@jafreck/lore 0.3.5 → 0.3.7

package/README.md

@@ -7,15 +7,17 @@
 [![Node.js](https://img.shields.io/badge/node-%3E%3D22.0.0-brightgreen)](https://nodejs.org)
 [![TypeScript](https://img.shields.io/badge/TypeScript-5.9+-blue)](https://www.typescriptlang.org)
 
-**The teammate that has seen it all** 
+**The teammate that knows it all** 
 
-Lore is your agent's institutional knowledge over the codebase — it knows what was built, why it changed, and how it all connects. Lore indexes your code and git history into a structured knowledge base that agents query through MCP. It maps symbols, imports, call relationships, type relationships, routes, annotations, and git history — with optional embeddings for semantic search — so agents can reason about your codebase
-without re-reading it from scratch.
+Lore holds your agent's institutional knowledge over the codebase — it knows what was built, why it changed, and how it all connects. Lore indexes your code and git history into a structured knowledge base that agents query through MCP. It maps symbols, imports, call relationships, type relationships, routes, annotations, docs, and all git data — with optional embeddings for semantic search — so agents can reason about your codebase without re-reading it from scratch.
+
+Lore-enabled agents achieve up to **8.8× faster** responses, up to **97% fewer tokens**, and up to **+33pp correctness improvement** on code intelligence tasks compared to a baseline agent with grep and file reads alone. See the [full benchmark results](docs/benchmark-results.md) for details.
 
 ## What Lore does
 
-- Parses source files and extracts symbols, imports, call refs, type refs, annotations, and API routes across all 23 supported languages
-- Resolves internal vs external imports and builds call/import/module/inheritance/type-dependency graph edges using a 3-tier resolution strategy (LSP containment, same-file name match, unique name match)
+- Indexes source files using SCIP indexers by default for pre-resolved symbols and edges, with tree-sitter parsing as a fallback for languages without a SCIP indexer
+- Extracts symbols, imports, call refs, type refs, annotations, and API routes across all 23 supported languages
+- Resolves internal vs external imports and builds call/import/module/inheritance/type-dependency graph edges using a 3-tier resolution strategy (SCIP/LSP containment, same-file name match, unique name match)
 - Discovers and indexes documentation (`.md`, `.rst`, `.adoc`, `.txt`) with inferred kinds/titles
 - Stores everything in a normalized SQL schema with optional vector search
 - Enables RAG-style retrieval with semantic/fused search across symbols and doc sections
@@ -35,36 +37,38 @@ flowchart LR
         COV[Coverage Reports]
     end
 
-    subgraph Lore Indexer
-      WALK[Walker] --> PARSE[Parser] --> EXTRACT[Extractors<br/>symbols · imports · call refs<br/>type refs · routes · annotations]
+    subgraph INDEXER[Lore Indexer]
+        SCIPDIRECT[SCIP Source<br/>pre-resolved symbols + refs] --> WALK
+        WALK[Walker] --> PARSE[Parser] --> EXTRACT[Extractors<br/>symbols · imports · call refs<br/>type refs · routes · annotations]
         EXTRACT --> RESOLVE[Import Resolver<br/>internal ↔ external]
-      EXTRACT --> CALLGRAPH[Relationship Resolver]
+        EXTRACT --> CALLGRAPH[Relationship Resolver]
         EXTRACT -.-> LSPENRICH[LSP Enrichment<br/>type signatures · definition locations]
         DOCSINGEST[Docs Ingest<br/>sections · headings · notes]
         GITHIST[Git History Ingest<br/>commits · diffs · refs]
         COVINGEST[Coverage Ingest<br/>lcov · cobertura]
     end
 
+    SRC --> SCIPDIRECT
+    SRC --> WALK
+    DOCS --> DOCSINGEST
+    GIT --> GITHIST
+    COV --> COVINGEST
+
     DB[(SQL DB)]
     EMBED([Embedding Model])
 
-    subgraph MCP Server
+    subgraph MCP_SERVER[MCP Server]
         LOOKUP[lore_lookup]
         SEARCH[lore_search]
         DOCS_TOOL[lore_docs]
-      ANNOT[lore_annotations]
         GRAPH[lore_graph]
-      ROUTES[lore_routes]
-      NOTES[lore_notes_read/write]
-      ARCH[lore_architecture]
+        ROUTES[lore_routes]
+        NOTES[lore_notes_read/write]
         TESTMAP[lore_test_map]
         SNIPPET[lore_snippet]
         BLAME[lore_blame]
         HISTORY[lore_history]
         METRICS[lore_metrics]
-        COVERAGE[lore_coverage]
-        WRITEBACK[lore_writeback]
-        ANALYZE[lore_analyze]
     end
 
     subgraph MCP_CLIENTS[MCP Clients — Agents]
@@ -75,20 +79,19 @@ flowchart LR
         CLAUDE_CODE ~~~ COPILOT ~~~ CURSOR ~~~ CUSTOM
     end
 
-    SRC --> WALK
-    DOCS --> DOCSINGEST --> DB
-    GIT --> GITHIST --> DB
-    COV --> COVINGEST --> DB
+    DOCSINGEST --> DB
+    GITHIST --> DB
+    COVINGEST --> DB
 
     RESOLVE & CALLGRAPH --> DB
     LSPENRICH -.->|optional| DB
     RESOLVE -.->|optional| EMBED
     EMBED -.-> DB
 
-    DB --- LOOKUP & SEARCH & DOCS_TOOL & ANNOT & GRAPH & ROUTES & NOTES & ARCH & TESTMAP & SNIPPET & BLAME & HISTORY & METRICS & COVERAGE & WRITEBACK & ANALYZE
+    DB --- LOOKUP & SEARCH & DOCS_TOOL & GRAPH & ROUTES & NOTES & TESTMAP & SNIPPET & BLAME & HISTORY & METRICS
     EMBED <-.->|semantic/fused| SEARCH
 
-    LOOKUP & SEARCH & DOCS_TOOL & ANNOT & GRAPH & ROUTES & NOTES & ARCH & TESTMAP & SNIPPET & BLAME & HISTORY & METRICS & COVERAGE & WRITEBACK & ANALYZE <--> MCP_CLIENTS
+    LOOKUP & SEARCH & DOCS_TOOL & GRAPH & ROUTES & NOTES & TESTMAP & SNIPPET & BLAME & HISTORY & METRICS <--> MCP_CLIENTS
 ```
 
 Lore sits between your codebase and any LLM-powered tool. A `LoreRuntime`
@@ -102,20 +105,22 @@ by `IndexPipeline`. `IndexBuilder` is now a thin façade (~310 lines, down from
 updates. The stage ordering enforces data dependencies structurally:
 
 ```
-SourceIndex → DocsIndex → ImportResolution → DependencyApi
-  → LspEnrichment → Resolution → TestMap → History → Embedding
+ScipSource → SourceIndex → DocsIndex → ImportResolution → DependencyApi
+  → ScipEnrichment → LspEnrichment → Resolution → TestMap → History → Embedding
 ```
 
-Each stage walks source files, parses them into ASTs, and extracts
-symbols/imports/call-refs via language-specific extractors, then resolves
-imports (internal vs external) and resolves symbol references using a
-**3-tier resolution** strategy: LSP containment → same-file name match →
-unique name match. An optional **LSP enrichment** stage queries language
-servers with batch-pipelined hover + definition requests. An optional
-**embedder** generates dense vectors for semantic search (with async
-initialization so the MCP server starts instantly), and a parallel **git
-history** ingest captures commits, diffs, and refs. Everything is persisted to
-a normalized SQL database.
+**SCIP is the default source stage.** `ScipSourceStage` runs first and
+populates symbols, refs, and pre-resolved edges for every language that has
+a SCIP indexer available. `SourceIndexStage` then handles remaining languages
+(or all languages if SCIP is explicitly disabled) via tree-sitter as a
+fallback. A **SCIP enrichment** stage then writes definition locations and
+type metadata from SCIP data, while an optional **LSP enrichment** stage can
+enrich symbols not already covered by SCIP. Symbol references are
+resolved using a **3-tier strategy**: SCIP/LSP containment → same-file name
+match → unique name match. An optional **embedder** generates dense vectors
+for semantic search (with async initialization so the MCP server starts
+instantly), and a parallel **git history** ingest captures commits, diffs,
+and refs. Everything is persisted to a normalized SQL database.
 
 The **MCP server** uses a `ToolRegistry` that auto-discovers tool modules
 from their exported `toolDef` / `handler` definitions — no duplicate schema
@@ -184,20 +189,15 @@ await builder.build();
 | `lore_lookup` | Find symbols by name or files by path, including external dependency API symbols and LSP-resolved metadata when available |
 | `lore_search` | Structural BM25, semantic vector, or fused RRF search across symbols and doc sections |
 | `lore_docs` | List, fetch, or search indexed documentation with branch, kind, and path filters |
-| `lore_annotations` | Return indexed TODO/FIXME/HACK/NOTE-style annotations with optional path and limit filters |
 | `lore_routes` | Query extracted API routes/endpoints with optional method, path prefix, and framework filters |
 | `lore_notes_write` | Upsert agent-authored notes by key and scope, with optional source hash for staleness tracking |
 | `lore_notes_read` | Read notes by exact key or key prefix with scope-aware staleness metadata |
-| `lore_architecture` | Build a component-level architecture view with edges, entry/leaf nodes, and external dependency usage |
-| `lore_graph` | Query call/import/module/inheritance/type-dependency edges; supports `source_id` for outbound and `target_id` for inbound/reverse queries; call edges include `callee_coverage_percent` |
+| `lore_graph` | Query call/import/inheritance/type-dependency edges; supports `source_id` for outbound and `target_id` for inbound/reverse queries; call edges include `callee_coverage_percent` |
 | `lore_snippet` | Return snippets from indexed source snapshots by file path + line range or by symbol name; path/symbol resolution is branch-aware and responses include containing-symbol context metadata (name, kind, start/end lines) when available |
 | `lore_test_map` | Return mapped test files (with confidence) for a given source file path |
 | `lore_blame` | Query blame, line-range history, or ownership aggregates with optional symbol targeting, commit-context enrichment, and risk signals |
 | `lore_history` | Query commit history by file, commit, author, ref, recency, or semantic commit-message similarity |
 | `lore_metrics` | Aggregate index metrics plus coverage/staleness fields |
-| `lore_coverage` | Symbol-level coverage, uncovered lines, and staleness metadata |
-| `lore_writeback` | Persist agent-authored symbol summaries |
-| `lore_analyze` | Run graph analysis primitives: symbol-level cycle detection (SCC), connected components (file or symbol scope), bounded-size symbol clustering, and condensed codebase summary |
 
 ### lore_lookup query options
 
@@ -288,10 +288,11 @@ has its own ingestion pipeline and can be enabled independently.
 
 ### Source code
 
-The indexer walks source files, parses them into ASTs via tree-sitter, and
-extracts symbols, imports, and call references through language-specific
-extractors. The import resolver classifies each import as internal or external,
-and a call-graph builder creates edges between symbols.
+The indexer uses a SCIP-first strategy: for languages with a SCIP indexer it
+produces symbols and pre-resolved edges directly, then falls back to tree-sitter
+parsing for remaining languages. Optional LSP enrichment can augment symbols
+from either path. The import resolver classifies each import as internal or
+external, and a call-graph builder creates edges between symbols.
 
 Programmatic example:
 
@@ -416,7 +417,7 @@ SQLite-only — language servers are never invoked at runtime.
 
 LSP precedence:
 
-1. CLI flags (`--lsp` / `--no-lsp`)
+1. CLI flag (`--lsp`)
 2. `.lore.config` `lsp.enabled`
 3. Built-in default (`false`)
 
@@ -514,7 +515,7 @@ are fast even on large repositories.
 Build or update a knowledge base.
 
 ```bash
-npx @jafreck/lore index --root <dir> --db <path> [--embedding-model <id>] [--blocking-embedder] [--index-deps] [--history] [--history-depth <n>] [--history-all] [--include <glob>] [--exclude <glob>] [--language <lang>] [--docs-include <glob>] [--docs-exclude <glob>] [--docs-extension <ext>] [--docs-auto-notes|--no-docs-auto-notes] [--lsp] [--no-lsp]
+npx @jafreck/lore index --root <dir> --db <path> [--embedding-model <id>] [--blocking-embedder] [--index-deps] [--history] [--history-depth <n>] [--history-all] [--include <glob>] [--exclude <glob>] [--language <lang>] [--docs-include <glob>] [--docs-exclude <glob>] [--docs-extension <ext>] [--docs-auto-notes|--no-docs-auto-notes] [--lsp] [--no-scip]
 ```
 
 ### lore refresh
@@ -522,9 +523,9 @@ npx @jafreck/lore index --root <dir> --db <path> [--embedding-model <id>] [--blo
 Incremental refresh (one-shot, watch, or poll).
 
 ```bash
-npx @jafreck/lore refresh --db <path> --root <dir> [--index-deps] [--history] [--history-depth <n>] [--history-all] [--docs-include <glob>] [--docs-exclude <glob>] [--docs-extension <ext>] [--docs-auto-notes|--no-docs-auto-notes] [--lsp] [--no-lsp]
-npx @jafreck/lore refresh --db <path> --root <dir> --watch [--index-deps] [--history] [--docs-include <glob>] [--docs-exclude <glob>] [--docs-extension <ext>] [--lsp] [--no-lsp]
-npx @jafreck/lore refresh --db <path> --root <dir> --poll [--index-deps] [--history] [--docs-include <glob>] [--docs-exclude <glob>] [--docs-extension <ext>] [--lsp] [--no-lsp]
+npx @jafreck/lore refresh --db <path> --root <dir> [--index-deps] [--history] [--history-depth <n>] [--history-all] [--docs-include <glob>] [--docs-exclude <glob>] [--docs-extension <ext>] [--docs-auto-notes|--no-docs-auto-notes] [--lsp] [--no-scip]
+npx @jafreck/lore refresh --db <path> --root <dir> --watch [--index-deps] [--history] [--docs-include <glob>] [--docs-exclude <glob>] [--docs-extension <ext>] [--lsp] [--no-scip]
+npx @jafreck/lore refresh --db <path> --root <dir> --poll [--index-deps] [--history] [--docs-include <glob>] [--docs-exclude <glob>] [--docs-extension <ext>] [--lsp] [--no-scip]
 ```
 
 ### lore hooks
@@ -532,7 +533,7 @@ npx @jafreck/lore refresh --db <path> --root <dir> --poll [--index-deps] [--hist
 Install repo-local git hooks for automatic refresh.
 
 ```bash
-npx @jafreck/lore hooks --root <repo> --db <path> [--history] [--lsp] [--no-lsp]
+npx @jafreck/lore hooks --root <repo> --db <path> [--history] [--lsp] [--no-scip]
 ```
 
 ### lore ingest-coverage
@@ -551,14 +552,6 @@ Start the MCP server over stdio.
 npx @jafreck/lore mcp --db <path> [--blocking-embedder]
 ```
 
-### lore analyze
-
-Run graph analysis on an indexed knowledge base.
-
-```bash
-npx @jafreck/lore analyze --db <path> [--mode <cycles|components|clusters|summary>] [--edge-kinds <call|type|both>] [--branch <name>] [--max-lines <n>]
-```
-
 ## Build from source
 
 ```bash

package/dist/cli.js

@@ -16,20 +16,21 @@
  *                         Ingest a coverage report file into the knowledge base.
  */
 import * as fs from 'node:fs';
-import { loadLspSettingsFromLoreConfig, resolveEffectiveLspSettings, } from './indexer/lsp/config.js';
+import { loadLspSettingsFromLoreConfig, resolveEffectiveLspSettings, } from './lsp/config.js';
+import { loadScipSettingsFromLoreConfig, resolveEffectiveScipSettings, } from './scip/config.js';
 import { initLogger, LogLevel, LOG_LEVEL_NAMES } from './logger.js';
 import { killAllTracked } from './process-tracker.js';
 import { LoreRuntime } from './runtime.js';
 // ─── Argument helpers ─────────────────────────────────────────────────────────
 function usage() {
     console.error(`Usage:
-  lore index --root <dir> --db <path> [--embedding-model <id>] [--index-deps] [--history] [--history-depth <n>] [--history-all]
+  lore index --root <dir> --db <path> [--embeddings] [--embedding-model <id>] [--index-deps] [--history] [--history-depth <n>] [--history-all]
                          Index a codebase into a knowledge-base SQLite file
   lore mcp --db <path> [--root <dir> --watch|--poll]  Start the Lore MCP server (stdio transport), optionally with live indexing
   lore refresh --db <path> --root <dir> [--index-deps] [--history] [--history-depth <n>] [--history-all]  Run an incremental index update and exit
   lore refresh --db <path> --root <dir> --watch [--embedding-model <id>] Watch for file changes and refresh automatically
   lore refresh --db <path> --root <dir> --poll [--embedding-model <id>]  Poll for file changes and refresh automatically
-  lore hooks --db <path> --root <dir> [--history] [--history-depth <n>] [--history-all] [--lsp] [--no-lsp]
+  lore hooks --db <path> --root <dir> [--history] [--history-depth <n>] [--history-all] [--lsp]
                          Install git hooks for automatic refresh on commit/merge/checkout
   lore ingest-coverage --db <path> --root <dir> --file <path> --format <lcov|cobertura> [--commit <sha>]
                          Ingest an explicit coverage report file into the knowledge base
@@ -39,7 +40,9 @@ function usage() {
 Options:
   --root <dir>             Root directory to index (required for index, refresh)
   --db <path>              Path to a Lore knowledge-base SQLite file (required for index, mcp, refresh)
-  --embedding-model <id>   Embedding model identifier (default: Qwen/Qwen3-Embedding-4B)
+  --embedding-model <id>   Embedding model identifier (default: Qwen3-Embedding-0.6B-ONNX)
+  --embeddings             Enable embedding generation during indexing (disabled by default)
+  --no-embeddings          Disable embedding generation during indexing (default)
   --index-deps             Enable dependency API indexing (disabled by default)
   --history                Enable git history ingestion
   --history-depth <n>      Limit commit ingestion to the most recent N commits
@@ -54,8 +57,8 @@ Options:
   --no-docs-auto-notes     Disable doc-based note seeding during indexing
   --watch                  Enable fs-event watch mode (low-latency, may miss events on some platforms)
   --poll                   Enable polling mode (reliable but higher CPU/IO cost)
-  --lsp                    Force-enable index-time LSP settings
-  --no-lsp                 Force-disable index-time LSP settings
+  --lsp                    Enable index-time LSP enrichment (disabled by default)
+  --no-scip                Disable index-time SCIP indexing (enabled by default)
   --file <path>            Coverage report path (required for ingest-coverage)
   --format <name>          Coverage format: lcov or cobertura (required for ingest-coverage)
   --commit <sha>           Commit SHA to associate with coverage ingestion (default: HEAD)
@@ -93,14 +96,12 @@ function docsAutoNotesFlag(args) {
     return true;
 }
 function explicitLspEnabled(args) {
-    const enabled = args.includes('--lsp');
-    const disabled = args.includes('--no-lsp');
-    if (enabled && disabled) {
-        throw new Error('cannot combine --lsp and --no-lsp');
-    }
-    if (enabled)
+    if (args.includes('--lsp'))
         return true;
-    if (disabled)
+    return undefined;
+}
+function explicitScipEnabled(args) {
+    if (args.includes('--no-scip'))
         return false;
     return undefined;
 }
@@ -143,6 +144,12 @@ async function main() {
             return;
         }
         const embeddingModel = flag(args, '--embedding-model');
+        const embeddingsEnabled = embeddingModel !== undefined || args.includes('--embeddings');
+        if (args.includes('--embeddings') && args.includes('--no-embeddings')) {
+            console.error('Error: --embeddings and --no-embeddings cannot be used together.\n');
+            usage();
+            return;
+        }
         const indexDependencies = args.includes('--index-deps');
         const historyEnabled = args.includes('--history');
         const historyAll = args.includes('--history-all');
@@ -158,8 +165,10 @@ async function main() {
             historyDepth = Math.floor(parsed);
         }
         let lspEnabled;
+        let scipEnabled;
         try {
             lspEnabled = explicitLspEnabled(args);
+            scipEnabled = explicitScipEnabled(args);
         }
         catch (error) {
             const message = error instanceof Error ? error.message : String(error);
@@ -178,6 +187,17 @@ async function main() {
             process.exit(1);
             return;
         }
+        let scipSettings;
+        try {
+            const scipConfig = loadScipSettingsFromLoreConfig(rootDir);
+            scipSettings = resolveEffectiveScipSettings(scipConfig, { ...(scipEnabled !== undefined && { enabled: scipEnabled }) });
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            console.error(`Error: ${message}\n`);
+            process.exit(1);
+            return;
+        }
         const includeGlobs = flags(args, '--include');
         const excludeGlobs = flags(args, '--exclude');
         const languageNames = flags(args, '--language');
@@ -226,11 +246,18 @@ async function main() {
             }
         }
         const { IndexBuilder } = await import('./indexer/index.js');
+        // Create an embedding provider when embeddings are enabled.
+        let embedder;
+        if (embeddingsEnabled) {
+            const { LazyEmbeddingProvider, DEFAULT_EMBEDDING_MODEL } = await import('./embeddings/embedder.js');
+            embedder = new LazyEmbeddingProvider(embeddingModel ?? DEFAULT_EMBEDDING_MODEL);
+        }
         const shouldEnableHistory = historyEnabled || historyAll || historyDepth !== undefined;
         const options = {
             docsAutoNotes,
             indexDependencies,
             lsp: lspSettings,
+            scip: scipSettings,
             ...(embeddingModel && { embeddingModel }),
             ...(shouldEnableHistory && {
                 history: {
@@ -247,7 +274,7 @@ async function main() {
             ...(docsIncludeGlobs.length > 0 && { docsIncludeGlobs }),
             ...(docsExcludeGlobs.length > 0 && { docsExcludeGlobs }),
             ...(docsExtensions.length > 0 && { docsExtensions }),
-        }, undefined, options);
+        }, embedder, options);
         await builder.build();
     }
     else if (subcommand === 'mcp') {
@@ -262,9 +289,9 @@ async function main() {
         // library entry point for consumers who only need the indexer.
         const { McpServer } = await import('@modelcontextprotocol/sdk/server/mcp.js');
         const { StdioServerTransport } = await import('@modelcontextprotocol/sdk/server/stdio.js');
-        const { openReadOnly } = await import('./lore-server/db.js');
-        const { createLoreMcpServer } = await import('./lore-server/server.js');
-        const { getLoreMeta } = await import('./indexer/db.js');
+        const { openReadOnly } = await import('./db/read-only.js');
+        const { createLoreMcpServer } = await import('./server/server.js');
+        const { getLoreMeta } = await import('./db/schema.js');
         const db = openReadOnly(dbPath);
         // Gather DB stats for startup log
         const totalFiles = db.prepare('SELECT COUNT(*) AS cnt FROM files').get().cnt;
@@ -297,6 +324,7 @@ async function main() {
             rootDir: rootDir ?? '.',
             walkerConfig: { rootDir: rootDir ?? '.' },
             lsp: null,
+            scip: null,
             history: false,
             indexDependencies: false,
             docsAutoNotes: true,
@@ -352,8 +380,10 @@ async function main() {
             historyDepth = Math.floor(parsed);
         }
         let lspEnabled;
+        let scipEnabled2;
         try {
             lspEnabled = explicitLspEnabled(args);
+            scipEnabled2 = explicitScipEnabled(args);
         }
         catch (error) {
             const message = error instanceof Error ? error.message : String(error);
@@ -372,6 +402,17 @@ async function main() {
             process.exit(1);
             return;
         }
+        let scipSettings;
+        try {
+            const scipConfig = loadScipSettingsFromLoreConfig(rootDir);
+            scipSettings = resolveEffectiveScipSettings(scipConfig, { ...(scipEnabled2 !== undefined && { enabled: scipEnabled2 }) });
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            console.error(`Error: ${message}\n`);
+            process.exit(1);
+            return;
+        }
         const shouldEnableHistory = historyEnabled || historyAll || historyDepth !== undefined;
         const historyOption = shouldEnableHistory
             ? {
@@ -392,6 +433,7 @@ async function main() {
         const refreshOptions = {
             indexDependencies,
             lsp: lspSettings,
+            scip: scipSettings,
             ...(shouldEnableHistory && { history: historyOption }),
         };
         // Build an optional long-lived embedder for watch/poll modes.
@@ -402,6 +444,7 @@ async function main() {
                 rootDir,
                 walkerConfig,
                 lsp: lspSettings,
+                scip: scipSettings,
                 history: shouldEnableHistory ? historyOption : false,
                 indexDependencies,
                 docsAutoNotes,
@@ -421,8 +464,8 @@ async function main() {
             const dbExists = fs.existsSync(dbPath);
             if (dbExists) {
                 const [{ openDb }, { walkFiles }] = await Promise.all([
-                    import('./indexer/db.js'),
-                    import('./indexer/walker.js'),
+                    import('./db/schema.js'),
+                    import('./discovery/walker.js'),
                 ]);
                 const files = await walkFiles(walkerConfig);
                 const db = openDb(dbPath);
@@ -456,8 +499,10 @@ async function main() {
         const historyDepthRaw = flag(args, '--history-depth');
         const includeHistory = historyEnabled || historyAll || historyDepthRaw !== undefined;
         let lspEnabled;
+        let scipEnabled3;
         try {
             lspEnabled = explicitLspEnabled(args);
+            scipEnabled3 = explicitScipEnabled(args);
         }
         catch (error) {
             const message = error instanceof Error ? error.message : String(error);
@@ -476,13 +521,22 @@ async function main() {
             process.exit(1);
             return;
         }
-        const { installGitHooks } = await import('./indexer/git-hooks.js');
+        let scipSettings;
+        try {
+            const scipConfig = loadScipSettingsFromLoreConfig(rootDir);
+            scipSettings = resolveEffectiveScipSettings(scipConfig, { ...(scipEnabled3 !== undefined && { enabled: scipEnabled3 }) });
+        }
+        catch {
+            // SCIP config errors in hooks are non-fatal.
+        }
+        const { installGitHooks } = await import('./git/hooks.js');
         const result = installGitHooks({
             repoRoot: rootDir,
             rootDir,
             dbPath,
             includeHistory,
             lspEnabled: lspSettings.enabled,
+            scipEnabled: scipSettings?.enabled ?? false,
         });
         process.stderr.write(JSON.stringify({
             level: 'info',
@@ -546,8 +600,8 @@ async function main() {
             }
             maxLines = Math.floor(parsed);
         }
-        const { openReadOnly } = await import('./lore-server/db.js');
-        const { detectSymbolCycles, findConnectedComponents, clusterSymbols, buildCodebaseSummary, } = await import('./indexer/graph-analysis.js');
+        const { openReadOnly } = await import('./db/read-only.js');
+        const { detectSymbolCycles, findConnectedComponents, clusterSymbols, buildCodebaseSummary, } = await import('./resolution/graph-analysis.js');
         const db = openReadOnly(dbPath);
         const opts = { edgeKinds, branch };
         let result;

package/dist/cli.js.map

@@ -1 +1 @@
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package/dist/{lore-server/db.d.ts → db/read-only.d.ts}

@@ -513,4 +513,4 @@ export declare function getSymbolCoverageAggregates(db: Database.Database, optio
 }): SymbolCoverageAggregate[];
 /** Return symbol coverage percentages for selected symbol ids from latest coverage run. */
 export declare function getCoveragePercentBySymbolIds(db: Database.Database, symbolIds: number[], branch?: string): Map<number, number | null>;
-//# sourceMappingURL=db.d.ts.map
+//# sourceMappingURL=read-only.d.ts.map

package/dist/db/read-only.d.ts.map

@@ -0,0 +1 @@
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package/dist/{lore-server/db.js → db/read-only.js}

@@ -1210,4 +1210,4 @@ export function getCoveragePercentBySymbolIds(db, symbolIds, branch) {
     const rows = getSymbolCoverageAggregates(db, { symbolIds, branch, limit: symbolIds.length });
     return new Map(rows.map((row) => [row.symbol_id, row.coverage_percent]));
 }
-//# sourceMappingURL=db.js.map
+//# sourceMappingURL=read-only.js.map