher retry budget | `PUBLISHER_RETRY_BUDGET = 5` | `db/manifest/publisher.rs` |
+| Internal manifest schema version | `INTERNAL_MANIFEST_SCHEMA_VERSION = 3` | `db/manifest/migrations.rs` |
+| Merge stage batch | `MERGE_STAGE_BATCH_ROWS = 8192` | `exec/merge.rs` |
+| Maintenance concurrency | `OMNIGRAPH_MAINTENANCE_CONCURRENCY=8` | `db/omnigraph/optimize.rs` |
+| Lance blob compaction support | `LANCE_SUPPORTS_BLOB_COMPACTION = false` | `db/omnigraph/optimize.rs` |
+| Graph index cache size | `8` (LRU) | `runtime_cache.rs` |
+| Expand indexed-path frontier ceiling | `OMNIGRAPH_EXPAND_INDEXED_MAX_FRONTIER=1024` | `exec/query.rs` |
+| Expand indexed-path hop ceiling | `OMNIGRAPH_EXPAND_INDEXED_MAX_HOPS=6` | `exec/query.rs` |
+| Expand CSR-build cost factor | `CSR_BUILD_FACTOR = 1.5` | `exec/query.rs` |
+| Expand mode override | `OMNIGRAPH_TRAVERSAL_MODE` (`indexed`\|`csr`; unset = cost-based auto) | `exec/query.rs` |
+| Default body limit | `1 MB` | `omnigraph-server/lib.rs` |
+| Ingest body limit | `32 MB` | `omnigraph-server/lib.rs` |
+| Engine embed model | `gemini-embedding-2-preview` | `omnigraph/embedding.rs` |
+| Compiler embed model | `text-embedding-3-small` | `omnigraph-compiler/embedding.rs` |
+| Embed timeout | `30 000 ms` | both clients |
+| Embed retries | `4` | both clients |
+| Embed retry backoff | `200 ms` | both clients |
+| LANCE memory pool default | `1 GB` (raised in v0.3.0) | runtime |
+
+**Expand traversal dispatch.** With `OMNIGRAPH_TRAVERSAL_MODE` unset, the engine
+chooses the indexed (per-hop BTREE) vs CSR (whole-graph in-memory) path with a
+cost model over cheap manifest counts (frontier size, |E|, source-vertex count,
+hops) plus the index-coverage signal: the indexed path is preferred when its
+frontier-relative work beats building the CSR (≈ when `hops × frontier` is a
+small fraction of the source-vertex set), and CSR is preferred for dense/deep
+traversals or when the BTREE coverage is degraded and a full scan would be paid
+per hop. The two ceilings bound the **initial dispatch** frontier/hops (beyond
+them CSR is always used); they are not a hard per-hop bound — the cost model
+*estimates* total indexed work as ~`hops × frontier × fanout`, so dense fan-out is
+priced toward CSR rather than capped mid-traversal. The override flag forces a path (the `auto` result is identical either way;
+only the path differs).