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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>
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# Constants & Tunables (cheat sheet)
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| Name | Value | Where |
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| Name | Value | Area |
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|---|---|---|
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| `MANIFEST_DIR` | `__manifest` | `db/manifest/layout.rs` |
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| Commit graph dir | `_graph_commits.lance` | `db/commit_graph.rs` |
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| Run registry dir (legacy, removed MR-771) | `_graph_runs.lance` | inert post-v0.4.0; bytes remain until a `delete_prefix` primitive lands |
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| Run branch prefix (legacy, removed MR-771/MR-770) | `__run__` | swept off `__manifest` by the v2→v3 migration; no longer a reserved name |
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| Schema apply lock | `__schema_apply_lock__` | `db/mod.rs` |
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| Manifest publisher retry budget | `PUBLISHER_RETRY_BUDGET = 5` | `db/manifest/publisher.rs` |
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| Internal manifest schema version | `INTERNAL_MANIFEST_SCHEMA_VERSION = 3` | `db/manifest/migrations.rs` |
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| Merge stage batch | `MERGE_STAGE_BATCH_ROWS = 8192` | `exec/merge.rs` |
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| Maintenance concurrency | `OMNIGRAPH_MAINTENANCE_CONCURRENCY=8` | `db/omnigraph/optimize.rs` |
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| Lance blob compaction support | `LANCE_SUPPORTS_BLOB_COMPACTION = false` | `db/omnigraph/optimize.rs` |
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| Graph index cache size | `8` (LRU) | `runtime_cache.rs` |
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| Expand indexed-path frontier ceiling | `OMNIGRAPH_EXPAND_INDEXED_MAX_FRONTIER=1024` | `exec/query.rs` |
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| Expand indexed-path hop ceiling | `OMNIGRAPH_EXPAND_INDEXED_MAX_HOPS=6` | `exec/query.rs` |
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| Expand CSR-build cost factor | `CSR_BUILD_FACTOR = 1.5` | `exec/query.rs` |
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| Expand mode override | `OMNIGRAPH_TRAVERSAL_MODE` (`indexed`\|`csr`; unset = cost-based auto) | `exec/query.rs` |
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| Default body limit | `1 MB` | `omnigraph-server/lib.rs` |
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| Ingest body limit | `32 MB` | `omnigraph-server/lib.rs` |
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| Engine embed model | `gemini-embedding-2-preview` | `omnigraph/embedding.rs` |
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| Compiler embed model | `text-embedding-3-small` | `omnigraph-compiler/embedding.rs` |
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| `MANIFEST_DIR` | `__manifest` | manifest layout |
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| Commit graph dir | `_graph_commits.lance` | commit graph |
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| Run registry dir (legacy, removed) | `_graph_runs.lance` | inert post-v0.4.0; bytes remain until a prefix-delete primitive lands |
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| Run branch prefix (legacy, removed) | `__run__` | swept off `__manifest` by the internal schema migration; no longer a reserved name |
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| Schema apply lock | `__schema_apply_lock__` | schema apply |
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| Manifest publisher retry budget | `PUBLISHER_RETRY_BUDGET = 5` | manifest publish |
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| Internal manifest schema version | `INTERNAL_MANIFEST_SCHEMA_VERSION = 3` | manifest migrations |
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| Merge stage batch | `MERGE_STAGE_BATCH_ROWS = 8192` | merge execution |
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| Maintenance concurrency | `OMNIGRAPH_MAINTENANCE_CONCURRENCY=8` | optimize/cleanup |
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| Lance blob compaction support | `LANCE_SUPPORTS_BLOB_COMPACTION = false` | optimize |
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| Graph index cache size | `8` (LRU) | runtime cache |
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| Expand indexed-path frontier ceiling | `OMNIGRAPH_EXPAND_INDEXED_MAX_FRONTIER=1024` | traversal |
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| Expand indexed-path hop ceiling | `OMNIGRAPH_EXPAND_INDEXED_MAX_HOPS=6` | traversal |
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| Expand CSR-build cost factor | `CSR_BUILD_FACTOR = 1.5` | traversal |
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| Expand mode override | `OMNIGRAPH_TRAVERSAL_MODE` (`indexed`\|`csr`; unset = cost-based auto) | traversal |
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| Default body limit | `1 MB` | HTTP server |
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| Ingest body limit | `32 MB` | HTTP server |
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| Engine embed model | `gemini-embedding-2-preview` | engine embedding |
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| Compiler embed model | `text-embedding-3-small` | compiler embedding |
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| Embed timeout | `30 000 ms` | both clients |
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| Embed retries | `4` | both clients |
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| Embed retry backoff | `200 ms` | both clients |
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