feat: Implemented graph-based RAG
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# Graph RAG Design Spec
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## Status: COMPLETE
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### Verified From Code (all claims backed by actual file reads)
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---
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## Goal
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Extend the existing two-signal hybrid search (vector HNSW + BM25 → RRF) to a three-signal hybrid
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(vector + BM25 + knowledge graph → RRF). The graph captures entity/relationship knowledge extracted
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from documents at ingestion time via an LLM call per chunk. At query time, graph traversal expands
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context beyond semantic similarity.
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---
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## Verified Current Architecture
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### `Rag` struct (`src/rag/mod.rs:48`)
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```rust
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pub struct Rag {
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app_config: Arc<AppConfig>,
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name: String,
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path: String,
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embedding_model: Model,
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hnsw: Hnsw<'static, f32, DistCosine>, // ephemeral, rebuilt on load
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bm25: SearchEngine<DocumentId>, // ephemeral, rebuilt on load
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data: RagData, // serialized to YAML
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last_sources: RwLock<Option<String>>,
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}
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```
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### `RagData` struct (`src/rag/mod.rs:892`)
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```rust
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pub struct RagData {
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pub embedding_model: String,
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pub chunk_size: usize,
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pub chunk_overlap: usize,
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pub reranker_model: Option<String>,
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pub top_k: usize,
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pub batch_size: Option<usize>,
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pub next_file_id: FileId,
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pub document_paths: Vec<String>,
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pub files: IndexMap<FileId, RagFile>,
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#[serde(with = "serde_vectors")]
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pub vectors: IndexMap<DocumentId, Vec<f32>>,
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}
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```
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### `RagData::new` callers (both need updating):
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1. `Rag::init` (`src/rag/mod.rs:219`) — interactive init path
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2. `Rag::resolve_init_data` (`src/rag/mod.rs:195`) — config-driven init path
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### `Rag::create` (`src/rag/mod.rs:253`) — all init paths converge here:
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```rust
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pub fn create(app: &AppConfig, name: &str, path: &Path, data: RagData) -> Result<Self> {
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let hnsw = data.build_hnsw();
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let bm25 = data.build_bm25();
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let embedding_model = Model::retrieve_model(app, &data.embedding_model, ModelType::Embedding)?;
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let rag = Rag { app_config: Arc::new(app.clone()), name: name.to_string(),
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path: path.display().to_string(), data, embedding_model, hnsw, bm25,
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last_sources: RwLock::new(None) };
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Ok(rag)
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}
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```
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### `hybrid_search` (`src/rag/mod.rs:710`)
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```rust
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async fn hybrid_search(&self, query: &str, top_k: usize, rerank_model: Option<&str>)
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-> Result<Vec<(DocumentId, String)>>
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```
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Runs `vector_search` + `keyword_search` in parallel via `tokio::join!`, then either reranks or
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applies `reciprocal_rank_fusion(vec![vector_ids, keyword_ids], vec![1.125, 1.0], top_k)`.
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### `reciprocal_rank_fusion` (`src/rag/mod.rs:1186`) — standalone fn, already weight-parameterized:
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```rust
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fn reciprocal_rank_fusion(
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list_of_document_ids: Vec<Vec<DocumentId>>,
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list_of_weights: Vec<f32>,
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top_k: usize,
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) -> Vec<DocumentId>
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```
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### `RagData::del` (`src/rag/mod.rs:953`):
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```rust
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pub fn del(&mut self, file_ids: Vec<FileId>) {
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for file_id in file_ids {
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if let Some(file) = self.files.swap_remove(&file_id) {
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for (document_index, _) in file.documents.iter().enumerate() {
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let document_id = DocumentId::new(file_id, document_index);
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self.vectors.swap_remove(&document_id);
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}
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}
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}
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}
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```
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### `RagNode` (`src/graph/types.rs:331`):
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```rust
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pub struct RagNode {
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pub documents: Vec<String>,
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pub query: Option<String>,
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pub top_k: Option<usize>,
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pub embedding_model: Option<String>,
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pub chunk_size: Option<usize>,
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pub chunk_overlap: Option<usize>,
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pub reranker_model: Option<String>,
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pub batch_size: Option<usize>,
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pub state_updates: Option<HashMap<String, String>>,
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pub timeout: Option<u64>,
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}
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```
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### `Client` trait (`src/client/common.rs:40`):
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- `async fn chat_completions(&self, input: Input) -> Result<ChatCompletionsOutput>` — needs `Input`
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- `async fn chat_completions_inner(&self, client: &ReqwestClient, data: ChatCompletionsData) -> Result<ChatCompletionsOutput>` — accessible on `Box<dyn Client>` via vtable
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- `async fn embeddings(&self, data: &EmbeddingsData) -> Result<Vec<Vec<f32>>>`
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- `async fn rerank(&self, data: &RerankData) -> Result<RerankOutput>`
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- `fn build_client(&self) -> Result<ReqwestClient>`
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- `fn model(&self) -> &Model`
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**Key finding**: `Input` cannot be constructed without `RequestContext` (which `Rag` doesn't have).
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Instead, `extract_entities` uses `chat_completions_inner` directly with manually built
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`ChatCompletionsData`. This is accessible via `Box<dyn Client>`.
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### `Message` (`src/client/message.rs:22`):
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```rust
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pub fn new(role: MessageRole, content: MessageContent) -> Self
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```
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`MessageRole::User`, `MessageContent::Text(String)` — both confirmed.
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### `AppConfig` RAG fields (`src/config/app_config.rs:71`):
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```rust
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pub rag_embedding_model: Option<String>,
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pub rag_reranker_model: Option<String>,
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pub rag_top_k: usize, // default: 5
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pub rag_chunk_size: Option<usize>,
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pub rag_chunk_overlap: Option<usize>,
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pub rag_template: Option<String>,
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```
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### `patch_messages` — confirmed exported from `crate::client::*` (used in `input.rs:5`)
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### `init_client(app_config, model)` — works for any `ModelType`, including `Chat`
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### `ModelType` variants: `Chat`, `Embedding`, `Reranker` (confirmed in `model.rs`)
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### petgraph serde: `NodeIndex` serializes as inner `u32`; `StableGraph` preserves index positions
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through roundtrip. `IndexMap<DocumentId, Vec<NodeIndex>>` safe for YAML (DocumentId is newtype over
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usize, serializes as integer key).
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---
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## New Dependency
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```toml
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petgraph = { version = "0.7", features = ["serde-1"] }
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```
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---
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## New File: `src/rag/graph.rs`
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All graph types and extraction logic. Module declared in `mod.rs` as `mod graph; use self::graph::*;`.
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### Types:
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- `Entity { name: String, entity_type: String, description: Option<String> }`
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- `Relationship { relation_type: String, weight: f32 }`
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- `ExtractionResult { entities: Vec<ExtractedEntity>, relationships: Vec<ExtractedRelationship> }`
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- `ExtractedEntity { name: String, r#type: String, description: Option<String> }`
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- `ExtractedRelationship { from: String, to: String, r#type: String, weight: Option<f32> }`
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- `KnowledgeGraph { graph: StableGraph<Entity, Relationship>, entity_index: IndexMap<String, NodeIndex>, document_entities: IndexMap<DocumentId, Vec<NodeIndex>> }`
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### Key methods on `KnowledgeGraph`:
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- `merge(doc_id: DocumentId, result: ExtractionResult)` — merges extraction into graph
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- `remove_documents(ids: &[DocumentId])` — removes entities exclusive to deleted documents
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- `build_node_to_docs(&self) -> IndexMap<NodeIndex, Vec<DocumentId>>` — ephemeral reverse map
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### `extract_entities(client: &dyn Client, chunk: &str) -> Result<ExtractionResult>`:
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- Builds `ChatCompletionsData` manually (no `Input` needed)
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- Calls `patch_messages` then `client.chat_completions_inner(&reqwest_client, data).await`
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- Strips markdown code fences from response before JSON parse
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- Temperature: `Some(0.0)` for deterministic extraction
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### Extraction prompt: structured JSON output requesting entities + relationships
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---
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## Changes to `src/rag/mod.rs`
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### `Rag` struct — add one ephemeral field:
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```rust
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node_to_docs: IndexMap<NodeIndex, Vec<DocumentId>>, // ephemeral, rebuilt on load
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```
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### `Rag::create` — build node_to_docs before moving data:
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```rust
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let node_to_docs = data.knowledge_graph.build_node_to_docs();
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// then add to struct literal
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```
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### `Rag` Clone impl — add:
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```rust
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node_to_docs: self.data.knowledge_graph.build_node_to_docs(),
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```
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### `RagData` struct — three new fields (all `#[serde(default)]` for backward compat):
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```rust
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#[serde(default)]
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pub graph_enabled: bool,
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#[serde(default, skip_serializing_if = "Option::is_none")]
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pub extractor_model: Option<String>,
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#[serde(default)]
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pub knowledge_graph: KnowledgeGraph,
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```
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### `RagData::new` — two new params: `graph_enabled: bool, extractor_model: Option<String>`
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### `RagData::del` — collect doc_ids during existing loop, call `remove_documents` at end:
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```rust
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let mut doc_ids_to_remove = vec![];
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for file_id in file_ids {
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if let Some(file) = self.files.swap_remove(&file_id) {
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for (document_index, _) in file.documents.iter().enumerate() {
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let document_id = DocumentId::new(file_id, document_index);
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self.vectors.swap_remove(&document_id);
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doc_ids_to_remove.push(document_id);
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}
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}
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}
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self.knowledge_graph.remove_documents(&doc_ids_to_remove);
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```
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### `Rag::init` (line 219) — add two params to `RagData::new`:
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```rust
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app.rag_graph_enabled,
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app.rag_extractor_model.clone(),
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```
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### `resolve_init_data` — resolve from config+app, pass to `RagData::new`:
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```rust
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let graph_enabled = config.graph_enabled.unwrap_or(app.rag_graph_enabled);
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let extractor_model = config.extractor_model.clone().or_else(|| app.rag_extractor_model.clone());
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```
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### `sync_documents` — entity extraction block after `rag_files` built, before embedding:
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```rust
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if self.data.graph_enabled {
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if let Some(extractor_model_id) = self.data.extractor_model.clone() {
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let model = Model::retrieve_model(&self.app_config, &extractor_model_id, ModelType::Chat)?;
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let client = self.create_embeddings_client(model)?;
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let total_chunks: usize = rag_files.iter().map(|f| f.documents.len()).sum();
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let mut chunk_num = 0;
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let file_offset = next_file_id;
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for (batch_file_idx, rag_file) in rag_files.iter().enumerate() {
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let file_id = file_offset + batch_file_idx;
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for (doc_idx, doc) in rag_file.documents.iter().enumerate() {
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chunk_num += 1;
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progress(&spinner, format!("Extracting entities [{chunk_num}/{total_chunks}]"));
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let doc_id = DocumentId::new(file_id, doc_idx);
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match extract_entities(client.as_ref(), &doc.page_content).await {
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Ok(result) => self.data.knowledge_graph.merge(doc_id, result),
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Err(e) => debug!("Entity extraction failed for {doc_id:?}: {e}"),
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}
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}
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}
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}
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}
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```
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### After line 705 (after hnsw/bm25 rebuild in sync_documents):
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```rust
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self.node_to_docs = self.data.knowledge_graph.build_node_to_docs();
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```
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### `hybrid_search` — add third signal:
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```rust
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let graph_search_ids: Vec<DocumentId> = if self.data.graph_enabled
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&& !self.data.knowledge_graph.entity_index.is_empty()
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{
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self.graph_search(query, &keyword_search_ids, top_k)
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} else {
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vec![]
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};
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// RRF: extend to 3-way when graph has results, fall back to 2-way otherwise
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```
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### New `graph_search` method (sync):
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```rust
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fn graph_search(&self, query: &str, bm25_anchor_ids: &[DocumentId], top_k: usize) -> Vec<DocumentId>
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```
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Phase 1: entity names from query via substring match in `entity_index`.
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Phase 2: fallback — entities from top BM25 document chunks.
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Phase 3: expand 1-hop neighbors in `StableGraph`.
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Phase 4: score docs by entity overlap ratio, return top_k.
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### `RagInitConfig` — two new fields:
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```rust
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pub graph_enabled: Option<bool>,
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pub extractor_model: Option<String>,
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```
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---
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## Changes to `src/config/app_config.rs`
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New fields alongside existing `rag_*` block:
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```rust
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pub rag_graph_enabled: bool, // default: false
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pub rag_extractor_model: Option<String>, // default: None
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```
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Defaults, env var overrides, and propagation all follow the same pattern as existing `rag_*` fields.
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---
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## Changes to `src/graph/types.rs` — `RagNode`
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```rust
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#[serde(default, skip_serializing_if = "Option::is_none")]
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pub graph_enabled: Option<bool>,
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#[serde(default, skip_serializing_if = "Option::is_none")]
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pub extractor_model: Option<String>,
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```
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---
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## Changes to `src/config/agent.rs`
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Pass new fields through to `RagInitConfig`:
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```rust
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graph_enabled: rag_node.graph_enabled,
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extractor_model: rag_node.extractor_model.clone(),
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```
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---
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## Backward Compatibility
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- All new `RagData` fields have `#[serde(default)]` — old YAML files load without migration
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- `graph_enabled` defaults `false` — existing RAG instances unchanged
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- `graph_search_ids` empty → 2-way RRF runs (identical to current behavior)
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- `node_to_docs` rebuild on `create()` is O(n) over empty map for old instances
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---
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## V1 Scope Exclusions
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- LLM entity extraction from query at search time (V1 uses substring match + BM25 anchoring)
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- Multi-hop traversal (field reserved, 1-hop only in V1)
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- Entity embeddings / fuzzy entity lookup
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- Bincode for large-corpus graph storage
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- Gleaning / multi-pass extraction
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---
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## Implementation Progress
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- [x] Cargo.toml — petgraph dependency
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- [x] src/rag/graph.rs — new file
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- [x] src/rag/mod.rs — mod/use, Rag struct, create, clone
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- [x] src/rag/mod.rs — RagData fields, new, del
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- [x] src/rag/mod.rs — Rag::init, resolve_init_data
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- [x] src/rag/mod.rs — sync_documents extraction block
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- [x] src/rag/mod.rs — hybrid_search + graph_search
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- [x] src/rag/mod.rs — RagInitConfig fields
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- [x] src/config/app_config.rs — new fields
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- [x] src/config/mod.rs — propagation
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- [x] src/graph/types.rs — RagNode fields
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- [x] src/config/agent.rs — propagation
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- [x] cargo check — clean (0 warnings, 1065 tests passing)
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