feat: rag-embedding-ai-chat (#1)

Co-authored-by: Sharang Parnerkar <parnerkarsharang@gmail.com>
Reviewed-on: #1

compliance-agent/src/agent.rs

@@ -20,6 +20,7 @@ impl ComplianceAgent {
             config.litellm_url.clone(),
             config.litellm_api_key.clone(),
             config.litellm_model.clone(),
+            config.litellm_embed_model.clone(),
         ));
         Self {
             config,

compliance-agent/src/api/handlers/chat.rs

@@ -0,0 +1,238 @@
+use std::sync::Arc;
+
+use axum::extract::{Extension, Path};
+use axum::http::StatusCode;
+use axum::Json;
+use mongodb::bson::doc;
+
+use compliance_core::models::chat::{ChatRequest, ChatResponse, SourceReference};
+use compliance_core::models::embedding::EmbeddingBuildRun;
+use compliance_graph::graph::embedding_store::EmbeddingStore;
+
+use crate::agent::ComplianceAgent;
+use crate::rag::pipeline::RagPipeline;
+
+use super::ApiResponse;
+
+type AgentExt = Extension<Arc<ComplianceAgent>>;
+
+/// POST /api/v1/chat/:repo_id — Send a chat message with RAG context
+pub async fn chat(
+    Extension(agent): AgentExt,
+    Path(repo_id): Path<String>,
+    Json(req): Json<ChatRequest>,
+) -> Result<Json<ApiResponse<ChatResponse>>, StatusCode> {
+    let pipeline = RagPipeline::new(agent.llm.clone(), agent.db.inner());
+
+    // Step 1: Embed the user's message
+    let query_vectors = agent
+        .llm
+        .embed(vec![req.message.clone()])
+        .await
+        .map_err(|e| {
+            tracing::error!("Failed to embed query: {e}");
+            StatusCode::INTERNAL_SERVER_ERROR
+        })?;
+
+    let query_embedding = query_vectors.into_iter().next().ok_or_else(|| {
+        tracing::error!("Empty embedding response");
+        StatusCode::INTERNAL_SERVER_ERROR
+    })?;
+
+    // Step 2: Vector search — retrieve top 8 chunks
+    let search_results = pipeline
+        .store()
+        .vector_search(&repo_id, query_embedding, 8, 0.5)
+        .await
+        .map_err(|e| {
+            tracing::error!("Vector search failed: {e}");
+            StatusCode::INTERNAL_SERVER_ERROR
+        })?;
+
+    // Step 3: Build system prompt with code context
+    let mut context_parts = Vec::new();
+    let mut sources = Vec::new();
+
+    for (embedding, score) in &search_results {
+        context_parts.push(format!(
+            "--- {} ({}, {}:L{}-L{}) ---\n{}",
+            embedding.qualified_name,
+            embedding.kind,
+            embedding.file_path,
+            embedding.start_line,
+            embedding.end_line,
+            embedding.content,
+        ));
+
+        // Truncate snippet for the response
+        let snippet: String = embedding
+            .content
+            .lines()
+            .take(10)
+            .collect::<Vec<_>>()
+            .join("\n");
+        sources.push(SourceReference {
+            file_path: embedding.file_path.clone(),
+            qualified_name: embedding.qualified_name.clone(),
+            start_line: embedding.start_line,
+            end_line: embedding.end_line,
+            language: embedding.language.clone(),
+            snippet,
+            score: *score,
+        });
+    }
+
+    let code_context = if context_parts.is_empty() {
+        "No relevant code context found.".to_string()
+    } else {
+        context_parts.join("\n\n")
+    };
+
+    let system_prompt = format!(
+        "You are an expert code assistant for a software repository. \
+         Answer the user's question based on the code context below. \
+         Reference specific files and functions when relevant. \
+         If the context doesn't contain enough information, say so.\n\n\
+         ## Code Context\n\n{code_context}"
+    );
+
+    // Step 4: Build messages array with history
+    let mut messages: Vec<(String, String)> = Vec::new();
+    messages.push(("system".to_string(), system_prompt));
+
+    for msg in &req.history {
+        messages.push((msg.role.clone(), msg.content.clone()));
+    }
+    messages.push(("user".to_string(), req.message));
+
+    // Step 5: Call LLM
+    let response_text = agent
+        .llm
+        .chat_with_messages(messages, Some(0.3))
+        .await
+        .map_err(|e| {
+            tracing::error!("LLM chat failed: {e}");
+            StatusCode::INTERNAL_SERVER_ERROR
+        })?;
+
+    Ok(Json(ApiResponse {
+        data: ChatResponse {
+            message: response_text,
+            sources,
+        },
+        total: None,
+        page: None,
+    }))
+}
+
+/// POST /api/v1/chat/:repo_id/build-embeddings — Trigger embedding build
+pub async fn build_embeddings(
+    Extension(agent): AgentExt,
+    Path(repo_id): Path<String>,
+) -> Result<Json<serde_json::Value>, StatusCode> {
+    let agent_clone = (*agent).clone();
+    tokio::spawn(async move {
+        let repo = match agent_clone
+            .db
+            .repositories()
+            .find_one(doc! { "_id": mongodb::bson::oid::ObjectId::parse_str(&repo_id).ok() })
+            .await
+        {
+            Ok(Some(r)) => r,
+            _ => {
+                tracing::error!("Repository {repo_id} not found for embedding build");
+                return;
+            }
+        };
+
+        // Get latest graph build
+        let build = match agent_clone
+            .db
+            .graph_builds()
+            .find_one(doc! { "repo_id": &repo_id })
+            .sort(doc! { "started_at": -1 })
+            .await
+        {
+            Ok(Some(b)) => b,
+            _ => {
+                tracing::error!("[{repo_id}] No graph build found — build graph first");
+                return;
+            }
+        };
+
+        let graph_build_id = build
+            .id
+            .map(|id| id.to_hex())
+            .unwrap_or_else(|| "unknown".to_string());
+
+        // Get nodes
+        let nodes: Vec<compliance_core::models::graph::CodeNode> = match agent_clone
+            .db
+            .graph_nodes()
+            .find(doc! { "repo_id": &repo_id })
+            .await
+        {
+            Ok(cursor) => {
+                use futures_util::StreamExt;
+                let mut items = Vec::new();
+                let mut cursor = cursor;
+                while let Some(Ok(item)) = cursor.next().await {
+                    items.push(item);
+                }
+                items
+            }
+            Err(e) => {
+                tracing::error!("[{repo_id}] Failed to fetch nodes: {e}");
+                return;
+            }
+        };
+
+        let git_ops = crate::pipeline::git::GitOps::new(&agent_clone.config.git_clone_base_path);
+        let repo_path = match git_ops.clone_or_fetch(&repo.git_url, &repo.name) {
+            Ok(p) => p,
+            Err(e) => {
+                tracing::error!("Failed to clone repo for embedding build: {e}");
+                return;
+            }
+        };
+
+        let pipeline = RagPipeline::new(agent_clone.llm.clone(), agent_clone.db.inner());
+        match pipeline
+            .build_embeddings(&repo_id, &repo_path, &graph_build_id, &nodes)
+            .await
+        {
+            Ok(run) => {
+                tracing::info!(
+                    "[{repo_id}] Embedding build complete: {}/{} chunks",
+                    run.embedded_chunks,
+                    run.total_chunks
+                );
+            }
+            Err(e) => {
+                tracing::error!("[{repo_id}] Embedding build failed: {e}");
+            }
+        }
+    });
+
+    Ok(Json(
+        serde_json::json!({ "status": "embedding_build_triggered" }),
+    ))
+}
+
+/// GET /api/v1/chat/:repo_id/status — Get latest embedding build status
+pub async fn embedding_status(
+    Extension(agent): AgentExt,
+    Path(repo_id): Path<String>,
+) -> Result<Json<ApiResponse<Option<EmbeddingBuildRun>>>, StatusCode> {
+    let store = EmbeddingStore::new(agent.db.inner());
+    let build = store.get_latest_build(&repo_id).await.map_err(|e| {
+        tracing::error!("Failed to get embedding status: {e}");
+        StatusCode::INTERNAL_SERVER_ERROR
+    })?;
+
+    Ok(Json(ApiResponse {
+        data: build,
+        total: None,
+        page: None,
+    }))
+}

compliance-agent/src/api/handlers/dast.rs

@@ -103,8 +103,7 @@ pub async fn trigger_scan(
     Extension(agent): AgentExt,
     Path(id): Path<String>,
 ) -> Result<Json<serde_json::Value>, StatusCode> {
-    let oid =
-        mongodb::bson::oid::ObjectId::parse_str(&id).map_err(|_| StatusCode::BAD_REQUEST)?;
+    let oid = mongodb::bson::oid::ObjectId::parse_str(&id).map_err(|_| StatusCode::BAD_REQUEST)?;
 
     let target = agent
         .db
@@ -207,8 +206,7 @@ pub async fn get_finding(
     Extension(agent): AgentExt,
     Path(id): Path<String>,
 ) -> Result<Json<ApiResponse<DastFinding>>, StatusCode> {
-    let oid =
-        mongodb::bson::oid::ObjectId::parse_str(&id).map_err(|_| StatusCode::BAD_REQUEST)?;
+    let oid = mongodb::bson::oid::ObjectId::parse_str(&id).map_err(|_| StatusCode::BAD_REQUEST)?;
 
     let finding = agent
         .db

compliance-agent/src/api/handlers/graph.rs

@@ -52,7 +52,7 @@ pub async fn get_graph(
         // so there is only one set of nodes/edges per repo.
         let filter = doc! { "repo_id": &repo_id };
 
-        let nodes: Vec<CodeNode> = match db.graph_nodes().find(filter.clone()).await {
+        let all_nodes: Vec<CodeNode> = match db.graph_nodes().find(filter.clone()).await {
             Ok(cursor) => collect_cursor_async(cursor).await,
             Err(_) => Vec::new(),
         };
@@ -60,6 +60,17 @@ pub async fn get_graph(
             Ok(cursor) => collect_cursor_async(cursor).await,
             Err(_) => Vec::new(),
         };
+
+        // Remove disconnected nodes (no edges) to keep the graph clean
+        let connected: std::collections::HashSet<&str> = edges
+            .iter()
+            .flat_map(|e| [e.source.as_str(), e.target.as_str()])
+            .collect();
+        let nodes = all_nodes
+            .into_iter()
+            .filter(|n| connected.contains(n.qualified_name.as_str()))
+            .collect();
+
         (nodes, edges)
     } else {
         (Vec::new(), Vec::new())
@@ -235,12 +246,7 @@ pub async fn get_file_content(
     // Cap at 10,000 lines
     let truncated: String = content.lines().take(10_000).collect::<Vec<_>>().join("\n");
 
-    let language = params
-        .path
-        .rsplit('.')
-        .next()
-        .unwrap_or("")
-        .to_string();
+    let language = params.path.rsplit('.').next().unwrap_or("").to_string();
 
     Ok(Json(ApiResponse {
         data: FileContent {

compliance-agent/src/api/handlers/mod.rs

@@ -1,3 +1,4 @@
+pub mod chat;
 pub mod dast;
 pub mod graph;
 
@@ -5,7 +6,8 @@ use std::sync::Arc;
 
 #[allow(unused_imports)]
 use axum::extract::{Extension, Path, Query};
-use axum::http::StatusCode;
+use axum::http::{header, StatusCode};
+use axum::response::IntoResponse;
 use axum::Json;
 use mongodb::bson::doc;
 use serde::{Deserialize, Serialize};
@@ -89,6 +91,72 @@ pub struct UpdateStatusRequest {
     pub status: String,
 }
 
+#[derive(Deserialize)]
+pub struct SbomFilter {
+    #[serde(default)]
+    pub repo_id: Option<String>,
+    #[serde(default)]
+    pub package_manager: Option<String>,
+    #[serde(default)]
+    pub q: Option<String>,
+    #[serde(default)]
+    pub has_vulns: Option<bool>,
+    #[serde(default)]
+    pub license: Option<String>,
+    #[serde(default = "default_page")]
+    pub page: u64,
+    #[serde(default = "default_limit")]
+    pub limit: i64,
+}
+
+#[derive(Deserialize)]
+pub struct SbomExportParams {
+    pub repo_id: String,
+    #[serde(default = "default_export_format")]
+    pub format: String,
+}
+
+fn default_export_format() -> String {
+    "cyclonedx".to_string()
+}
+
+#[derive(Deserialize)]
+pub struct SbomDiffParams {
+    pub repo_a: String,
+    pub repo_b: String,
+}
+
+#[derive(Serialize)]
+pub struct LicenseSummary {
+    pub license: String,
+    pub count: u64,
+    pub is_copyleft: bool,
+    pub packages: Vec<String>,
+}
+
+#[derive(Serialize)]
+pub struct SbomDiffResult {
+    pub only_in_a: Vec<SbomDiffEntry>,
+    pub only_in_b: Vec<SbomDiffEntry>,
+    pub version_changed: Vec<SbomVersionDiff>,
+    pub common_count: u64,
+}
+
+#[derive(Serialize)]
+pub struct SbomDiffEntry {
+    pub name: String,
+    pub version: String,
+    pub package_manager: String,
+}
+
+#[derive(Serialize)]
+pub struct SbomVersionDiff {
+    pub name: String,
+    pub package_manager: String,
+    pub version_a: String,
+    pub version_b: String,
+}
+
 type AgentExt = Extension<Arc<ComplianceAgent>>;
 type ApiResult<T> = Result<Json<ApiResponse<T>>, StatusCode>;
 
@@ -235,6 +303,52 @@ pub async fn trigger_scan(
     Ok(Json(serde_json::json!({ "status": "scan_triggered" })))
 }
 
+pub async fn delete_repository(
+    Extension(agent): AgentExt,
+    Path(id): Path<String>,
+) -> Result<Json<serde_json::Value>, StatusCode> {
+    let oid = mongodb::bson::oid::ObjectId::parse_str(&id).map_err(|_| StatusCode::BAD_REQUEST)?;
+    let db = &agent.db;
+
+    // Delete the repository
+    let result = db
+        .repositories()
+        .delete_one(doc! { "_id": oid })
+        .await
+        .map_err(|_| StatusCode::INTERNAL_SERVER_ERROR)?;
+
+    if result.deleted_count == 0 {
+        return Err(StatusCode::NOT_FOUND);
+    }
+
+    // Cascade delete all related data
+    let _ = db.findings().delete_many(doc! { "repo_id": &id }).await;
+    let _ = db.sbom_entries().delete_many(doc! { "repo_id": &id }).await;
+    let _ = db.scan_runs().delete_many(doc! { "repo_id": &id }).await;
+    let _ = db.cve_alerts().delete_many(doc! { "repo_id": &id }).await;
+    let _ = db
+        .tracker_issues()
+        .delete_many(doc! { "repo_id": &id })
+        .await;
+    let _ = db.graph_nodes().delete_many(doc! { "repo_id": &id }).await;
+    let _ = db.graph_edges().delete_many(doc! { "repo_id": &id }).await;
+    let _ = db.graph_builds().delete_many(doc! { "repo_id": &id }).await;
+    let _ = db
+        .impact_analyses()
+        .delete_many(doc! { "repo_id": &id })
+        .await;
+    let _ = db
+        .code_embeddings()
+        .delete_many(doc! { "repo_id": &id })
+        .await;
+    let _ = db
+        .embedding_builds()
+        .delete_many(doc! { "repo_id": &id })
+        .await;
+
+    Ok(Json(serde_json::json!({ "status": "deleted" })))
+}
+
 pub async fn list_findings(
     Extension(agent): AgentExt,
     Query(filter): Query<FindingsFilter>,
@@ -322,21 +436,46 @@ pub async fn update_finding_status(
 
 pub async fn list_sbom(
     Extension(agent): AgentExt,
-    Query(params): Query<PaginationParams>,
+    Query(filter): Query<SbomFilter>,
 ) -> ApiResult<Vec<SbomEntry>> {
     let db = &agent.db;
-    let skip = (params.page.saturating_sub(1)) * params.limit as u64;
+    let mut query = doc! {};
+
+    if let Some(repo_id) = &filter.repo_id {
+        query.insert("repo_id", repo_id);
+    }
+    if let Some(pm) = &filter.package_manager {
+        query.insert("package_manager", pm);
+    }
+    if let Some(q) = &filter.q {
+        if !q.is_empty() {
+            query.insert("name", doc! { "$regex": q, "$options": "i" });
+        }
+    }
+    if let Some(has_vulns) = filter.has_vulns {
+        if has_vulns {
+            query.insert("known_vulnerabilities", doc! { "$exists": true, "$ne": [] });
+        } else {
+            query.insert("known_vulnerabilities", doc! { "$size": 0 });
+        }
+    }
+    if let Some(license) = &filter.license {
+        query.insert("license", license);
+    }
+
+    let skip = (filter.page.saturating_sub(1)) * filter.limit as u64;
     let total = db
         .sbom_entries()
-        .count_documents(doc! {})
+        .count_documents(query.clone())
         .await
         .unwrap_or(0);
 
     let entries = match db
         .sbom_entries()
-        .find(doc! {})
+        .find(query)
+        .sort(doc! { "name": 1 })
         .skip(skip)
-        .limit(params.limit)
+        .limit(filter.limit)
         .await
     {
         Ok(cursor) => collect_cursor_async(cursor).await,
@@ -346,7 +485,272 @@ pub async fn list_sbom(
     Ok(Json(ApiResponse {
         data: entries,
         total: Some(total),
-        page: Some(params.page),
+        page: Some(filter.page),
+    }))
+}
+
+pub async fn export_sbom(
+    Extension(agent): AgentExt,
+    Query(params): Query<SbomExportParams>,
+) -> Result<impl IntoResponse, StatusCode> {
+    let db = &agent.db;
+    let entries: Vec<SbomEntry> = match db
+        .sbom_entries()
+        .find(doc! { "repo_id": &params.repo_id })
+        .await
+    {
+        Ok(cursor) => collect_cursor_async(cursor).await,
+        Err(_) => Vec::new(),
+    };
+
+    let body = if params.format == "spdx" {
+        // SPDX 2.3 format
+        let packages: Vec<serde_json::Value> = entries
+            .iter()
+            .enumerate()
+            .map(|(i, e)| {
+                serde_json::json!({
+                    "SPDXID": format!("SPDXRef-Package-{i}"),
+                    "name": e.name,
+                    "versionInfo": e.version,
+                    "downloadLocation": "NOASSERTION",
+                    "licenseConcluded": e.license.as_deref().unwrap_or("NOASSERTION"),
+                    "externalRefs": e.purl.as_ref().map(|p| vec![serde_json::json!({
+                        "referenceCategory": "PACKAGE-MANAGER",
+                        "referenceType": "purl",
+                        "referenceLocator": p,
+                    })]).unwrap_or_default(),
+                })
+            })
+            .collect();
+
+        serde_json::json!({
+            "spdxVersion": "SPDX-2.3",
+            "dataLicense": "CC0-1.0",
+            "SPDXID": "SPDXRef-DOCUMENT",
+            "name": format!("sbom-{}", params.repo_id),
+            "documentNamespace": format!("https://compliance-scanner/sbom/{}", params.repo_id),
+            "packages": packages,
+        })
+    } else {
+        // CycloneDX 1.5 format
+        let components: Vec<serde_json::Value> = entries
+            .iter()
+            .map(|e| {
+                let mut comp = serde_json::json!({
+                    "type": "library",
+                    "name": e.name,
+                    "version": e.version,
+                    "group": e.package_manager,
+                });
+                if let Some(purl) = &e.purl {
+                    comp["purl"] = serde_json::Value::String(purl.clone());
+                }
+                if let Some(license) = &e.license {
+                    comp["licenses"] = serde_json::json!([{ "license": { "id": license } }]);
+                }
+                if !e.known_vulnerabilities.is_empty() {
+                    comp["vulnerabilities"] = serde_json::json!(
+                        e.known_vulnerabilities.iter().map(|v| serde_json::json!({
+                            "id": v.id,
+                            "source": { "name": v.source },
+                            "ratings": v.severity.as_ref().map(|s| vec![serde_json::json!({"severity": s})]).unwrap_or_default(),
+                        })).collect::<Vec<_>>()
+                    );
+                }
+                comp
+            })
+            .collect();
+
+        serde_json::json!({
+            "bomFormat": "CycloneDX",
+            "specVersion": "1.5",
+            "version": 1,
+            "metadata": {
+                "component": {
+                    "type": "application",
+                    "name": format!("repo-{}", params.repo_id),
+                }
+            },
+            "components": components,
+        })
+    };
+
+    let json_str =
+        serde_json::to_string_pretty(&body).map_err(|_| StatusCode::INTERNAL_SERVER_ERROR)?;
+    let filename = if params.format == "spdx" {
+        format!("sbom-{}-spdx.json", params.repo_id)
+    } else {
+        format!("sbom-{}-cyclonedx.json", params.repo_id)
+    };
+
+    let disposition = format!("attachment; filename=\"{filename}\"");
+    Ok((
+        [
+            (
+                header::CONTENT_TYPE,
+                header::HeaderValue::from_static("application/json"),
+            ),
+            (
+                header::CONTENT_DISPOSITION,
+                header::HeaderValue::from_str(&disposition)
+                    .unwrap_or_else(|_| header::HeaderValue::from_static("attachment")),
+            ),
+        ],
+        json_str,
+    ))
+}
+
+const COPYLEFT_LICENSES: &[&str] = &[
+    "GPL-2.0",
+    "GPL-2.0-only",
+    "GPL-2.0-or-later",
+    "GPL-3.0",
+    "GPL-3.0-only",
+    "GPL-3.0-or-later",
+    "AGPL-3.0",
+    "AGPL-3.0-only",
+    "AGPL-3.0-or-later",
+    "LGPL-2.1",
+    "LGPL-2.1-only",
+    "LGPL-2.1-or-later",
+    "LGPL-3.0",
+    "LGPL-3.0-only",
+    "LGPL-3.0-or-later",
+    "MPL-2.0",
+];
+
+pub async fn license_summary(
+    Extension(agent): AgentExt,
+    Query(params): Query<SbomFilter>,
+) -> ApiResult<Vec<LicenseSummary>> {
+    let db = &agent.db;
+    let mut query = doc! {};
+    if let Some(repo_id) = &params.repo_id {
+        query.insert("repo_id", repo_id);
+    }
+
+    let entries: Vec<SbomEntry> = match db.sbom_entries().find(query).await {
+        Ok(cursor) => collect_cursor_async(cursor).await,
+        Err(_) => Vec::new(),
+    };
+
+    let mut license_map: std::collections::HashMap<String, Vec<String>> =
+        std::collections::HashMap::new();
+    for entry in &entries {
+        let lic = entry.license.as_deref().unwrap_or("Unknown").to_string();
+        license_map.entry(lic).or_default().push(entry.name.clone());
+    }
+
+    let mut summaries: Vec<LicenseSummary> = license_map
+        .into_iter()
+        .map(|(license, packages)| {
+            let is_copyleft = COPYLEFT_LICENSES
+                .iter()
+                .any(|c| license.to_uppercase().contains(&c.to_uppercase()));
+            LicenseSummary {
+                license,
+                count: packages.len() as u64,
+                is_copyleft,
+                packages,
+            }
+        })
+        .collect();
+    summaries.sort_by(|a, b| b.count.cmp(&a.count));
+
+    Ok(Json(ApiResponse {
+        data: summaries,
+        total: None,
+        page: None,
+    }))
+}
+
+pub async fn sbom_diff(
+    Extension(agent): AgentExt,
+    Query(params): Query<SbomDiffParams>,
+) -> ApiResult<SbomDiffResult> {
+    let db = &agent.db;
+
+    let entries_a: Vec<SbomEntry> = match db
+        .sbom_entries()
+        .find(doc! { "repo_id": &params.repo_a })
+        .await
+    {
+        Ok(cursor) => collect_cursor_async(cursor).await,
+        Err(_) => Vec::new(),
+    };
+
+    let entries_b: Vec<SbomEntry> = match db
+        .sbom_entries()
+        .find(doc! { "repo_id": &params.repo_b })
+        .await
+    {
+        Ok(cursor) => collect_cursor_async(cursor).await,
+        Err(_) => Vec::new(),
+    };
+
+    // Build maps by (name, package_manager) -> version
+    let map_a: std::collections::HashMap<(String, String), String> = entries_a
+        .iter()
+        .map(|e| {
+            (
+                (e.name.clone(), e.package_manager.clone()),
+                e.version.clone(),
+            )
+        })
+        .collect();
+    let map_b: std::collections::HashMap<(String, String), String> = entries_b
+        .iter()
+        .map(|e| {
+            (
+                (e.name.clone(), e.package_manager.clone()),
+                e.version.clone(),
+            )
+        })
+        .collect();
+
+    let mut only_in_a = Vec::new();
+    let mut version_changed = Vec::new();
+    let mut common_count: u64 = 0;
+
+    for (key, ver_a) in &map_a {
+        match map_b.get(key) {
+            None => only_in_a.push(SbomDiffEntry {
+                name: key.0.clone(),
+                version: ver_a.clone(),
+                package_manager: key.1.clone(),
+            }),
+            Some(ver_b) if ver_a != ver_b => {
+                version_changed.push(SbomVersionDiff {
+                    name: key.0.clone(),
+                    package_manager: key.1.clone(),
+                    version_a: ver_a.clone(),
+                    version_b: ver_b.clone(),
+                });
+            }
+            Some(_) => common_count += 1,
+        }
+    }
+
+    let only_in_b: Vec<SbomDiffEntry> = map_b
+        .iter()
+        .filter(|(key, _)| !map_a.contains_key(key))
+        .map(|(key, ver)| SbomDiffEntry {
+            name: key.0.clone(),
+            version: ver.clone(),
+            package_manager: key.1.clone(),
+        })
+        .collect();
+
+    Ok(Json(ApiResponse {
+        data: SbomDiffResult {
+            only_in_a,
+            only_in_b,
+            version_changed,
+            common_count,
+        },
+        total: None,
+        page: None,
     }))
 }
 

compliance-agent/src/api/routes.rs

@@ -1,4 +1,4 @@
-use axum::routing::{get, patch, post};
+use axum::routing::{delete, get, patch, post};
 use axum::Router;
 
 use crate::api::handlers;
@@ -13,6 +13,10 @@ pub fn build_router() -> Router {
             "/api/v1/repositories/{id}/scan",
             post(handlers::trigger_scan),
         )
+        .route(
+            "/api/v1/repositories/{id}",
+            delete(handlers::delete_repository),
+        )
         .route("/api/v1/findings", get(handlers::list_findings))
         .route("/api/v1/findings/{id}", get(handlers::get_finding))
         .route(
@@ -20,13 +24,13 @@ pub fn build_router() -> Router {
             patch(handlers::update_finding_status),
         )
         .route("/api/v1/sbom", get(handlers::list_sbom))
+        .route("/api/v1/sbom/export", get(handlers::export_sbom))
+        .route("/api/v1/sbom/licenses", get(handlers::license_summary))
+        .route("/api/v1/sbom/diff", get(handlers::sbom_diff))
         .route("/api/v1/issues", get(handlers::list_issues))
         .route("/api/v1/scan-runs", get(handlers::list_scan_runs))
         // Graph API endpoints
-        .route(
-            "/api/v1/graph/{repo_id}",
-            get(handlers::graph::get_graph),
-        )
+        .route("/api/v1/graph/{repo_id}", get(handlers::graph::get_graph))
         .route(
             "/api/v1/graph/{repo_id}/nodes",
             get(handlers::graph::get_nodes),
@@ -52,14 +56,8 @@ pub fn build_router() -> Router {
             post(handlers::graph::trigger_build),
         )
         // DAST API endpoints
-        .route(
-            "/api/v1/dast/targets",
-            get(handlers::dast::list_targets),
-        )
-        .route(
-            "/api/v1/dast/targets",
-            post(handlers::dast::add_target),
-        )
+        .route("/api/v1/dast/targets", get(handlers::dast::list_targets))
+        .route("/api/v1/dast/targets", post(handlers::dast::add_target))
         .route(
             "/api/v1/dast/targets/{id}/scan",
             post(handlers::dast::trigger_scan),
@@ -68,12 +66,19 @@ pub fn build_router() -> Router {
             "/api/v1/dast/scan-runs",
             get(handlers::dast::list_scan_runs),
         )
-        .route(
-            "/api/v1/dast/findings",
-            get(handlers::dast::list_findings),
-        )
+        .route("/api/v1/dast/findings", get(handlers::dast::list_findings))
         .route(
             "/api/v1/dast/findings/{id}",
             get(handlers::dast::get_finding),
         )
+        // Chat / RAG API endpoints
+        .route("/api/v1/chat/{repo_id}", post(handlers::chat::chat))
+        .route(
+            "/api/v1/chat/{repo_id}/build-embeddings",
+            post(handlers::chat::build_embeddings),
+        )
+        .route(
+            "/api/v1/chat/{repo_id}/status",
+            get(handlers::chat::embedding_status),
+        )
 }

compliance-agent/src/config.rs

@@ -24,6 +24,8 @@ pub fn load_config() -> Result<AgentConfig, AgentError> {
             .unwrap_or_else(|| "http://localhost:4000".to_string()),
         litellm_api_key: SecretString::from(env_var_opt("LITELLM_API_KEY").unwrap_or_default()),
         litellm_model: env_var_opt("LITELLM_MODEL").unwrap_or_else(|| "gpt-4o".to_string()),
+        litellm_embed_model: env_var_opt("LITELLM_EMBED_MODEL")
+            .unwrap_or_else(|| "text-embedding-3-small".to_string()),
         github_token: env_secret_opt("GITHUB_TOKEN"),
         github_webhook_secret: env_secret_opt("GITHUB_WEBHOOK_SECRET"),
         gitlab_url: env_var_opt("GITLAB_URL"),

compliance-agent/src/database.rs

@@ -127,11 +127,7 @@ impl Database {
 
         // dast_targets: index on repo_id
         self.dast_targets()
-            .create_index(
-                IndexModel::builder()
-                    .keys(doc! { "repo_id": 1 })
-                    .build(),
-            )
+            .create_index(IndexModel::builder().keys(doc! { "repo_id": 1 }).build())
             .await?;
 
         // dast_scan_runs: compound (target_id, started_at DESC)
@@ -152,6 +148,24 @@ impl Database {
             )
             .await?;
 
+        // code_embeddings: compound (repo_id, graph_build_id)
+        self.code_embeddings()
+            .create_index(
+                IndexModel::builder()
+                    .keys(doc! { "repo_id": 1, "graph_build_id": 1 })
+                    .build(),
+            )
+            .await?;
+
+        // embedding_builds: compound (repo_id, started_at DESC)
+        self.embedding_builds()
+            .create_index(
+                IndexModel::builder()
+                    .keys(doc! { "repo_id": 1, "started_at": -1 })
+                    .build(),
+            )
+            .await?;
+
         tracing::info!("Database indexes ensured");
         Ok(())
     }
@@ -210,6 +224,17 @@ impl Database {
         self.inner.collection("dast_findings")
     }
 
+    // Embedding collections
+    pub fn code_embeddings(&self) -> Collection<compliance_core::models::embedding::CodeEmbedding> {
+        self.inner.collection("code_embeddings")
+    }
+
+    pub fn embedding_builds(
+        &self,
+    ) -> Collection<compliance_core::models::embedding::EmbeddingBuildRun> {
+        self.inner.collection("embedding_builds")
+    }
+
     #[allow(dead_code)]
     pub fn raw_collection(&self, name: &str) -> Collection<mongodb::bson::Document> {
         self.inner.collection(name)

compliance-agent/src/llm/client.rs

@@ -8,6 +8,7 @@ pub struct LlmClient {
     base_url: String,
     api_key: SecretString,
     model: String,
+    embed_model: String,
     http: reqwest::Client,
 }
 
@@ -42,16 +43,46 @@ struct ChatResponseMessage {
     content: String,
 }
 
+/// Request body for the embeddings API
+#[derive(Serialize)]
+struct EmbeddingRequest {
+    model: String,
+    input: Vec<String>,
+}
+
+/// Response from the embeddings API
+#[derive(Deserialize)]
+struct EmbeddingResponse {
+    data: Vec<EmbeddingData>,
+}
+
+/// A single embedding result
+#[derive(Deserialize)]
+struct EmbeddingData {
+    embedding: Vec<f64>,
+    index: usize,
+}
+
 impl LlmClient {
-    pub fn new(base_url: String, api_key: SecretString, model: String) -> Self {
+    pub fn new(
+        base_url: String,
+        api_key: SecretString,
+        model: String,
+        embed_model: String,
+    ) -> Self {
         Self {
             base_url,
             api_key,
             model,
+            embed_model,
             http: reqwest::Client::new(),
         }
     }
 
+    pub fn embed_model(&self) -> &str {
+        &self.embed_model
+    }
+
     pub async fn chat(
         &self,
         system_prompt: &str,
@@ -169,4 +200,49 @@ impl LlmClient {
             .map(|c| c.message.content.clone())
             .ok_or_else(|| AgentError::Other("Empty response from LiteLLM".to_string()))
     }
+
+    /// Generate embeddings for a batch of texts
+    pub async fn embed(&self, texts: Vec<String>) -> Result<Vec<Vec<f64>>, AgentError> {
+        let url = format!("{}/v1/embeddings", self.base_url.trim_end_matches('/'));
+
+        let request_body = EmbeddingRequest {
+            model: self.embed_model.clone(),
+            input: texts,
+        };
+
+        let mut req = self
+            .http
+            .post(&url)
+            .header("content-type", "application/json")
+            .json(&request_body);
+
+        let key = self.api_key.expose_secret();
+        if !key.is_empty() {
+            req = req.header("Authorization", format!("Bearer {key}"));
+        }
+
+        let resp = req
+            .send()
+            .await
+            .map_err(|e| AgentError::Other(format!("Embedding request failed: {e}")))?;
+
+        if !resp.status().is_success() {
+            let status = resp.status();
+            let body = resp.text().await.unwrap_or_default();
+            return Err(AgentError::Other(format!(
+                "Embedding API returned {status}: {body}"
+            )));
+        }
+
+        let body: EmbeddingResponse = resp
+            .json()
+            .await
+            .map_err(|e| AgentError::Other(format!("Failed to parse embedding response: {e}")))?;
+
+        // Sort by index to maintain input order
+        let mut data = body.data;
+        data.sort_by_key(|d| d.index);
+
+        Ok(data.into_iter().map(|d| d.embedding).collect())
+    }
 }

compliance-agent/src/main.rs

@@ -7,6 +7,7 @@ mod database;
 mod error;
 mod llm;
 mod pipeline;
+mod rag;
 mod scheduler;
 #[allow(dead_code)]
 mod trackers;

compliance-agent/src/pipeline/orchestrator.rs

@@ -185,7 +185,9 @@ impl PipelineOrchestrator {
         // Stage 4.5: Graph Building
         tracing::info!("[{repo_id}] Stage 4.5: Graph Building");
         self.update_phase(scan_run_id, "graph_building").await;
-        let graph_context = match self.build_code_graph(&repo_path, &repo_id, &all_findings).await
+        let graph_context = match self
+            .build_code_graph(&repo_path, &repo_id, &all_findings)
+            .await
         {
             Ok(ctx) => Some(ctx),
             Err(e) => {
@@ -296,9 +298,10 @@ impl PipelineOrchestrator {
         let graph_build_id = uuid::Uuid::new_v4().to_string();
         let engine = compliance_graph::GraphEngine::new(50_000);
 
-        let (mut code_graph, build_run) = engine
-            .build_graph(repo_path, repo_id, &graph_build_id)
-            .map_err(|e| AgentError::Other(format!("Graph build error: {e}")))?;
+        let (mut code_graph, build_run) =
+            engine
+                .build_graph(repo_path, repo_id, &graph_build_id)
+                .map_err(|e| AgentError::Other(format!("Graph build error: {e}")))?;
 
         // Apply community detection
         compliance_graph::graph::community::apply_communities(&mut code_graph);
@@ -348,15 +351,11 @@ impl PipelineOrchestrator {
         use futures_util::TryStreamExt;
 
         let filter = mongodb::bson::doc! { "repo_id": repo_id };
-        let targets: Vec<compliance_core::models::DastTarget> = match self
-            .db
-            .dast_targets()
-            .find(filter)
-            .await
-        {
-            Ok(cursor) => cursor.try_collect().await.unwrap_or_default(),
-            Err(_) => return,
-        };
+        let targets: Vec<compliance_core::models::DastTarget> =
+            match self.db.dast_targets().find(filter).await {
+                Ok(cursor) => cursor.try_collect().await.unwrap_or_default(),
+                Err(_) => return,
+            };
 
         if targets.is_empty() {
             tracing::info!("[{repo_id}] No DAST targets configured, skipping");
@@ -379,10 +378,7 @@ impl PipelineOrchestrator {
                                 tracing::error!("Failed to store DAST finding: {e}");
                             }
                         }
-                        tracing::info!(
-                            "DAST scan complete: {} findings",
-                            findings.len()
-                        );
+                        tracing::info!("DAST scan complete: {} findings", findings.len());
                     }
                     Err(e) => {
                         tracing::error!("DAST scan failed: {e}");

compliance-agent/src/rag/mod.rs

@@ -0,0 +1 @@
+pub mod pipeline;

compliance-agent/src/rag/pipeline.rs

@@ -0,0 +1,164 @@
+use std::path::Path;
+use std::sync::Arc;
+
+use chrono::Utc;
+use compliance_core::models::embedding::{CodeEmbedding, EmbeddingBuildRun, EmbeddingBuildStatus};
+use compliance_core::models::graph::CodeNode;
+use compliance_graph::graph::chunking::extract_chunks;
+use compliance_graph::graph::embedding_store::EmbeddingStore;
+use tracing::{error, info};
+
+use crate::error::AgentError;
+use crate::llm::LlmClient;
+
+/// RAG pipeline for building embeddings and performing retrieval
+pub struct RagPipeline {
+    llm: Arc<LlmClient>,
+    embedding_store: EmbeddingStore,
+}
+
+impl RagPipeline {
+    pub fn new(llm: Arc<LlmClient>, db: &mongodb::Database) -> Self {
+        Self {
+            llm,
+            embedding_store: EmbeddingStore::new(db),
+        }
+    }
+
+    pub fn store(&self) -> &EmbeddingStore {
+        &self.embedding_store
+    }
+
+    /// Build embeddings for all code nodes in a repository
+    pub async fn build_embeddings(
+        &self,
+        repo_id: &str,
+        repo_path: &Path,
+        graph_build_id: &str,
+        nodes: &[CodeNode],
+    ) -> Result<EmbeddingBuildRun, AgentError> {
+        let embed_model = self.llm.embed_model().to_string();
+        let mut build =
+            EmbeddingBuildRun::new(repo_id.to_string(), graph_build_id.to_string(), embed_model);
+
+        // Step 1: Extract chunks
+        let chunks = extract_chunks(repo_path, nodes, 2048);
+        build.total_chunks = chunks.len() as u32;
+        info!(
+            "[{repo_id}] Extracted {} chunks for embedding",
+            chunks.len()
+        );
+
+        // Store the initial build record
+        self.embedding_store
+            .store_build(&build)
+            .await
+            .map_err(|e| AgentError::Other(format!("Failed to store build: {e}")))?;
+
+        if chunks.is_empty() {
+            build.status = EmbeddingBuildStatus::Completed;
+            build.completed_at = Some(Utc::now());
+            self.embedding_store
+                .update_build(
+                    repo_id,
+                    graph_build_id,
+                    EmbeddingBuildStatus::Completed,
+                    0,
+                    None,
+                )
+                .await
+                .map_err(|e| AgentError::Other(format!("Failed to update build: {e}")))?;
+            return Ok(build);
+        }
+
+        // Step 2: Delete old embeddings for this repo
+        self.embedding_store
+            .delete_repo_embeddings(repo_id)
+            .await
+            .map_err(|e| AgentError::Other(format!("Failed to delete old embeddings: {e}")))?;
+
+        // Step 3: Batch embed (small batches to stay within model limits)
+        let batch_size = 20;
+        let mut all_embeddings = Vec::new();
+        let mut embedded_count = 0u32;
+
+        for batch_start in (0..chunks.len()).step_by(batch_size) {
+            let batch_end = (batch_start + batch_size).min(chunks.len());
+            let batch_chunks = &chunks[batch_start..batch_end];
+
+            // Prepare texts: context_header + content
+            let texts: Vec<String> = batch_chunks
+                .iter()
+                .map(|c| format!("{}\n{}", c.context_header, c.content))
+                .collect();
+
+            match self.llm.embed(texts).await {
+                Ok(vectors) => {
+                    for (chunk, embedding) in batch_chunks.iter().zip(vectors) {
+                        all_embeddings.push(CodeEmbedding {
+                            id: None,
+                            repo_id: repo_id.to_string(),
+                            graph_build_id: graph_build_id.to_string(),
+                            qualified_name: chunk.qualified_name.clone(),
+                            kind: chunk.kind.clone(),
+                            file_path: chunk.file_path.clone(),
+                            start_line: chunk.start_line,
+                            end_line: chunk.end_line,
+                            language: chunk.language.clone(),
+                            content: chunk.content.clone(),
+                            context_header: chunk.context_header.clone(),
+                            embedding,
+                            token_estimate: chunk.token_estimate,
+                            created_at: Utc::now(),
+                        });
+                    }
+                    embedded_count += batch_chunks.len() as u32;
+                }
+                Err(e) => {
+                    error!("[{repo_id}] Embedding batch failed: {e}");
+                    build.status = EmbeddingBuildStatus::Failed;
+                    build.error_message = Some(e.to_string());
+                    build.completed_at = Some(Utc::now());
+                    let _ = self
+                        .embedding_store
+                        .update_build(
+                            repo_id,
+                            graph_build_id,
+                            EmbeddingBuildStatus::Failed,
+                            embedded_count,
+                            Some(e.to_string()),
+                        )
+                        .await;
+                    return Ok(build);
+                }
+            }
+        }
+
+        // Step 4: Store all embeddings
+        self.embedding_store
+            .store_embeddings(&all_embeddings)
+            .await
+            .map_err(|e| AgentError::Other(format!("Failed to store embeddings: {e}")))?;
+
+        // Step 5: Update build status
+        build.status = EmbeddingBuildStatus::Completed;
+        build.embedded_chunks = embedded_count;
+        build.completed_at = Some(Utc::now());
+        self.embedding_store
+            .update_build(
+                repo_id,
+                graph_build_id,
+                EmbeddingBuildStatus::Completed,
+                embedded_count,
+                None,
+            )
+            .await
+            .map_err(|e| AgentError::Other(format!("Failed to update build: {e}")))?;
+
+        info!(
+            "[{repo_id}] Embedding build complete: {embedded_count}/{} chunks",
+            build.total_chunks
+        );
+        Ok(build)
+    }
+}