docs(user): de-dev polish — strip internal scaffolding from user docs (Phase 3a) (#226)

Remove developer-only scaffolding that leaked into the public user/operator
docs, while preserving every user-facing behavior, command, flag, endpoint,
constant, and env var. No behavior changes.

Removed across 18 files:
- internal ticket / sequencing refs (MR-NNN, RFC-NNN, "Phase N");
- source-code paths (crates/**/*.rs, *.pest) and internal struct/function
  dumps (e.g. the QueryIR / GraphCommit / SchemaMigrationPlan Rust types,
  internal fn names like fork_branch_from_state, optimize_all_tables);
- Lance-internal blocker prose (upstream issue numbers, blob-decode cause,
  sidecar Phase-B/C mechanics) — keeping the user-visible behavior (e.g.
  "optimize skips Blob-column tables; reads/writes unaffected");
- pre-v0.4.0 Run-state-machine archaeology.

Internal IR/lowering/recovery-internals sections were either trimmed to a
brief user-facing note (e.g. "Traversal execution", "interrupted writes
recover automatically; recovery commits are recorded under actor
omnigraph:recovery") or removed.

Kept: all language syntax, lint codes, Cedar actions/scopes, endpoints,
error taxonomy, every constant and env var (verified none dropped from the
constants cheat-sheet), and the operator-facing explanations of on-disk
artifacts. Residual "legacy" mentions are all user-facing (the deprecated
omnigraph.yaml, the legacy token chain, old command names).

Verified: zero internal-scaffolding leaks (MR/RFC/Phase/.rs/.pest = 0) across
docs/user; zero broken links; check-agents-md.sh green.

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

docs/user/search/embeddings.md

@@ -2,14 +2,14 @@
 
 OmniGraph has **two** embedding clients with different defaults and purposes.
 
-## Compiler-side client (`omnigraph-compiler/src/embedding.rs`) — query-time normalization
+## Compiler-side client — query-time normalization
 
 - Default model: `text-embedding-3-small` (OpenAI-style schema)
 - Env: `NANOGRAPH_EMBED_MODEL`, `OPENAI_API_KEY`, `OPENAI_BASE_URL` (default `https://api.openai.com/v1`), `NANOGRAPH_EMBEDDINGS_MOCK`, `NANOGRAPH_EMBED_TIMEOUT_MS=30000`, `NANOGRAPH_EMBED_RETRY_ATTEMPTS=4`, `NANOGRAPH_EMBED_RETRY_BACKOFF_MS=200`
 - Methods: `embed_text(input, expected_dim)`, `embed_texts(inputs, expected_dim)`
 - Mock mode: deterministic FNV-1a + xorshift64 → L2-normalized vectors
 
-## Engine-side client (`omnigraph/src/embedding.rs`) — runtime ingest
+## Engine-side client — runtime ingest
 
 - Model: `gemini-embedding-2-preview`
 - Env: `GEMINI_API_KEY`, `OMNIGRAPH_GEMINI_BASE_URL` (default Google generativelanguage v1beta), `OMNIGRAPH_EMBED_TIMEOUT_MS=30000`, `OMNIGRAPH_EMBED_RETRY_ATTEMPTS=4`, `OMNIGRAPH_EMBED_RETRY_BACKOFF_MS=200`, `OMNIGRAPH_EMBEDDINGS_MOCK`

docs/user/search/indexes.md

@@ -15,12 +15,11 @@
 - **Lazy branch forking for indexes**: a branch that hasn't mutated a sub-table doesn't need its own index — the main lineage's index is reused until the first write triggers a copy-on-write fork.
 - Vector index parameters (metric, nlist, nprobe, etc.) are not exposed in the schema; they default at the Lance layer and are picked up automatically when an index is asked for on a Vector column.
 
-## L2 — Graph topology index (`graph_index/mod.rs`)
+## L2 — Graph topology index
 
 This is OmniGraph-specific (not Lance):
 
-- `TypeIndex`: dense `u32 ↔ String id` mapping per node type.
-- `CsrIndex`: Compressed Sparse Row representation of edges per edge type — `offsets[i]..offsets[i+1]` slices into `targets`.
-- `GraphIndex { type_indices, csr (out), csc (in) }` — built on demand from a snapshot's edge tables, **lazily**: only when an `Expand` the planner routes to the CSR path (dense / large frontier) or an `AntiJoin` actually needs it.
-- Cached in `RuntimeCache::graph_indices` (LRU, max 8 entries, keyed by snapshot id + edge table versions).
-- Selective `Expand`s resolve neighbors from the persisted `src`/`dst` BTREE instead (one indexed scan per hop) and never trigger the CSR build; see [query-language](../queries/index.md) → Expand. Pure scans, and queries served entirely by the indexed traversal path, skip it.
+- A Compressed Sparse Row (CSR) adjacency representation of edges, with both out- (CSR) and in- (CSC) directions, plus a dense per-node-type id mapping.
+- Built on demand from a snapshot's edge tables, **lazily**: only when an `Expand` the planner routes to the CSR path (dense / large frontier) or an `AntiJoin` actually needs it.
+- Cached per snapshot (LRU, keyed by snapshot id + edge table versions), so repeat traversals over the same snapshot reuse it.
+- Selective `Expand`s resolve neighbors from the persisted `src`/`dst` BTREE instead (one indexed scan per hop) and never trigger the CSR build; see [query-language](../queries/index.md) → Traversal execution. Pure scans, and queries served entirely by the indexed traversal path, skip it.