@wrongstack/tools 0.307.0 → 0.307.1

package/dist/patch.js

@@ -4427,10 +4427,16 @@ function buildFileGraphNodeState(pkgSyms, localFiles, packageOf) {
   }
   return { fileNodes, symToFile, fileStats, ensureFileNode };
 }
-function buildSymbolGraphNodes(symById, relatedIds, fileFilter, packageOf) {
+function buildSymbolGraphNodes(symById, relatedIds, localFiles, packageOf) {
+  const local = new Set(
+    [...typeof localFiles === "string" ? [localFiles] : localFiles].map(
+      (file) => file.replace(/\\/g, "/")
+    )
+  );
+  const isLocal = (file) => local.has(file.replace(/\\/g, "/"));
   return [...relatedIds].map((id) => symById.get(id)).filter((symbol) => symbol !== void 0).sort((a, b) => {
-    const aExternal = a.file === fileFilter ? 0 : 1;
-    const bExternal = b.file === fileFilter ? 0 : 1;
+    const aExternal = isLocal(a.file) ? 0 : 1;
+    const bExternal = isLocal(b.file) ? 0 : 1;
     return aExternal - bExternal || a.file.localeCompare(b.file) || a.line - b.line || a.id - b.id;
   }).map((s) => ({
     id: `sym:${s.id}`,
@@ -4444,7 +4450,7 @@ function buildSymbolGraphNodes(symById, relatedIds, fileFilter, packageOf) {
     line: s.line,
     signature: s.signature,
     scope: s.scope,
-    external: s.file !== fileFilter
+    external: !isLocal(s.file)
   }));
 }
 function addWeightedEdge(edgeMap, source, target, callType, weight) {
@@ -4479,6 +4485,52 @@ function materializeWeightedEdges(edgeMap, idPrefix) {
   return edges;
 }
 
+// src/codebase-index/writer-helpers.ts
+import { resolveWstackPaths } from "@wrongstack/core/utils";
+function escapeLike(value) {
+  return value.replace(/[\\%_]/g, (char) => `\\${char}`);
+}
+function posixIndexPath(file) {
+  return file.replace(/\\/g, "/").replace(/^\.\//, "");
+}
+function indexedFileMatchSql(column = "file") {
+  return `(${column} = ? OR replace(${column}, '\\', '/') = ? OR replace(${column}, '\\', '/') LIKE ? ESCAPE '\\')`;
+}
+function indexedFileMatchArgs(file) {
+  const posix4 = posixIndexPath(file.trim());
+  return [file, posix4, `%/${escapeLike(posix4)}`];
+}
+function matchesIndexedPackageFilter(storedFile, packageLabel, filter) {
+  if (packageLabel === filter) return true;
+  const posixFile = posixIndexPath(storedFile);
+  const posixFilter = posixIndexPath(filter.trim());
+  if (!posixFilter) return false;
+  return posixFile === posixFilter || posixFile.endsWith(`/${posixFilter}`) || posixFile.includes(`/${posixFilter}/`);
+}
+function assignRefsToSymbols(refs, symbols) {
+  if (refs.length === 0 || symbols.length === 0) return [];
+  const ordered = [...symbols].sort((a, b) => a.line - b.line || a.col - b.col || a.id - b.id);
+  const seen = /* @__PURE__ */ new Set();
+  const assigned = [];
+  for (const ref of refs) {
+    let owner;
+    for (const symbol of ordered) {
+      if (symbol.line > ref.line) break;
+      owner = symbol;
+    }
+    if (!owner && ref.callType === "import") owner = ordered[0];
+    if (!owner || owner.id <= 0) continue;
+    const key = `${owner.id}:${ref.toName}:${ref.callType}:${ref.module ?? ""}`;
+    if (seen.has(key)) continue;
+    seen.add(key);
+    assigned.push({ ...ref, fromId: owner.id });
+  }
+  return assigned;
+}
+function resolveIndexDir(projectRoot, override) {
+  return override ?? resolveWstackPaths({ projectRoot }).projectCodebaseIndex;
+}
+
 // src/codebase-index/writer-ref-mapper.ts
 function mapWriterRefRow(row) {
   return {
@@ -4534,10 +4586,23 @@ function mapCallSiteRow(row) {
     line: row.ref_line
   };
 }
+function resolveIndexedFiles(stmt, file) {
+  const rows = stmt(
+    `SELECT DISTINCT file FROM symbols WHERE ${indexedFileMatchSql("file")} ORDER BY length(file), file`
+  ).all(...indexedFileMatchArgs(file));
+  return rows.map((row) => row.file);
+}
 function resolveSymbolIds(stmt, symbolName, file) {
-  const baseSql = file ? `SELECT id FROM symbols WHERE name = ? AND file = ? ORDER BY id` : `SELECT id FROM symbols WHERE name = ? ORDER BY id`;
-  const args = file ? [symbolName, file] : [symbolName];
-  const rows = stmt(baseSql).all(...args);
+  if (!file) {
+    const rows2 = stmt("SELECT id FROM symbols WHERE name = ? ORDER BY id").all(symbolName);
+    return rows2.map((r) => r.id);
+  }
+  const indexedFiles = resolveIndexedFiles(stmt, file);
+  if (indexedFiles.length === 0) return [];
+  const placeholders = indexedFiles.map(() => "?").join(",");
+  const rows = stmt(
+    `SELECT id FROM symbols WHERE name = ? AND file IN (${placeholders}) ORDER BY id`
+  ).all(symbolName, ...indexedFiles);
   return rows.map((r) => r.id);
 }
 function findIncomingCallsByName(stmt, symbolName, file, limit) {
@@ -4859,7 +4924,7 @@ function getFileGraphWithStatement(stmt, packageFilter) {
   const allFiles = stmt("SELECT DISTINCT file FROM symbols").all();
   const packageOf = readPackageLabeller(stmt);
   const langOf = (file) => detectLang(file) ?? "other";
-  const pkgFilePaths = allFiles.filter((f) => packageOf(f.file) === packageFilter).map((f) => f.file);
+  const pkgFilePaths = allFiles.filter((f) => matchesIndexedPackageFilter(f.file, packageOf(f.file), packageFilter)).map((f) => f.file);
   const localFiles = new Set(pkgFilePaths);
   if (localFiles.size === 0) return { nodes: [], edges: [] };
   const filePlaceholders = [...localFiles].map(() => "?").join(",");
@@ -4935,9 +5000,12 @@ function getFileGraphWithStatement(stmt, packageFilter) {
   return { nodes: [...fileNodes.values()], edges };
 }
 function getSymbolGraphWithStatement(stmt, fileFilter) {
+  const indexedFiles = resolveIndexedFiles(stmt, fileFilter);
+  if (indexedFiles.length === 0) return { nodes: [], edges: [] };
+  const filePlaceholders = indexedFiles.map(() => "?").join(",");
   const syms = stmt(
-    "SELECT id, name, kind, lang, file, line, signature, scope FROM symbols WHERE file = ? ORDER BY line, id"
-  ).all(fileFilter);
+    `SELECT id, name, kind, lang, file, line, signature, scope FROM symbols WHERE file IN (${filePlaceholders}) ORDER BY line, id`
+  ).all(...indexedFiles);
   if (syms.length === 0) return { nodes: [], edges: [] };
   const symById = new Map(syms.map((symbol) => [symbol.id, symbol]));
   const relatedIds = new Set(syms.map((symbol) => symbol.id));
@@ -4947,16 +5015,16 @@ function getSymbolGraphWithStatement(stmt, fileFilter) {
          SELECT r.from_id, r.to_id, r.to_name, r.call_type, r.line
          FROM refs r
          JOIN symbols s ON s.id = r.from_id
-         WHERE s.file = ?
+         WHERE s.file IN (${filePlaceholders})
          UNION
          SELECT r.from_id, r.to_id, r.to_name, r.call_type, r.line
          FROM refs r
          JOIN symbols s ON s.id = r.to_id
-         WHERE s.file = ?
+         WHERE s.file IN (${filePlaceholders})
        )
        WHERE to_id IS NOT NULL
        GROUP BY from_id, to_id, call_type`
-  ).all(fileFilter, fileFilter);
+  ).all(...indexedFiles, ...indexedFiles);
   const edgeMap = /* @__PURE__ */ new Map();
   for (const r of refRows) {
     if (r.to_id == null) continue;
@@ -4975,39 +5043,15 @@ function getSymbolGraphWithStatement(stmt, fileFilter) {
     ).all(...missingIds);
     for (const s of extras) symById.set(s.id, s);
   }
-  const nodes = buildSymbolGraphNodes(symById, relatedIds, fileFilter, readPackageLabeller(stmt));
+  const nodes = buildSymbolGraphNodes(
+    symById,
+    relatedIds,
+    new Set(syms.map((symbol) => symbol.file)),
+    readPackageLabeller(stmt)
+  );
   return { nodes, edges };
 }
 
-// src/codebase-index/writer-helpers.ts
-import { resolveWstackPaths } from "@wrongstack/core/utils";
-function escapeLike(value) {
-  return value.replace(/[\\%_]/g, (char) => `\\${char}`);
-}
-function assignRefsToSymbols(refs, symbols) {
-  if (refs.length === 0 || symbols.length === 0) return [];
-  const ordered = [...symbols].sort((a, b) => a.line - b.line || a.col - b.col || a.id - b.id);
-  const seen = /* @__PURE__ */ new Set();
-  const assigned = [];
-  for (const ref of refs) {
-    let owner;
-    for (const symbol of ordered) {
-      if (symbol.line > ref.line) break;
-      owner = symbol;
-    }
-    if (!owner && ref.callType === "import") owner = ordered[0];
-    if (!owner || owner.id <= 0) continue;
-    const key = `${owner.id}:${ref.toName}:${ref.callType}:${ref.module ?? ""}`;
-    if (seen.has(key)) continue;
-    seen.add(key);
-    assigned.push({ ...ref, fromId: owner.id });
-  }
-  return assigned;
-}
-function resolveIndexDir(projectRoot, override) {
-  return override ?? resolveWstackPaths({ projectRoot }).projectCodebaseIndex;
-}
-
 // src/codebase-index/vector-search.ts
 var RRF_K = 60;
 var VECTOR_DIMENSIONS = 384;

package/dist/read.js

@@ -4426,10 +4426,16 @@ function buildFileGraphNodeState(pkgSyms, localFiles, packageOf) {
   }
   return { fileNodes, symToFile, fileStats, ensureFileNode };
 }
-function buildSymbolGraphNodes(symById, relatedIds, fileFilter, packageOf) {
+function buildSymbolGraphNodes(symById, relatedIds, localFiles, packageOf) {
+  const local = new Set(
+    [...typeof localFiles === "string" ? [localFiles] : localFiles].map(
+      (file) => file.replace(/\\/g, "/")
+    )
+  );
+  const isLocal = (file) => local.has(file.replace(/\\/g, "/"));
   return [...relatedIds].map((id) => symById.get(id)).filter((symbol) => symbol !== void 0).sort((a, b) => {
-    const aExternal = a.file === fileFilter ? 0 : 1;
-    const bExternal = b.file === fileFilter ? 0 : 1;
+    const aExternal = isLocal(a.file) ? 0 : 1;
+    const bExternal = isLocal(b.file) ? 0 : 1;
     return aExternal - bExternal || a.file.localeCompare(b.file) || a.line - b.line || a.id - b.id;
   }).map((s) => ({
     id: `sym:${s.id}`,
@@ -4443,7 +4449,7 @@ function buildSymbolGraphNodes(symById, relatedIds, fileFilter, packageOf) {
     line: s.line,
     signature: s.signature,
     scope: s.scope,
-    external: s.file !== fileFilter
+    external: !isLocal(s.file)
   }));
 }
 function addWeightedEdge(edgeMap, source, target, callType, weight) {
@@ -4478,6 +4484,56 @@ function materializeWeightedEdges(edgeMap, idPrefix) {
   return edges;
 }
 
+// src/codebase-index/writer-helpers.ts
+import { resolveWstackPaths } from "@wrongstack/core/utils";
+function escapeLike(value) {
+  return value.replace(/[\\%_]/g, (char) => `\\${char}`);
+}
+function posixIndexPath(file) {
+  return file.replace(/\\/g, "/").replace(/^\.\//, "");
+}
+function indexedFileMatchSql(column = "file") {
+  return `(${column} = ? OR replace(${column}, '\\', '/') = ? OR replace(${column}, '\\', '/') LIKE ? ESCAPE '\\')`;
+}
+function indexedFileMatchArgs(file) {
+  const posix4 = posixIndexPath(file.trim());
+  return [file, posix4, `%/${escapeLike(posix4)}`];
+}
+function matchesIndexedPackageFilter(storedFile, packageLabel, filter) {
+  if (packageLabel === filter) return true;
+  const posixFile = posixIndexPath(storedFile);
+  const posixFilter = posixIndexPath(filter.trim());
+  if (!posixFilter) return false;
+  return posixFile === posixFilter || posixFile.endsWith(`/${posixFilter}`) || posixFile.includes(`/${posixFilter}/`);
+}
+function assignRefsToSymbols(refs, symbols) {
+  if (refs.length === 0 || symbols.length === 0) return [];
+  const ordered = [...symbols].sort((a, b) => a.line - b.line || a.col - b.col || a.id - b.id);
+  const seen = /* @__PURE__ */ new Set();
+  const assigned = [];
+  for (const ref of refs) {
+    let owner;
+    for (const symbol of ordered) {
+      if (symbol.line > ref.line) break;
+      owner = symbol;
+    }
+    if (!owner && ref.callType === "import") owner = ordered[0];
+    if (!owner || owner.id <= 0) continue;
+    const key = `${owner.id}:${ref.toName}:${ref.callType}:${ref.module ?? ""}`;
+    if (seen.has(key)) continue;
+    seen.add(key);
+    assigned.push({ ...ref, fromId: owner.id });
+  }
+  return assigned;
+}
+function resolveIndexDir(projectRoot, override) {
+  return override ?? resolveWstackPaths({ projectRoot }).projectCodebaseIndex;
+}
+function codebaseIndexDirOverride(ctx) {
+  const v = ctx.meta?.["codebaseIndexDir"];
+  return typeof v === "string" ? v : void 0;
+}
+
 // src/codebase-index/writer-ref-mapper.ts
 function mapWriterRefRow(row) {
   return {
@@ -4533,10 +4589,23 @@ function mapCallSiteRow(row) {
     line: row.ref_line
   };
 }
+function resolveIndexedFiles(stmt, file) {
+  const rows = stmt(
+    `SELECT DISTINCT file FROM symbols WHERE ${indexedFileMatchSql("file")} ORDER BY length(file), file`
+  ).all(...indexedFileMatchArgs(file));
+  return rows.map((row) => row.file);
+}
 function resolveSymbolIds(stmt, symbolName, file) {
-  const baseSql = file ? `SELECT id FROM symbols WHERE name = ? AND file = ? ORDER BY id` : `SELECT id FROM symbols WHERE name = ? ORDER BY id`;
-  const args = file ? [symbolName, file] : [symbolName];
-  const rows = stmt(baseSql).all(...args);
+  if (!file) {
+    const rows2 = stmt("SELECT id FROM symbols WHERE name = ? ORDER BY id").all(symbolName);
+    return rows2.map((r) => r.id);
+  }
+  const indexedFiles = resolveIndexedFiles(stmt, file);
+  if (indexedFiles.length === 0) return [];
+  const placeholders = indexedFiles.map(() => "?").join(",");
+  const rows = stmt(
+    `SELECT id FROM symbols WHERE name = ? AND file IN (${placeholders}) ORDER BY id`
+  ).all(symbolName, ...indexedFiles);
   return rows.map((r) => r.id);
 }
 function findIncomingCallsByName(stmt, symbolName, file, limit) {
@@ -4858,7 +4927,7 @@ function getFileGraphWithStatement(stmt, packageFilter) {
   const allFiles = stmt("SELECT DISTINCT file FROM symbols").all();
   const packageOf = readPackageLabeller(stmt);
   const langOf = (file) => detectLang(file) ?? "other";
-  const pkgFilePaths = allFiles.filter((f) => packageOf(f.file) === packageFilter).map((f) => f.file);
+  const pkgFilePaths = allFiles.filter((f) => matchesIndexedPackageFilter(f.file, packageOf(f.file), packageFilter)).map((f) => f.file);
   const localFiles = new Set(pkgFilePaths);
   if (localFiles.size === 0) return { nodes: [], edges: [] };
   const filePlaceholders = [...localFiles].map(() => "?").join(",");
@@ -4934,9 +5003,12 @@ function getFileGraphWithStatement(stmt, packageFilter) {
   return { nodes: [...fileNodes.values()], edges };
 }
 function getSymbolGraphWithStatement(stmt, fileFilter) {
+  const indexedFiles = resolveIndexedFiles(stmt, fileFilter);
+  if (indexedFiles.length === 0) return { nodes: [], edges: [] };
+  const filePlaceholders = indexedFiles.map(() => "?").join(",");
   const syms = stmt(
-    "SELECT id, name, kind, lang, file, line, signature, scope FROM symbols WHERE file = ? ORDER BY line, id"
-  ).all(fileFilter);
+    `SELECT id, name, kind, lang, file, line, signature, scope FROM symbols WHERE file IN (${filePlaceholders}) ORDER BY line, id`
+  ).all(...indexedFiles);
   if (syms.length === 0) return { nodes: [], edges: [] };
   const symById = new Map(syms.map((symbol) => [symbol.id, symbol]));
   const relatedIds = new Set(syms.map((symbol) => symbol.id));
@@ -4946,16 +5018,16 @@ function getSymbolGraphWithStatement(stmt, fileFilter) {
          SELECT r.from_id, r.to_id, r.to_name, r.call_type, r.line
          FROM refs r
          JOIN symbols s ON s.id = r.from_id
-         WHERE s.file = ?
+         WHERE s.file IN (${filePlaceholders})
          UNION
          SELECT r.from_id, r.to_id, r.to_name, r.call_type, r.line
          FROM refs r
          JOIN symbols s ON s.id = r.to_id
-         WHERE s.file = ?
+         WHERE s.file IN (${filePlaceholders})
        )
        WHERE to_id IS NOT NULL
        GROUP BY from_id, to_id, call_type`
-  ).all(fileFilter, fileFilter);
+  ).all(...indexedFiles, ...indexedFiles);
   const edgeMap = /* @__PURE__ */ new Map();
   for (const r of refRows) {
     if (r.to_id == null) continue;
@@ -4974,43 +5046,15 @@ function getSymbolGraphWithStatement(stmt, fileFilter) {
     ).all(...missingIds);
     for (const s of extras) symById.set(s.id, s);
   }
-  const nodes = buildSymbolGraphNodes(symById, relatedIds, fileFilter, readPackageLabeller(stmt));
+  const nodes = buildSymbolGraphNodes(
+    symById,
+    relatedIds,
+    new Set(syms.map((symbol) => symbol.file)),
+    readPackageLabeller(stmt)
+  );
   return { nodes, edges };
 }
 
-// src/codebase-index/writer-helpers.ts
-import { resolveWstackPaths } from "@wrongstack/core/utils";
-function escapeLike(value) {
-  return value.replace(/[\\%_]/g, (char) => `\\${char}`);
-}
-function assignRefsToSymbols(refs, symbols) {
-  if (refs.length === 0 || symbols.length === 0) return [];
-  const ordered = [...symbols].sort((a, b) => a.line - b.line || a.col - b.col || a.id - b.id);
-  const seen = /* @__PURE__ */ new Set();
-  const assigned = [];
-  for (const ref of refs) {
-    let owner;
-    for (const symbol of ordered) {
-      if (symbol.line > ref.line) break;
-      owner = symbol;
-    }
-    if (!owner && ref.callType === "import") owner = ordered[0];
-    if (!owner || owner.id <= 0) continue;
-    const key = `${owner.id}:${ref.toName}:${ref.callType}:${ref.module ?? ""}`;
-    if (seen.has(key)) continue;
-    seen.add(key);
-    assigned.push({ ...ref, fromId: owner.id });
-  }
-  return assigned;
-}
-function resolveIndexDir(projectRoot, override) {
-  return override ?? resolveWstackPaths({ projectRoot }).projectCodebaseIndex;
-}
-function codebaseIndexDirOverride(ctx) {
-  const v = ctx.meta?.["codebaseIndexDir"];
-  return typeof v === "string" ? v : void 0;
-}
-
 // src/codebase-index/vector-search.ts
 var RRF_K = 60;
 var VECTOR_DIMENSIONS = 384;

package/dist/replace.js

@@ -4592,10 +4592,16 @@ function buildFileGraphNodeState(pkgSyms, localFiles, packageOf) {
   }
   return { fileNodes, symToFile, fileStats, ensureFileNode };
 }
-function buildSymbolGraphNodes(symById, relatedIds, fileFilter, packageOf) {
+function buildSymbolGraphNodes(symById, relatedIds, localFiles, packageOf) {
+  const local = new Set(
+    [...typeof localFiles === "string" ? [localFiles] : localFiles].map(
+      (file) => file.replace(/\\/g, "/")
+    )
+  );
+  const isLocal = (file) => local.has(file.replace(/\\/g, "/"));
   return [...relatedIds].map((id) => symById.get(id)).filter((symbol) => symbol !== void 0).sort((a, b) => {
-    const aExternal = a.file === fileFilter ? 0 : 1;
-    const bExternal = b.file === fileFilter ? 0 : 1;
+    const aExternal = isLocal(a.file) ? 0 : 1;
+    const bExternal = isLocal(b.file) ? 0 : 1;
     return aExternal - bExternal || a.file.localeCompare(b.file) || a.line - b.line || a.id - b.id;
   }).map((s) => ({
     id: `sym:${s.id}`,
@@ -4609,7 +4615,7 @@ function buildSymbolGraphNodes(symById, relatedIds, fileFilter, packageOf) {
     line: s.line,
     signature: s.signature,
     scope: s.scope,
-    external: s.file !== fileFilter
+    external: !isLocal(s.file)
   }));
 }
 function addWeightedEdge(edgeMap, source, target, callType, weight) {
@@ -4644,6 +4650,52 @@ function materializeWeightedEdges(edgeMap, idPrefix) {
   return edges;
 }
 
+// src/codebase-index/writer-helpers.ts
+import { resolveWstackPaths } from "@wrongstack/core/utils";
+function escapeLike(value) {
+  return value.replace(/[\\%_]/g, (char) => `\\${char}`);
+}
+function posixIndexPath(file) {
+  return file.replace(/\\/g, "/").replace(/^\.\//, "");
+}
+function indexedFileMatchSql(column = "file") {
+  return `(${column} = ? OR replace(${column}, '\\', '/') = ? OR replace(${column}, '\\', '/') LIKE ? ESCAPE '\\')`;
+}
+function indexedFileMatchArgs(file) {
+  const posix4 = posixIndexPath(file.trim());
+  return [file, posix4, `%/${escapeLike(posix4)}`];
+}
+function matchesIndexedPackageFilter(storedFile, packageLabel, filter) {
+  if (packageLabel === filter) return true;
+  const posixFile = posixIndexPath(storedFile);
+  const posixFilter = posixIndexPath(filter.trim());
+  if (!posixFilter) return false;
+  return posixFile === posixFilter || posixFile.endsWith(`/${posixFilter}`) || posixFile.includes(`/${posixFilter}/`);
+}
+function assignRefsToSymbols(refs, symbols) {
+  if (refs.length === 0 || symbols.length === 0) return [];
+  const ordered = [...symbols].sort((a, b) => a.line - b.line || a.col - b.col || a.id - b.id);
+  const seen = /* @__PURE__ */ new Set();
+  const assigned = [];
+  for (const ref of refs) {
+    let owner;
+    for (const symbol of ordered) {
+      if (symbol.line > ref.line) break;
+      owner = symbol;
+    }
+    if (!owner && ref.callType === "import") owner = ordered[0];
+    if (!owner || owner.id <= 0) continue;
+    const key = `${owner.id}:${ref.toName}:${ref.callType}:${ref.module ?? ""}`;
+    if (seen.has(key)) continue;
+    seen.add(key);
+    assigned.push({ ...ref, fromId: owner.id });
+  }
+  return assigned;
+}
+function resolveIndexDir(projectRoot, override) {
+  return override ?? resolveWstackPaths({ projectRoot }).projectCodebaseIndex;
+}
+
 // src/codebase-index/writer-ref-mapper.ts
 function mapWriterRefRow(row) {
   return {
@@ -4699,10 +4751,23 @@ function mapCallSiteRow(row) {
     line: row.ref_line
   };
 }
+function resolveIndexedFiles(stmt, file) {
+  const rows = stmt(
+    `SELECT DISTINCT file FROM symbols WHERE ${indexedFileMatchSql("file")} ORDER BY length(file), file`
+  ).all(...indexedFileMatchArgs(file));
+  return rows.map((row) => row.file);
+}
 function resolveSymbolIds(stmt, symbolName, file) {
-  const baseSql = file ? `SELECT id FROM symbols WHERE name = ? AND file = ? ORDER BY id` : `SELECT id FROM symbols WHERE name = ? ORDER BY id`;
-  const args = file ? [symbolName, file] : [symbolName];
-  const rows = stmt(baseSql).all(...args);
+  if (!file) {
+    const rows2 = stmt("SELECT id FROM symbols WHERE name = ? ORDER BY id").all(symbolName);
+    return rows2.map((r) => r.id);
+  }
+  const indexedFiles = resolveIndexedFiles(stmt, file);
+  if (indexedFiles.length === 0) return [];
+  const placeholders = indexedFiles.map(() => "?").join(",");
+  const rows = stmt(
+    `SELECT id FROM symbols WHERE name = ? AND file IN (${placeholders}) ORDER BY id`
+  ).all(symbolName, ...indexedFiles);
   return rows.map((r) => r.id);
 }
 function findIncomingCallsByName(stmt, symbolName, file, limit) {
@@ -5024,7 +5089,7 @@ function getFileGraphWithStatement(stmt, packageFilter) {
   const allFiles = stmt("SELECT DISTINCT file FROM symbols").all();
   const packageOf = readPackageLabeller(stmt);
   const langOf = (file) => detectLang(file) ?? "other";
-  const pkgFilePaths = allFiles.filter((f) => packageOf(f.file) === packageFilter).map((f) => f.file);
+  const pkgFilePaths = allFiles.filter((f) => matchesIndexedPackageFilter(f.file, packageOf(f.file), packageFilter)).map((f) => f.file);
   const localFiles = new Set(pkgFilePaths);
   if (localFiles.size === 0) return { nodes: [], edges: [] };
   const filePlaceholders = [...localFiles].map(() => "?").join(",");
@@ -5100,9 +5165,12 @@ function getFileGraphWithStatement(stmt, packageFilter) {
   return { nodes: [...fileNodes.values()], edges };
 }
 function getSymbolGraphWithStatement(stmt, fileFilter) {
+  const indexedFiles = resolveIndexedFiles(stmt, fileFilter);
+  if (indexedFiles.length === 0) return { nodes: [], edges: [] };
+  const filePlaceholders = indexedFiles.map(() => "?").join(",");
   const syms = stmt(
-    "SELECT id, name, kind, lang, file, line, signature, scope FROM symbols WHERE file = ? ORDER BY line, id"
-  ).all(fileFilter);
+    `SELECT id, name, kind, lang, file, line, signature, scope FROM symbols WHERE file IN (${filePlaceholders}) ORDER BY line, id`
+  ).all(...indexedFiles);
   if (syms.length === 0) return { nodes: [], edges: [] };
   const symById = new Map(syms.map((symbol) => [symbol.id, symbol]));
   const relatedIds = new Set(syms.map((symbol) => symbol.id));
@@ -5112,16 +5180,16 @@ function getSymbolGraphWithStatement(stmt, fileFilter) {
          SELECT r.from_id, r.to_id, r.to_name, r.call_type, r.line
          FROM refs r
          JOIN symbols s ON s.id = r.from_id
-         WHERE s.file = ?
+         WHERE s.file IN (${filePlaceholders})
          UNION
          SELECT r.from_id, r.to_id, r.to_name, r.call_type, r.line
          FROM refs r
          JOIN symbols s ON s.id = r.to_id
-         WHERE s.file = ?
+         WHERE s.file IN (${filePlaceholders})
        )
        WHERE to_id IS NOT NULL
        GROUP BY from_id, to_id, call_type`
-  ).all(fileFilter, fileFilter);
+  ).all(...indexedFiles, ...indexedFiles);
   const edgeMap = /* @__PURE__ */ new Map();
   for (const r of refRows) {
     if (r.to_id == null) continue;
@@ -5140,39 +5208,15 @@ function getSymbolGraphWithStatement(stmt, fileFilter) {
     ).all(...missingIds);
     for (const s of extras) symById.set(s.id, s);
   }
-  const nodes = buildSymbolGraphNodes(symById, relatedIds, fileFilter, readPackageLabeller(stmt));
+  const nodes = buildSymbolGraphNodes(
+    symById,
+    relatedIds,
+    new Set(syms.map((symbol) => symbol.file)),
+    readPackageLabeller(stmt)
+  );
   return { nodes, edges };
 }
 
-// src/codebase-index/writer-helpers.ts
-import { resolveWstackPaths } from "@wrongstack/core/utils";
-function escapeLike(value) {
-  return value.replace(/[\\%_]/g, (char) => `\\${char}`);
-}
-function assignRefsToSymbols(refs, symbols) {
-  if (refs.length === 0 || symbols.length === 0) return [];
-  const ordered = [...symbols].sort((a, b) => a.line - b.line || a.col - b.col || a.id - b.id);
-  const seen = /* @__PURE__ */ new Set();
-  const assigned = [];
-  for (const ref of refs) {
-    let owner;
-    for (const symbol of ordered) {
-      if (symbol.line > ref.line) break;
-      owner = symbol;
-    }
-    if (!owner && ref.callType === "import") owner = ordered[0];
-    if (!owner || owner.id <= 0) continue;
-    const key = `${owner.id}:${ref.toName}:${ref.callType}:${ref.module ?? ""}`;
-    if (seen.has(key)) continue;
-    seen.add(key);
-    assigned.push({ ...ref, fromId: owner.id });
-  }
-  return assigned;
-}
-function resolveIndexDir(projectRoot, override) {
-  return override ?? resolveWstackPaths({ projectRoot }).projectCodebaseIndex;
-}
-
 // src/codebase-index/vector-search.ts
 var RRF_K = 60;
 var VECTOR_DIMENSIONS = 384;