scip-query 0.4.1 → 0.4.2

package/dist/index.d.ts

@@ -43,6 +43,7 @@ export { dataflow } from './queries/dataflow.js';
 export { slice } from './queries/slice.js';
 export { redundantReexports } from './queries/redundant-reexports.js';
 export { similarSignatures } from './queries/similar-signatures.js';
+import { Index } from '@c4312/scip';
 import 'better-sqlite3';
 
 /**
@@ -88,6 +89,22 @@ declare const INDEXER_CONFIGS: Record<SupportedLanguage, IndexerConfig>;
 /** Get the indexer config for a language */
 declare function getIndexerConfig(language: SupportedLanguage): IndexerConfig;
 
+interface MergeScipResult {
+    documentCount: number;
+    externalSymbolCount: number;
+    inputCount: number;
+}
+/**
+ * Merge multiple SCIP indices into a single index message.
+ *
+ * A SCIP index is a code graph snapshot: metadata about one indexed project plus
+ * the documents and external symbols discovered by one or more indexers. Merging
+ * means producing one unified snapshot so later conversion to SQLite sees the
+ * whole repo instead of whichever language indexed last.
+ */
+declare function mergeScipIndexes(indexes: readonly Index[]): Index;
+declare function mergeScipFiles(inputPaths: readonly string[], outputPath: string): MergeScipResult;
+
 /**
  * Check if a binary is available on PATH.
  */
@@ -250,4 +267,4 @@ declare function installSkills(opts?: {
     quiet?: boolean;
 }): InstallSkillsResult;
 
-export { INDEXER_CONFIGS, IndexerConfig, ProjectConfig, ScipLocalSymbol, ScipSymbol, SupportedLanguage, Watcher, WatcherStatus, detectLanguages, getIndexerConfig, getScipVersion, initProjectConfig, installSkills, isBinaryAvailable, isIndexerInstalled, isScipInstalled, leafName, loadProjectConfig, parseSymbol, printScipInstallInstructions, reindex, resolveCacheDir, resolveIndexPaths, shortenSymbol, tryInstallIndexer, tryInstallScipCli };
+export { INDEXER_CONFIGS, IndexerConfig, ProjectConfig, ScipLocalSymbol, ScipSymbol, SupportedLanguage, Watcher, WatcherStatus, detectLanguages, getIndexerConfig, getScipVersion, initProjectConfig, installSkills, isBinaryAvailable, isIndexerInstalled, isScipInstalled, leafName, loadProjectConfig, mergeScipFiles, mergeScipIndexes, parseSymbol, printScipInstallInstructions, reindex, resolveCacheDir, resolveIndexPaths, shortenSymbol, tryInstallIndexer, tryInstallScipCli };

package/dist/index.js

@@ -254,7 +254,7 @@ var ScipDatabase = class {
 // src/gitignore-filter.ts
 import ignore from "ignore";
 import { readFileSync, existsSync } from "fs";
-import { join, dirname } from "path";
+import { dirname, isAbsolute, join, relative, resolve } from "path";
 function createGitignoreFilter(projectRoot) {
   const ig = ignore();
   let loaded = false;
@@ -271,8 +271,8 @@ function createGitignoreFilter(projectRoot) {
     ig.add(DEFAULT_IGNORES);
   }
   return {
-    isIgnored: (relativePath) => ig.ignores(relativePath),
-    filter: (paths) => paths.filter((p) => !ig.ignores(p))
+    isIgnored: (relativePath) => safeIgnores(ig, projectRoot, relativePath),
+    filter: (paths) => paths.filter((p) => !safeIgnores(ig, projectRoot, p))
   };
 }
 function findGitignoreFiles(projectRoot) {
@@ -352,11 +352,36 @@ Thumbs.db
 # Type definitions (often noise in queries)
 *.d.ts
 `;
+function safeIgnores(ig, projectRoot, inputPath) {
+  const relativePath = normalizeForIgnore(projectRoot, inputPath);
+  if (!relativePath) {
+    return false;
+  }
+  try {
+    return ig.ignores(relativePath);
+  } catch {
+    return false;
+  }
+}
+function normalizeForIgnore(projectRoot, inputPath) {
+  if (!inputPath || inputPath === ".") {
+    return null;
+  }
+  if (!isAbsolute(inputPath) && !inputPath.startsWith("..")) {
+    return inputPath.replaceAll("\\", "/");
+  }
+  const absolutePath = isAbsolute(inputPath) ? inputPath : resolve(projectRoot, inputPath);
+  const relativePath = relative(projectRoot, absolutePath).replaceAll("\\", "/");
+  if (!relativePath || relativePath === "." || relativePath.startsWith("..")) {
+    return null;
+  }
+  return relativePath;
+}
 
 // src/reindex/index.ts
 import { execFileSync as execFileSync3 } from "child_process";
-import { existsSync as existsSync5, renameSync } from "fs";
-import { join as join5 } from "path";
+import { existsSync as existsSync5, renameSync, rmSync } from "fs";
+import { basename, dirname as dirname2, extname as extname2, join as join5 } from "path";
 
 // src/scip-cli.ts
 import { execFileSync as execFileSync2 } from "child_process";
@@ -991,6 +1016,128 @@ function resolveDotnetProject(projectRoot, suffixes) {
   return null;
 }
 
+// src/reindex/merge.ts
+import { readFileSync as readFileSync2, writeFileSync } from "fs";
+import { create } from "@bufbuild/protobuf";
+import {
+  deserializeSCIP,
+  serializeSCIP,
+  DocumentSchema,
+  IndexSchema,
+  SymbolInformationSchema
+} from "@c4312/scip";
+function mergeScipIndexes(indexes) {
+  if (indexes.length === 0) {
+    throw new Error("Cannot merge zero SCIP indexes");
+  }
+  if (indexes.length === 1) {
+    return indexes[0];
+  }
+  const metadata = mergeMetadata(indexes);
+  const documents = mergeDocuments(indexes.flatMap((index) => index.documents ?? []));
+  const externalSymbols = mergeSymbolInfos(indexes.flatMap((index) => index.externalSymbols ?? []));
+  return create(IndexSchema, {
+    metadata,
+    documents,
+    externalSymbols
+  });
+}
+function mergeScipFiles(inputPaths, outputPath) {
+  if (inputPaths.length === 0) {
+    throw new Error("Cannot merge zero SCIP files");
+  }
+  const indexes = inputPaths.map((path) => deserializeSCIP(readFileSync2(path)));
+  const merged = mergeScipIndexes(indexes);
+  writeFileSync(outputPath, Buffer.from(serializeSCIP(merged)));
+  return {
+    documentCount: merged.documents.length,
+    externalSymbolCount: merged.externalSymbols.length,
+    inputCount: inputPaths.length
+  };
+}
+function mergeMetadata(indexes) {
+  const first = indexes[0]?.metadata;
+  if (!first) {
+    return void 0;
+  }
+  const expectedProjectRoot = first.projectRoot;
+  for (const index of indexes.slice(1)) {
+    const actualProjectRoot = index.metadata?.projectRoot;
+    if (expectedProjectRoot && actualProjectRoot && actualProjectRoot !== expectedProjectRoot) {
+      throw new Error(
+        `Cannot merge SCIP indexes with different project roots: ${expectedProjectRoot} vs ${actualProjectRoot}`
+      );
+    }
+  }
+  return first;
+}
+function mergeDocuments(documents) {
+  const byPath = /* @__PURE__ */ new Map();
+  for (const document of documents) {
+    const existing = byPath.get(document.relativePath);
+    if (!existing) {
+      byPath.set(document.relativePath, document);
+      continue;
+    }
+    byPath.set(document.relativePath, create(DocumentSchema, {
+      language: existing.language || document.language,
+      relativePath: existing.relativePath || document.relativePath,
+      occurrences: [...existing.occurrences, ...document.occurrences],
+      symbols: mergeSymbolInfos([...existing.symbols, ...document.symbols]),
+      text: chooseText(existing.text, document.text),
+      positionEncoding: existing.positionEncoding || document.positionEncoding
+    }));
+  }
+  return [...byPath.values()];
+}
+function mergeSymbolInfos(symbols2) {
+  const bySymbol = /* @__PURE__ */ new Map();
+  for (const symbol of symbols2) {
+    const existing = bySymbol.get(symbol.symbol);
+    if (!existing) {
+      bySymbol.set(symbol.symbol, symbol);
+      continue;
+    }
+    bySymbol.set(symbol.symbol, create(SymbolInformationSchema, {
+      symbol: existing.symbol,
+      documentation: uniqueStrings([...existing.documentation, ...symbol.documentation]),
+      relationships: mergeRelationships([...existing.relationships, ...symbol.relationships]),
+      kind: existing.kind || symbol.kind,
+      displayName: existing.displayName || symbol.displayName,
+      enclosingSymbol: existing.enclosingSymbol || symbol.enclosingSymbol,
+      signatureDocumentation: existing.signatureDocumentation ?? symbol.signatureDocumentation
+    }));
+  }
+  return [...bySymbol.values()];
+}
+function mergeRelationships(relationships) {
+  const seen = /* @__PURE__ */ new Set();
+  const merged = [];
+  for (const relationship of relationships) {
+    const key = [
+      relationship.symbol,
+      relationship.isReference ? "1" : "0",
+      relationship.isImplementation ? "1" : "0",
+      relationship.isTypeDefinition ? "1" : "0",
+      relationship.isDefinition ? "1" : "0"
+    ].join("|");
+    if (seen.has(key)) {
+      continue;
+    }
+    seen.add(key);
+    merged.push(relationship);
+  }
+  return merged;
+}
+function chooseText(left, right) {
+  if (!left) return right;
+  if (!right) return left;
+  return left.length >= right.length ? left : right;
+}
+function uniqueStrings(values) {
+  return [...new Set(values)];
+}
+
 // src/reindex/index.ts
 async function reindex(opts) {
   const {
@@ -1026,7 +1173,11 @@ async function reindex(opts) {
     ...process.env,
     NODE_OPTIONS: `--max-old-space-size=${maxHeapMb}`
   };
-  for (const lang of languages) {
+  const languageOutputs = languages.map((language, index) => ({
+    language,
+    scipPath: languages.length > 1 ? tempScipPath(outputScip, language, index) : outputScip
+  }));
+  for (const { language: lang, scipPath } of languageOutputs) {
     const config = getIndexerConfig(lang);
     const binaryLabel = describeIndexerBinary(config);
     const projectLocalBinary = resolveProjectLocalIndexerBinary(config, projectRoot);
@@ -1056,7 +1207,7 @@ async function reindex(opts) {
     const indexerEnv = getIndexerExecutionEnv(config, env, resolvedBinary);
     const { binary, args } = config.indexArgs({
       projectRoot,
-      outputPath: outputScip,
+      outputPath: scipPath,
       pnpmWorkspaces: opts.pnpmWorkspaces,
       indexerBinary: resolvedBinary
     });
@@ -1075,7 +1226,11 @@ Make sure ${binaryLabel} is installed and available on PATH.`,
         { cause: err }
       );
     }
-    moveDefaultOutputIfNeeded(config, projectRoot, outputScip);
+    moveDefaultOutputIfNeeded(config, projectRoot, scipPath);
+  }
+  if (languageOutputs.length > 1) {
+    onStatus(`Merging ${languageOutputs.length} language indexes...`);
+    mergeScipFiles(languageOutputs.map((entry) => entry.scipPath), outputScip);
   }
   onStatus("Converting to SQLite...");
   if (!existsSync5(outputScip)) {
@@ -1090,6 +1245,12 @@ Make sure ${binaryLabel} is installed and available on PATH.`,
   } catch (err) {
     const msg = err instanceof Error ? err.message : String(err);
     throw new Error(`Failed to convert SCIP index to SQLite: ${msg}`, { cause: err });
+  } finally {
+    for (const { scipPath } of languageOutputs) {
+      if (scipPath !== outputScip) {
+        rmSync(scipPath, { force: true });
+      }
+    }
   }
   const durationMs = Date.now() - start;
   onStatus(`Done in ${(durationMs / 1e3).toFixed(1)}s`);
@@ -1104,10 +1265,15 @@ function moveDefaultOutputIfNeeded(config, projectRoot, outputScip) {
     renameSync(defaultOutputPath, outputScip);
   }
 }
+function tempScipPath(outputScip, language, index) {
+  const extension = extname2(outputScip) || ".scip";
+  const stem = basename(outputScip, extension);
+  return join5(dirname2(outputScip), `${stem}.${index + 1}.${language}${extension}`);
+}
 
 // src/config.ts
-import { readFileSync as readFileSync2, writeFileSync, existsSync as existsSync6, mkdirSync } from "fs";
-import { join as join6, resolve } from "path";
+import { readFileSync as readFileSync3, writeFileSync as writeFileSync2, existsSync as existsSync6, mkdirSync } from "fs";
+import { join as join6, resolve as resolve2 } from "path";
 import { createHash } from "crypto";
 import { homedir } from "os";
 var CONFIG_FILENAME = ".scipquery.json";
@@ -1123,7 +1289,7 @@ function loadProjectConfig(projectRoot) {
     return {};
   }
   try {
-    const raw = readFileSync2(configPath, "utf-8");
+    const raw = readFileSync3(configPath, "utf-8");
     return JSON.parse(raw);
   } catch {
     return {};
@@ -1138,10 +1304,10 @@ function resolveWatchConfig(config) {
 function resolveCacheDir(projectRoot, config) {
   const envOverride = process.env["SCIP_QUERY_CACHE_DIR"];
   if (envOverride) return ensureDir(envOverride);
-  if (config?.dbPath) return ensureDir(resolve(projectRoot, config.dbPath));
+  if (config?.dbPath) return ensureDir(resolve2(projectRoot, config.dbPath));
   const xdgCache = process.env["XDG_CACHE_HOME"];
   const cacheBase = xdgCache || join6(homedir(), ".cache");
-  const projectHash = createHash("sha256").update(resolve(projectRoot)).digest("hex").slice(0, 12);
+  const projectHash = createHash("sha256").update(resolve2(projectRoot)).digest("hex").slice(0, 12);
   const dir = join6(cacheBase, "scip-query", "projects", projectHash);
   return ensureDir(dir);
 }
@@ -1167,7 +1333,7 @@ function initProjectConfig(projectRoot, languages) {
       cooldownMs: 6e4
     }
   };
-  writeFileSync(configPath, JSON.stringify(config, null, 2) + "\n");
+  writeFileSync2(configPath, JSON.stringify(config, null, 2) + "\n");
   return configPath;
 }
 function ensureDir(dir) {
@@ -1178,7 +1344,7 @@ function ensureDir(dir) {
 // src/watch.ts
 import { watch } from "fs";
 import { existsSync as existsSync7, renameSync as renameSync2 } from "fs";
-import { join as join7, relative } from "path";
+import { join as join7, relative as relative2 } from "path";
 import { fork } from "child_process";
 import ignore2 from "ignore";
 var Watcher = class {
@@ -1256,7 +1422,7 @@ var Watcher = class {
   }
   // ── Internal ─────────────────────────────────────────────
   handleFileChange(filename) {
-    const rel = relative(this.projectRoot, join7(this.projectRoot, filename));
+    const rel = relative2(this.projectRoot, join7(this.projectRoot, filename));
     if (this.gitignoreFilter.isIgnored(rel)) return;
     if (this.extraIgnore.ignores(rel)) return;
     if (filename.endsWith("index.db") || filename.endsWith("index.scip") || filename.endsWith("index.db.tmp") || filename.endsWith(".scipquery.json")) {
@@ -1337,10 +1503,10 @@ var Watcher = class {
    * Writes to index.db.tmp, then atomically renames to index.db.
    */
   runReindex() {
-    return new Promise((resolve3, reject) => {
+    return new Promise((resolve4, reject) => {
       const start = Date.now();
       const tmpDb = this.indexPaths.dbPath + ".tmp";
-      const tmpScip = tempScipPath(this.indexPaths.indexPath);
+      const tmpScip = tempScipPath2(this.indexPaths.indexPath);
       const child = fork(
         new URL("./reindex-worker.js", import.meta.url).pathname,
         [],
@@ -1365,7 +1531,7 @@ var Watcher = class {
             if (existsSync7(tmpScip)) {
               renameSync2(tmpScip, this.indexPaths.indexPath);
             }
-            resolve3(Date.now() - start);
+            resolve4(Date.now() - start);
           } catch (err) {
             reject(new Error(`Atomic swap failed: ${err}`));
           }
@@ -1381,7 +1547,7 @@ var Watcher = class {
     this.onStatus(status);
   }
 };
-function tempScipPath(indexPath) {
+function tempScipPath2(indexPath) {
   return indexPath.endsWith(".scip") ? indexPath.slice(0, -".scip".length) + ".tmp.scip" : indexPath + ".tmp.scip";
 }
 
@@ -1393,7 +1559,7 @@ import {
   readlinkSync,
   unlinkSync
 } from "fs";
-import { join as join8, dirname as dirname2, resolve as resolve2 } from "path";
+import { join as join8, dirname as dirname3, resolve as resolve3 } from "path";
 import { homedir as homedir2, platform as platform3 } from "os";
 import { fileURLToPath } from "url";
 var IS_WINDOWS3 = platform3() === "win32";
@@ -1408,7 +1574,7 @@ function installSkills(opts = {}) {
   const log = opts.quiet ? () => {
   } : console.log;
   const thisFile = fileURLToPath(import.meta.url);
-  const skillsSource = resolve2(dirname2(thisFile), "..", "skills");
+  const skillsSource = resolve3(dirname3(thisFile), "..", "skills");
   const targets = [
     join8(homedir2(), ".claude", "skills"),
     join8(homedir2(), ".codex", "skills")
@@ -1419,7 +1585,7 @@ function installSkills(opts = {}) {
     alreadyLinked: []
   };
   for (const targetDir of targets) {
-    const parentDir = dirname2(targetDir);
+    const parentDir = dirname3(targetDir);
     if (!existsSync8(parentDir)) {
       continue;
     }
@@ -1435,7 +1601,7 @@ function installSkills(opts = {}) {
       if (existsSync8(target)) {
         try {
           const existing = readlinkSync(target);
-          if (resolve2(existing) === resolve2(source)) {
+          if (resolve3(existing) === resolve3(source)) {
             result.alreadyLinked.push(`${toolName}/${skill}`);
             log(`  ok:   ${skill} \u2192 ${toolName} (already linked)`);
             continue;
@@ -1498,6 +1664,8 @@ export {
   leafName,
   loadProjectConfig,
   members,
+  mergeScipFiles,
+  mergeScipIndexes,
   methods,
   outline,
   parseSymbol,

package/dist/reindex-worker.js

@@ -11,8 +11,8 @@ import {
 
 // src/reindex/index.ts
 import { execFileSync } from "child_process";
-import { existsSync as existsSync3, renameSync } from "fs";
-import { join as join3 } from "path";
+import { existsSync as existsSync3, renameSync, rmSync } from "fs";
+import { basename, dirname, extname as extname2, join as join3 } from "path";
 
 // src/reindex/detect.ts
 import { existsSync, readdirSync } from "fs";
@@ -390,6 +390,128 @@ function resolveDotnetProject(projectRoot2, suffixes) {
   return null;
 }
 
+// src/reindex/merge.ts
+import { readFileSync, writeFileSync } from "fs";
+import { create } from "@bufbuild/protobuf";
+import {
+  deserializeSCIP,
+  serializeSCIP,
+  DocumentSchema,
+  IndexSchema,
+  SymbolInformationSchema
+} from "@c4312/scip";
+function mergeScipIndexes(indexes) {
+  if (indexes.length === 0) {
+    throw new Error("Cannot merge zero SCIP indexes");
+  }
+  if (indexes.length === 1) {
+    return indexes[0];
+  }
+  const metadata = mergeMetadata(indexes);
+  const documents = mergeDocuments(indexes.flatMap((index) => index.documents ?? []));
+  const externalSymbols = mergeSymbolInfos(indexes.flatMap((index) => index.externalSymbols ?? []));
+  return create(IndexSchema, {
+    metadata,
+    documents,
+    externalSymbols
+  });
+}
+function mergeScipFiles(inputPaths, outputPath) {
+  if (inputPaths.length === 0) {
+    throw new Error("Cannot merge zero SCIP files");
+  }
+  const indexes = inputPaths.map((path) => deserializeSCIP(readFileSync(path)));
+  const merged = mergeScipIndexes(indexes);
+  writeFileSync(outputPath, Buffer.from(serializeSCIP(merged)));
+  return {
+    documentCount: merged.documents.length,
+    externalSymbolCount: merged.externalSymbols.length,
+    inputCount: inputPaths.length
+  };
+}
+function mergeMetadata(indexes) {
+  const first = indexes[0]?.metadata;
+  if (!first) {
+    return void 0;
+  }
+  const expectedProjectRoot = first.projectRoot;
+  for (const index of indexes.slice(1)) {
+    const actualProjectRoot = index.metadata?.projectRoot;
+    if (expectedProjectRoot && actualProjectRoot && actualProjectRoot !== expectedProjectRoot) {
+      throw new Error(
+        `Cannot merge SCIP indexes with different project roots: ${expectedProjectRoot} vs ${actualProjectRoot}`
+      );
+    }
+  }
+  return first;
+}
+function mergeDocuments(documents) {
+  const byPath = /* @__PURE__ */ new Map();
+  for (const document of documents) {
+    const existing = byPath.get(document.relativePath);
+    if (!existing) {
+      byPath.set(document.relativePath, document);
+      continue;
+    }
+    byPath.set(document.relativePath, create(DocumentSchema, {
+      language: existing.language || document.language,
+      relativePath: existing.relativePath || document.relativePath,
+      occurrences: [...existing.occurrences, ...document.occurrences],
+      symbols: mergeSymbolInfos([...existing.symbols, ...document.symbols]),
+      text: chooseText(existing.text, document.text),
+      positionEncoding: existing.positionEncoding || document.positionEncoding
+    }));
+  }
+  return [...byPath.values()];
+}
+function mergeSymbolInfos(symbols) {
+  const bySymbol = /* @__PURE__ */ new Map();
+  for (const symbol of symbols) {
+    const existing = bySymbol.get(symbol.symbol);
+    if (!existing) {
+      bySymbol.set(symbol.symbol, symbol);
+      continue;
+    }
+    bySymbol.set(symbol.symbol, create(SymbolInformationSchema, {
+      symbol: existing.symbol,
+      documentation: uniqueStrings([...existing.documentation, ...symbol.documentation]),
+      relationships: mergeRelationships([...existing.relationships, ...symbol.relationships]),
+      kind: existing.kind || symbol.kind,
+      displayName: existing.displayName || symbol.displayName,
+      enclosingSymbol: existing.enclosingSymbol || symbol.enclosingSymbol,
+      signatureDocumentation: existing.signatureDocumentation ?? symbol.signatureDocumentation
+    }));
+  }
+  return [...bySymbol.values()];
+}
+function mergeRelationships(relationships) {
+  const seen = /* @__PURE__ */ new Set();
+  const merged = [];
+  for (const relationship of relationships) {
+    const key = [
+      relationship.symbol,
+      relationship.isReference ? "1" : "0",
+      relationship.isImplementation ? "1" : "0",
+      relationship.isTypeDefinition ? "1" : "0",
+      relationship.isDefinition ? "1" : "0"
+    ].join("|");
+    if (seen.has(key)) {
+      continue;
+    }
+    seen.add(key);
+    merged.push(relationship);
+  }
+  return merged;
+}
+function chooseText(left, right) {
+  if (!left) return right;
+  if (!right) return left;
+  return left.length >= right.length ? left : right;
+}
+function uniqueStrings(values) {
+  return [...new Set(values)];
+}
+
 // src/reindex/index.ts
 async function reindex(opts) {
   const {
@@ -425,7 +547,11 @@ async function reindex(opts) {
     ...process.env,
     NODE_OPTIONS: `--max-old-space-size=${maxHeapMb}`
   };
-  for (const lang of languages2) {
+  const languageOutputs = languages2.map((language, index) => ({
+    language,
+    scipPath: languages2.length > 1 ? tempScipPath(outputScip2, language, index) : outputScip2
+  }));
+  for (const { language: lang, scipPath } of languageOutputs) {
     const config = getIndexerConfig(lang);
     const binaryLabel = describeIndexerBinary(config);
     const projectLocalBinary = resolveProjectLocalIndexerBinary(config, projectRoot2);
@@ -455,7 +581,7 @@ async function reindex(opts) {
     const indexerEnv = getIndexerExecutionEnv(config, env, resolvedBinary);
     const { binary, args } = config.indexArgs({
       projectRoot: projectRoot2,
-      outputPath: outputScip2,
+      outputPath: scipPath,
       pnpmWorkspaces: opts.pnpmWorkspaces,
       indexerBinary: resolvedBinary
     });
@@ -474,7 +600,11 @@ Make sure ${binaryLabel} is installed and available on PATH.`,
         { cause: err }
       );
     }
-    moveDefaultOutputIfNeeded(config, projectRoot2, outputScip2);
+    moveDefaultOutputIfNeeded(config, projectRoot2, scipPath);
+  }
+  if (languageOutputs.length > 1) {
+    onStatus(`Merging ${languageOutputs.length} language indexes...`);
+    mergeScipFiles(languageOutputs.map((entry) => entry.scipPath), outputScip2);
   }
   onStatus("Converting to SQLite...");
   if (!existsSync3(outputScip2)) {
@@ -489,6 +619,12 @@ Make sure ${binaryLabel} is installed and available on PATH.`,
   } catch (err) {
     const msg = err instanceof Error ? err.message : String(err);
     throw new Error(`Failed to convert SCIP index to SQLite: ${msg}`, { cause: err });
+  } finally {
+    for (const { scipPath } of languageOutputs) {
+      if (scipPath !== outputScip2) {
+        rmSync(scipPath, { force: true });
+      }
+    }
   }
   const durationMs = Date.now() - start;
   onStatus(`Done in ${(durationMs / 1e3).toFixed(1)}s`);
@@ -503,6 +639,11 @@ function moveDefaultOutputIfNeeded(config, projectRoot2, outputScip2) {
     renameSync(defaultOutputPath, outputScip2);
   }
 }
+function tempScipPath(outputScip2, language, index) {
+  const extension = extname2(outputScip2) || ".scip";
+  const stem = basename(outputScip2, extension);
+  return join3(dirname(outputScip2), `${stem}.${index + 1}.${language}${extension}`);
+}
 
 // src/reindex-worker.ts
 var projectRoot = process.env["SCIP_REINDEX_PROJECT_ROOT"];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "scip-query",
-  "version": "0.4.1",
+  "version": "0.4.2",
   "description": "Language-agnostic code intelligence CLI powered by SCIP indexes",
   "type": "module",
   "main": "dist/index.js",
@@ -60,6 +60,8 @@
     "node": ">=18.0.0"
   },
   "dependencies": {
+    "@bufbuild/protobuf": "^2.11.0",
+    "@c4312/scip": "^0.1.0",
     "better-sqlite3": "^11.7.0",
     "commander": "^13.1.0",
     "ignore": "^7.0.3"