@danielblomma/cortex-mcp 0.4.5 → 1.0.0

package/scaffold/scripts/ingest.mjs

@@ -4,7 +4,19 @@ import fs from "node:fs";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
 import { execSync } from "node:child_process";
-import { parseCode } from "./parsers/javascript.mjs";
+import { parseCode as parseJavaScriptCode } from "./parsers/javascript.mjs";
+import {
+  isVbNetParserAvailable,
+  parseCode as parseVbNetCode
+} from "./parsers/vbnet.mjs";
+import {
+  isCppParserAvailable,
+  parseCode as parseCppCode
+} from "./parsers/cpp.mjs";
+import { parseCode as parseConfigCode } from "./parsers/config.mjs";
+import { parseCode as parseResourcesCode } from "./parsers/resources.mjs";
+import { parseCode as parseSqlCode } from "./parsers/sql.mjs";
+import { parseCode as parseRustCode } from "./parsers/rust.mjs";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -34,6 +46,16 @@ const SUPPORTED_TEXT_EXTENSIONS = new Set([
   ".go",
   ".java",
   ".cs",
+  ".vb",
+  ".sln",
+  ".vbproj",
+  ".csproj",
+  ".fsproj",
+  ".props",
+  ".targets",
+  ".config",
+  ".resx",
+  ".settings",
   ".rb",
   ".rs",
   ".php",
@@ -52,6 +74,216 @@ const SUPPORTED_TEXT_EXTENSIONS = new Set([
   ".hh"
 ]);
 
+const LEGACY_DOTNET_METADATA_EXTENSIONS = new Set([
+  ".sln",
+  ".vbproj",
+  ".csproj",
+  ".fsproj",
+  ".props",
+  ".targets",
+  ".config",
+  ".resx",
+  ".settings"
+]);
+
+const PROJECT_DEFINITION_EXTENSIONS = new Set([".sln", ".vbproj", ".csproj", ".fsproj"]);
+const STRUCTURED_NON_CODE_CHUNK_EXTENSIONS = new Set([".config", ".resx", ".settings"]);
+
+const CODE_FILE_EXTENSIONS = new Set([
+  ".ts",
+  ".tsx",
+  ".js",
+  ".jsx",
+  ".mjs",
+  ".cjs",
+  ".py",
+  ".go",
+  ".java",
+  ".cs",
+  ".vb",
+  ".rb",
+  ".rs",
+  ".php",
+  ".swift",
+  ".kt",
+  ".sql",
+  ".sh",
+  ".bash",
+  ".zsh",
+  ".ps1",
+  ".c",
+  ".h",
+  ".cpp",
+  ".hpp",
+  ".cc",
+  ".hh"
+]);
+
+const SQL_REFERENCE_SOURCE_EXTENSIONS = new Set([
+  ".vb",
+  ".cs",
+  ".config",
+  ".resx",
+  ".settings"
+]);
+const NAMED_RESOURCE_REFERENCE_SOURCE_EXTENSIONS = new Set([".vb", ".cs"]);
+
+const SQL_OBJECT_REFERENCE_PATTERNS = [
+  /\b(?:SqlCommand|OleDbCommand|OdbcCommand)\s*\(\s*"([^"\r\n]{2,200})"/gi,
+  /\bCommandText\s*=\s*"([^"\r\n]{2,500})"/gi,
+  /\bCommandType\s*=\s*(?:CommandType\.)?StoredProcedure[\s\S]{0,240}?"([^"\r\n]{2,200})"/gi,
+  /"([^"\r\n]{2,200})"[\s\S]{0,240}?\bCommandType\s*=\s*(?:CommandType\.)?StoredProcedure/gi
+];
+
+const SQL_STRING_REFERENCE_PATTERNS = [
+  /\bexec(?:ute)?\s+([#@]?[A-Za-z0-9_[\].]+)/gi,
+  /\bfrom\s+([#@]?[A-Za-z0-9_[\].]+)/gi,
+  /\bjoin\s+([#@]?[A-Za-z0-9_[\].]+)/gi,
+  /\bupdate\s+([#@]?[A-Za-z0-9_[\].]+)/gi,
+  /\binsert\s+into\s+([#@]?[A-Za-z0-9_[\].]+)/gi,
+  /\bdelete\s+from\s+([#@]?[A-Za-z0-9_[\].]+)/gi,
+  /\bmerge\s+into\s+([#@]?[A-Za-z0-9_[\].]+)/gi
+];
+
+const SQL_RESOURCE_KEY_PATTERNS = [
+  /\bMy\.Resources\.([A-Za-z_][A-Za-z0-9_]*)/g,
+  /\bResources\.([A-Za-z_][A-Za-z0-9_]*)/g,
+  /\bMy\.Settings\.([A-Za-z_][A-Za-z0-9_]*)/g,
+  /\b(?:[A-Za-z_][A-Za-z0-9_]*\.)?Settings\.Default\.([A-Za-z_][A-Za-z0-9_]*)/g,
+  /\bGetString\(\s*"([^"\r\n]+)"/g,
+  /\bGetObject\(\s*"([^"\r\n]+)"/g
+];
+const CONFIG_KEY_REFERENCE_PATTERNS = [
+  /\bConfigurationManager\.ConnectionStrings\s*\[\s*"([^"\r\n]+)"\s*\]/g,
+  /\bConfigurationManager\.ConnectionStrings\s*\(\s*"([^"\r\n]+)"\s*\)/g,
+  /\bConfigurationManager\.AppSettings\s*\[\s*"([^"\r\n]+)"\s*\]/g,
+  /\bConfigurationManager\.AppSettings\s*\(\s*"([^"\r\n]+)"\s*\)/g,
+  /\bGetConnectionString\(\s*"([^"\r\n]+)"\s*\)/g,
+  /\bGetAppSetting\(\s*"([^"\r\n]+)"\s*\)/g
+];
+
+const CHUNK_PARSERS = new Map([
+  [
+    ".js",
+    {
+      language: "javascript",
+      parse: parseJavaScriptCode
+    }
+  ],
+  [
+    ".mjs",
+    {
+      language: "javascript",
+      parse: parseJavaScriptCode
+    }
+  ],
+  [
+    ".cjs",
+    {
+      language: "javascript",
+      parse: parseJavaScriptCode
+    }
+  ],
+  [
+    ".ts",
+    {
+      language: "typescript",
+      parse: parseJavaScriptCode
+    }
+  ],
+  [
+    ".vb",
+    {
+      language: "vbnet",
+      parse: parseVbNetCode,
+      isAvailable: isVbNetParserAvailable
+    }
+  ],
+  [
+    ".sql",
+    {
+      language: "sql",
+      parse: parseSqlCode
+    }
+  ],
+  [
+    ".config",
+    {
+      language: "config",
+      parse: parseConfigCode
+    }
+  ],
+  [
+    ".resx",
+    {
+      language: "resource",
+      parse: parseResourcesCode
+    }
+  ],
+  [
+    ".settings",
+    {
+      language: "settings",
+      parse: parseResourcesCode
+    }
+  ],
+  [
+    ".c",
+    {
+      language: "c",
+      parse: parseCppCode,
+      isAvailable: isCppParserAvailable
+    }
+  ],
+  [
+    ".h",
+    {
+      language: "c",
+      parse: parseCppCode,
+      isAvailable: isCppParserAvailable
+    }
+  ],
+  [
+    ".cpp",
+    {
+      language: "cpp",
+      parse: parseCppCode,
+      isAvailable: isCppParserAvailable
+    }
+  ],
+  [
+    ".cc",
+    {
+      language: "cpp",
+      parse: parseCppCode,
+      isAvailable: isCppParserAvailable
+    }
+  ],
+  [
+    ".hpp",
+    {
+      language: "cpp",
+      parse: parseCppCode,
+      isAvailable: isCppParserAvailable
+    }
+  ],
+  [
+    ".hh",
+    {
+      language: "cpp",
+      parse: parseCppCode,
+      isAvailable: isCppParserAvailable
+    }
+  ],
+  [
+    ".rs",
+    {
+      language: "rust",
+      parse: parseRustCode
+    }
+  ]
+]);
+
 const SKIP_DIRECTORIES = new Set([
   ".git",
   ".idea",
@@ -69,6 +301,14 @@ const MAX_FILE_BYTES = 1024 * 1024;
 const MAX_CONTENT_CHARS = 60000;
 const MAX_BODY_CHARS = 12000;
 const RULE_KEYWORD_LIMIT = 20;
+const DEFAULT_CHUNK_WINDOW_LINES = 80;
+const DEFAULT_CHUNK_OVERLAP_LINES = 16;
+const DEFAULT_CHUNK_SPLIT_MIN_LINES = 120;
+const DEFAULT_CHUNK_MAX_WINDOWS = 8;
+const IMPORT_RESOLUTION_EXTENSIONS = [".ts", ".tsx", ".js", ".jsx", ".mjs", ".cjs", ".json"];
+const IMPORT_RUNTIME_JS_EXTENSIONS = new Set([".js", ".jsx", ".mjs", ".cjs"]);
+const IMPORT_RUNTIME_JS_RESOLUTION_EXTENSIONS = [".ts", ".tsx", ".js", ".jsx", ".mjs", ".cjs"];
+const CPP_IMPORT_RESOLUTION_EXTENSIONS = [".h", ".hh", ".hpp", ".c", ".cc", ".cpp"];
 
 const STOP_WORDS = new Set([
   "the",
@@ -183,6 +423,30 @@ function uniqueSorted(values) {
   return [...new Set(values)].sort();
 }
 
+function parsePositiveIntegerEnv(name, fallback) {
+  const rawValue = process.env[name];
+  if (!rawValue) {
+    return fallback;
+  }
+  const parsed = Number(rawValue);
+  if (!Number.isFinite(parsed) || parsed < 1) {
+    return fallback;
+  }
+  return Math.floor(parsed);
+}
+
+function parseNonNegativeIntegerEnv(name, fallback) {
+  const rawValue = process.env[name];
+  if (!rawValue) {
+    return fallback;
+  }
+  const parsed = Number(rawValue);
+  if (!Number.isFinite(parsed) || parsed < 0) {
+    return fallback;
+  }
+  return Math.floor(parsed);
+}
+
 function parseSourcePaths(configText) {
   const sourcePaths = [];
   const lines = configText.split(/\r?\n/);
@@ -290,6 +554,60 @@ function hasSourcePrefix(relPath, sourcePaths) {
   });
 }
 
+function pushImportResolutionCandidate(candidates, seenCandidates, candidatePath) {
+  if (!seenCandidates.has(candidatePath)) {
+    seenCandidates.add(candidatePath);
+    candidates.push(candidatePath);
+  }
+}
+
+function isCppLikeFilePath(filePath) {
+  return [".c", ".h", ".cc", ".cpp", ".hh", ".hpp"].includes(path.posix.extname(filePath).toLowerCase());
+}
+
+function resolveRelativeImportTargetId(filePath, importPath, indexedFileIds) {
+  const isCppLike = isCppLikeFilePath(filePath);
+  const isRelativeImport = importPath.startsWith(".");
+  const isLocalCppInclude =
+    isCppLike && !path.posix.isAbsolute(importPath) && !/^[A-Za-z]:[\\/]/.test(importPath);
+
+  if (!isRelativeImport && !isLocalCppInclude) {
+    return null;
+  }
+
+  const basePath = path.posix.normalize(path.posix.join(path.posix.dirname(filePath), importPath));
+  const candidates = [];
+  const seenCandidates = new Set();
+  pushImportResolutionCandidate(candidates, seenCandidates, basePath);
+
+  if (path.posix.extname(basePath) === "") {
+    const extensions = isCppLike ? CPP_IMPORT_RESOLUTION_EXTENSIONS : IMPORT_RESOLUTION_EXTENSIONS;
+    for (const extension of extensions) {
+      pushImportResolutionCandidate(candidates, seenCandidates, `${basePath}${extension}`);
+    }
+    if (!isCppLike) {
+      for (const extension of IMPORT_RESOLUTION_EXTENSIONS) {
+        pushImportResolutionCandidate(candidates, seenCandidates, path.posix.join(basePath, `index${extension}`));
+      }
+    }
+  } else if (IMPORT_RUNTIME_JS_EXTENSIONS.has(path.posix.extname(basePath))) {
+    const extension = path.posix.extname(basePath);
+    const stemPath = basePath.slice(0, -extension.length);
+    for (const candidateExtension of IMPORT_RUNTIME_JS_RESOLUTION_EXTENSIONS) {
+      pushImportResolutionCandidate(candidates, seenCandidates, `${stemPath}${candidateExtension}`);
+    }
+  }
+
+  for (const candidate of candidates) {
+    const targetFileId = `file:${candidate}`;
+    if (indexedFileIds.has(targetFileId)) {
+      return targetFileId;
+    }
+  }
+
+  return null;
+}
+
 function getGitChanges() {
   try {
     const output = execSync("git status --porcelain", {
@@ -428,9 +746,17 @@ function detectKind(relPath) {
     return "DOC";
   }
 
+  if (LEGACY_DOTNET_METADATA_EXTENSIONS.has(ext) || !CODE_FILE_EXTENSIONS.has(ext)) {
+    return "DOC";
+  }
+
   return "CODE";
 }
 
+function getChunkParserForExtension(ext) {
+  return CHUNK_PARSERS.get(ext) ?? null;
+}
+
 function trustLevelForKind(kind) {
   if (kind === "ADR") return 95;
   if (kind === "CODE") return 80;
@@ -509,32 +835,1217 @@ function sanitizeTsvCell(value) {
   return String(value).replace(/\t/g, " ").replace(/\r?\n/g, " ");
 }
 
-function writeTsv(filePath, headers, rows) {
-  const lines = [headers.join("\t")];
-  for (const row of rows) {
-    lines.push(row.map((value) => sanitizeTsvCell(value)).join("\t"));
+function writeTsv(filePath, headers, rows) {
+  const lines = [headers.join("\t")];
+  for (const row of rows) {
+    lines.push(row.map((value) => sanitizeTsvCell(value)).join("\t"));
+  }
+  fs.writeFileSync(filePath, `${lines.join("\n")}\n`, "utf8");
+}
+
+function readJsonlSafe(filePath) {
+  if (!fs.existsSync(filePath)) {
+    return [];
+  }
+
+  return fs
+    .readFileSync(filePath, "utf8")
+    .split(/\r?\n/)
+    .map((line) => line.trim())
+    .filter(Boolean)
+    .map((line) => {
+      try {
+        return JSON.parse(line);
+      } catch {
+        return null;
+      }
+    })
+    .filter((record) => record !== null);
+}
+
+function relationKey(...parts) {
+  return parts.map((part) => String(part ?? "")).join("|");
+}
+
+function uniqueRelations(relations) {
+  const deduped = new Map();
+  for (const relation of relations) {
+    const key = relationKey(relation.from, relation.to, relation.note);
+    if (!deduped.has(key)) {
+      deduped.set(key, relation);
+    }
+  }
+  return [...deduped.values()].sort((a, b) =>
+    relationKey(a.from, a.to, a.note).localeCompare(relationKey(b.from, b.to, b.note))
+  );
+}
+
+function normalizeSqlName(value) {
+  if (!value) {
+    return "";
+  }
+
+  return String(value)
+    .trim()
+    .replace(/[;"`]/g, "")
+    .replace(/\[(.+?)\]/g, "$1")
+    .replace(/\s+/g, "")
+    .replace(/^\.+|\.+$/g, "")
+    .replace(/\.\.+/g, ".")
+    .toLowerCase();
+}
+
+function sqlChunkAliases(name) {
+  const normalized = normalizeSqlName(name);
+  if (!normalized) {
+    return [];
+  }
+
+  const aliases = new Set([normalized]);
+  const parts = normalized.split(".").filter(Boolean);
+  if (parts.length > 1) {
+    aliases.add(parts[parts.length - 1]);
+  }
+  return [...aliases];
+}
+
+function configChunkAliases(chunk) {
+  const aliases = new Set();
+  const rawKey = String(chunk?.configKey ?? chunk?.name ?? "");
+  const normalizedKey = normalizeToken(rawKey);
+  if (normalizedKey) {
+    aliases.add(normalizedKey);
+  }
+  const chunkName = String(chunk?.name ?? "");
+  const tail = chunkName.split(".").pop() ?? "";
+  const normalizedTail = normalizeToken(tail);
+  if (normalizedTail) {
+    aliases.add(normalizedTail);
+  }
+  return [...aliases];
+}
+
+function namedEntryChunkAliases(chunk) {
+  const aliases = new Set();
+  const rawKey = String(chunk?.resourceKey ?? chunk?.configKey ?? chunk?.name ?? "");
+  const normalizedKey = normalizeToken(rawKey);
+  if (normalizedKey) {
+    aliases.add(normalizedKey);
+  }
+  const chunkName = String(chunk?.name ?? "");
+  const tail = chunkName.split(".").pop() ?? "";
+  const normalizedTail = normalizeToken(tail);
+  if (normalizedTail) {
+    aliases.add(normalizedTail);
+  }
+  return [...aliases];
+}
+
+function extractSqlReferenceNamesFromString(text) {
+  const refs = new Set();
+
+  const normalizedName = normalizeSqlName(text);
+  if (/^[a-z0-9_.]+$/i.test(normalizedName) && normalizedName.includes(".")) {
+    refs.add(normalizedName);
+  }
+
+  for (const pattern of SQL_STRING_REFERENCE_PATTERNS) {
+    let match;
+    while ((match = pattern.exec(text)) !== null) {
+      const name = normalizeSqlName(match[1]);
+      if (!name || name.startsWith("@") || name.startsWith("#")) {
+        continue;
+      }
+      refs.add(name);
+    }
+  }
+
+  return [...refs];
+}
+
+function parseResxSqlReferenceMap(content) {
+  const refsByKey = new Map();
+  const dataPattern = /<data\b[^>]*\bname="([^"]+)"[^>]*>([\s\S]*?)<\/data>/gi;
+  let match;
+
+  while ((match = dataPattern.exec(content)) !== null) {
+    const key = normalizeToken(decodeXmlEntities(match[1]));
+    if (!key) {
+      continue;
+    }
+
+    const valueMatch = match[2].match(/<value>([\s\S]*?)<\/value>/i);
+    if (!valueMatch) {
+      continue;
+    }
+
+    const value = decodeXmlEntities(valueMatch[1]).trim();
+    const refs = extractSqlReferenceNamesFromString(value);
+    if (refs.length === 0) {
+      continue;
+    }
+
+    const existing = refsByKey.get(key) ?? [];
+    refsByKey.set(key, uniqueSorted([...existing, ...refs]));
+  }
+
+  return refsByKey;
+}
+
+function parseResxKeyMap(content) {
+  const fileKeys = new Map();
+  const dataPattern = /<data\b[^>]*\bname="([^"]+)"[^>]*>/gi;
+  let match;
+
+  while ((match = dataPattern.exec(content)) !== null) {
+    const key = normalizeToken(decodeXmlEntities(match[1]));
+    if (!key) {
+      continue;
+    }
+    fileKeys.set(key, true);
+  }
+
+  return fileKeys;
+}
+
+function parseSettingsSqlReferenceMap(content) {
+  const refsByKey = new Map();
+  const settingPattern = /<Setting\b[^>]*\bName="([^"]+)"[^>]*>([\s\S]*?)<\/Setting>/gi;
+  let match;
+
+  while ((match = settingPattern.exec(content)) !== null) {
+    const key = normalizeToken(decodeXmlEntities(match[1]));
+    if (!key) {
+      continue;
+    }
+
+    const valueMatch = match[2].match(/<Value(?:\s[^>]*)?>([\s\S]*?)<\/Value>/i);
+    if (!valueMatch) {
+      continue;
+    }
+
+    const value = decodeXmlEntities(valueMatch[1]).trim();
+    const refs = extractSqlReferenceNamesFromString(value);
+    if (refs.length === 0) {
+      continue;
+    }
+
+    const existing = refsByKey.get(key) ?? [];
+    refsByKey.set(key, uniqueSorted([...existing, ...refs]));
+  }
+
+  return refsByKey;
+}
+
+function parseSettingsKeyMap(content) {
+  const fileKeys = new Map();
+  const settingPattern = /<Setting\b[^>]*\bName="([^"]+)"[^>]*>/gi;
+  let match;
+
+  while ((match = settingPattern.exec(content)) !== null) {
+    const key = normalizeToken(decodeXmlEntities(match[1]));
+    if (!key) {
+      continue;
+    }
+    fileKeys.set(key, true);
+  }
+
+  return fileKeys;
+}
+
+function parseConfigKeyMap(content) {
+  const fileKeys = new Map();
+  const addPattern = /<add\b([^>]+?)\/?>/gi;
+  let match;
+
+  while ((match = addPattern.exec(content)) !== null) {
+    const attributes = match[1];
+    const nameMatch = attributes.match(/\bname="([^"]+)"/i);
+    const keyMatch = attributes.match(/\bkey="([^"]+)"/i);
+    const normalized = normalizeToken(decodeXmlEntities(nameMatch?.[1] ?? keyMatch?.[1] ?? ""));
+    if (!normalized) {
+      continue;
+    }
+    fileKeys.set(normalized, true);
+  }
+
+  return fileKeys;
+}
+
+function buildSqlResourceReferenceMap(fileRecords) {
+  const refsByKey = new Map();
+
+  for (const fileRecord of fileRecords) {
+    const ext = path.extname(fileRecord.path).toLowerCase();
+    let fileRefs = null;
+    if (ext === ".resx") {
+      fileRefs = parseResxSqlReferenceMap(fileRecord.content);
+    } else if (ext === ".settings") {
+      fileRefs = parseSettingsSqlReferenceMap(fileRecord.content);
+    }
+
+    if (!fileRefs) {
+      continue;
+    }
+
+    for (const [key, refs] of fileRefs.entries()) {
+      const existing = refsByKey.get(key) ?? [];
+      refsByKey.set(key, uniqueSorted([...existing, ...refs]));
+    }
+  }
+
+  return refsByKey;
+}
+
+function buildNamedResourceFileMaps(fileRecords) {
+  const resourceFilesByKey = new Map();
+  const settingFilesByKey = new Map();
+  const configFilesByKey = new Map();
+
+  for (const fileRecord of fileRecords) {
+    const ext = path.extname(fileRecord.path).toLowerCase();
+    const keyMap =
+      ext === ".resx"
+        ? parseResxKeyMap(fileRecord.content)
+        : ext === ".settings"
+          ? parseSettingsKeyMap(fileRecord.content)
+          : ext === ".config"
+            ? parseConfigKeyMap(fileRecord.content)
+          : null;
+
+    if (!keyMap) {
+      continue;
+    }
+
+    for (const key of keyMap.keys()) {
+      const targetMap =
+        ext === ".resx" ? resourceFilesByKey : ext === ".settings" ? settingFilesByKey : configFilesByKey;
+      const list = targetMap.get(key) ?? [];
+      list.push(fileRecord.id);
+      targetMap.set(key, uniqueSorted(list));
+    }
+  }
+
+  return { resourceFilesByKey, settingFilesByKey, configFilesByKey };
+}
+
+function extractSqlResourceKeyReferences(content) {
+  const keys = new Set();
+
+  for (const pattern of SQL_RESOURCE_KEY_PATTERNS) {
+    let match;
+    while ((match = pattern.exec(content)) !== null) {
+      const key = normalizeToken(match[1]);
+      if (key) {
+        keys.add(key);
+      }
+    }
+  }
+
+  return [...keys];
+}
+
+function extractConfigKeyReferences(content) {
+  const keys = new Set();
+
+  for (const pattern of CONFIG_KEY_REFERENCE_PATTERNS) {
+    let match;
+    while ((match = pattern.exec(content)) !== null) {
+      const key = normalizeToken(match[1]);
+      if (key) {
+        keys.add(key);
+      }
+    }
+  }
+
+  return [...keys];
+}
+
+function shouldExtractNamedResourceReferences(filePath) {
+  return NAMED_RESOURCE_REFERENCE_SOURCE_EXTENSIONS.has(path.extname(filePath).toLowerCase());
+}
+
+function generateNamedResourceRelations(fileRecords) {
+  const { resourceFilesByKey, settingFilesByKey, configFilesByKey } = buildNamedResourceFileMaps(fileRecords);
+  const usesResourceRelations = [];
+  const usesSettingRelations = [];
+  const usesConfigRelations = [];
+  const resourceSeen = new Set();
+  const settingSeen = new Set();
+  const configSeen = new Set();
+
+  for (const fileRecord of fileRecords) {
+    if (!shouldExtractNamedResourceReferences(fileRecord.path)) {
+      continue;
+    }
+
+    for (const key of extractSqlResourceKeyReferences(fileRecord.content)) {
+      for (const targetFileId of resourceFilesByKey.get(key) ?? []) {
+        const relKey = relationKey(fileRecord.id, targetFileId, key);
+        if (!resourceSeen.has(relKey) && fileRecord.id !== targetFileId) {
+          resourceSeen.add(relKey);
+          usesResourceRelations.push({
+            from: fileRecord.id,
+            to: targetFileId,
+            note: key
+          });
+        }
+      }
+
+      for (const targetFileId of settingFilesByKey.get(key) ?? []) {
+        const relKey = relationKey(fileRecord.id, targetFileId, key);
+        if (!settingSeen.has(relKey) && fileRecord.id !== targetFileId) {
+          settingSeen.add(relKey);
+          usesSettingRelations.push({
+            from: fileRecord.id,
+            to: targetFileId,
+            note: key
+          });
+        }
+      }
+    }
+
+    for (const key of extractConfigKeyReferences(fileRecord.content)) {
+      for (const targetFileId of configFilesByKey.get(key) ?? []) {
+        const relKey = relationKey(fileRecord.id, targetFileId, key);
+        if (!configSeen.has(relKey) && fileRecord.id !== targetFileId) {
+          configSeen.add(relKey);
+          usesConfigRelations.push({
+            from: fileRecord.id,
+            to: targetFileId,
+            note: key
+          });
+        }
+      }
+    }
+  }
+
+  usesResourceRelations.sort((a, b) =>
+    relationKey(a.from, a.to, a.note).localeCompare(relationKey(b.from, b.to, b.note))
+  );
+  usesSettingRelations.sort((a, b) =>
+    relationKey(a.from, a.to, a.note).localeCompare(relationKey(b.from, b.to, b.note))
+  );
+  usesConfigRelations.sort((a, b) =>
+    relationKey(a.from, a.to, a.note).localeCompare(relationKey(b.from, b.to, b.note))
+  );
+
+  return { usesResourceRelations, usesSettingRelations, usesConfigRelations };
+}
+
+function parseConfigIncludeTargets(fileRecord) {
+  const relPath = toPosixPath(String(fileRecord?.path ?? "").trim());
+  const lowerPath = relPath.toLowerCase();
+  if (!lowerPath.endsWith(".config")) {
+    return [];
+  }
+
+  const content = String(fileRecord?.content ?? "");
+  const dir = path.posix.dirname(relPath);
+  const includes = [];
+  const sectionPattern =
+    /<([A-Za-z_][A-Za-z0-9_.:-]*)\b([^>]*?)\b(configSource|file)="([^"]+)"([^>]*)>/gi;
+  let match;
+
+  while ((match = sectionPattern.exec(content)) !== null) {
+    const sectionName = String(match[1] ?? "").trim().toLowerCase();
+    const attributeName = String(match[3] ?? "").trim().toLowerCase();
+    const includePath = decodeXmlEntities(match[4] ?? "").trim().replace(/\\/g, "/");
+    if (!sectionName || !attributeName || !includePath) {
+      continue;
+    }
+    if (includePath.startsWith("/") || includePath.startsWith("~")) {
+      continue;
+    }
+
+    const resolvedPath = path.posix.normalize(dir === "." ? includePath : `${dir}/${includePath}`);
+    if (!resolvedPath || resolvedPath.startsWith("../")) {
+      continue;
+    }
+
+    includes.push({
+      targetPath: resolvedPath,
+      note: `${sectionName}:${attributeName}`
+    });
+  }
+
+  return includes;
+}
+
+function generateConfigIncludeRelations(fileRecords) {
+  const fileIdByPath = new Map(fileRecords.map((record) => [toPosixPath(record.path), record.id]));
+  const relations = [];
+  const seen = new Set();
+
+  for (const fileRecord of fileRecords) {
+    for (const include of parseConfigIncludeTargets(fileRecord)) {
+      const targetFileId = fileIdByPath.get(include.targetPath);
+      if (!targetFileId || targetFileId === fileRecord.id) {
+        continue;
+      }
+      const key = relationKey(fileRecord.id, targetFileId, include.note);
+      if (seen.has(key)) {
+        continue;
+      }
+      seen.add(key);
+      relations.push({
+        from: fileRecord.id,
+        to: targetFileId,
+        note: include.note
+      });
+    }
+  }
+
+  relations.sort((a, b) => relationKey(a.from, a.to, a.note).localeCompare(relationKey(b.from, b.to, b.note)));
+  return relations;
+}
+
+function parseSectionHandlerDeclarations(content) {
+  const declarations = [];
+  const sectionPattern = /<section\b([^>]*?)\/?>/gi;
+  let match;
+
+  while ((match = sectionPattern.exec(String(content ?? ""))) !== null) {
+    const attrs = match[1] ?? "";
+    const nameMatch = attrs.match(/\bname="([^"]+)"/i);
+    const typeMatch = attrs.match(/\btype="([^"]+)"/i);
+    const sectionName = normalizeToken(decodeXmlEntities(nameMatch?.[1] ?? ""));
+    const typeValue = decodeXmlEntities(typeMatch?.[1] ?? "").trim();
+    if (!sectionName || !typeValue) {
+      continue;
+    }
+
+    const typeParts = typeValue.split(",").map((part) => part.trim()).filter(Boolean);
+    const fullTypeName = typeParts[0] ?? "";
+    const assemblyName = typeParts[1] ?? "";
+    const shortTypeName = fullTypeName.split(".").pop()?.split("+").pop() ?? "";
+    const normalizedTypeName = normalizeToken(shortTypeName);
+    const normalizedAssemblyName = normalizeToken(assemblyName);
+    if (!normalizedTypeName && !normalizedAssemblyName) {
+      continue;
+    }
+
+    declarations.push({
+      sectionName,
+      normalizedTypeName,
+      normalizedAssemblyName
+    });
+  }
+
+  return declarations;
+}
+
+function buildProjectAssemblyFileMap(fileRecords) {
+  const aliasMap = new Map();
+
+  for (const fileRecord of fileRecords) {
+    const ext = path.extname(fileRecord.path).toLowerCase();
+    if (!PROJECT_DEFINITION_EXTENSIONS.has(ext) || ext === ".sln") {
+      continue;
+    }
+
+    const aliases = uniqueSorted([
+      normalizeToken(extractXmlTagValue(fileRecord.content, "AssemblyName")),
+      normalizeToken(extractXmlTagValue(fileRecord.content, "RootNamespace")),
+      normalizeToken(path.basename(fileRecord.path, ext))
+    ].filter(Boolean));
+
+    for (const alias of aliases) {
+      const existing = aliasMap.get(alias) ?? [];
+      aliasMap.set(alias, uniqueSorted([...existing, fileRecord.id]));
+    }
+  }
+
+  return aliasMap;
+}
+
+function extractDeclaredTypeNames(fileRecord) {
+  const ext = path.extname(fileRecord.path).toLowerCase();
+  const pattern =
+    ext === ".vb"
+      ? /\b(?:Public|Friend|Private|Protected|Partial|MustInherit|NotInheritable|Shadows|Default|Overridable|Overrides|Shared|\s)*(?:Class|Module|Structure|Interface|Enum)\s+([A-Za-z_][A-Za-z0-9_]*)/gi
+      : ext === ".cs"
+        ? /\b(?:public|internal|private|protected|abstract|sealed|static|partial|\s)*(?:class|struct|interface|enum)\s+([A-Za-z_][A-Za-z0-9_]*)/gi
+        : null;
+
+  if (!pattern) {
+    return [];
+  }
+
+  const typeNames = new Set();
+  let match;
+  while ((match = pattern.exec(String(fileRecord.content ?? ""))) !== null) {
+    const normalized = normalizeToken(match[1] ?? "");
+    if (normalized) {
+      typeNames.add(normalized);
+    }
+  }
+
+  return [...typeNames];
+}
+
+function buildCodeTypeFileMap(fileRecords) {
+  const typeMap = new Map();
+
+  for (const fileRecord of fileRecords) {
+    if (fileRecord.kind !== "CODE") {
+      continue;
+    }
+    for (const typeName of extractDeclaredTypeNames(fileRecord)) {
+      const existing = typeMap.get(typeName) ?? [];
+      typeMap.set(typeName, uniqueSorted([...existing, fileRecord.id]));
+    }
+  }
+
+  return typeMap;
+}
+
+function longestCommonPathPrefixLength(pathA, pathB) {
+  const partsA = toPosixPath(pathA).split("/").filter(Boolean);
+  const partsB = toPosixPath(pathB).split("/").filter(Boolean);
+  const limit = Math.min(partsA.length, partsB.length);
+  let count = 0;
+  while (count < limit && partsA[count] === partsB[count]) {
+    count += 1;
+  }
+  return count;
+}
+
+function generateMachineConfigRelations(fileRecords) {
+  const machineConfigs = fileRecords.filter(
+    (record) => path.basename(record.path).toLowerCase() === "machine.config"
+  );
+  if (machineConfigs.length === 0) {
+    return [];
+  }
+
+  const relations = [];
+  const seen = new Set();
+
+  for (const fileRecord of fileRecords) {
+    const lowerPath = fileRecord.path.toLowerCase();
+    if (
+      !lowerPath.endsWith(".config") ||
+      path.basename(lowerPath) === "machine.config" ||
+      !/<configuration\b/i.test(String(fileRecord.content ?? "")) ||
+      parseConfigTransformTarget(fileRecord)
+    ) {
+      continue;
+    }
+
+    const rankedTargets = machineConfigs
+      .filter((candidate) => candidate.id !== fileRecord.id)
+      .map((candidate) => ({
+        id: candidate.id,
+        score: longestCommonPathPrefixLength(fileRecord.path, candidate.path)
+      }))
+      .sort((a, b) => b.score - a.score || a.id.localeCompare(b.id));
+
+    const target = rankedTargets[0];
+    if (!target) {
+      continue;
+    }
+
+    const key = relationKey(fileRecord.id, target.id, "inherits:machine");
+    if (seen.has(key)) {
+      continue;
+    }
+    seen.add(key);
+    relations.push({
+      from: fileRecord.id,
+      to: target.id,
+      note: "inherits:machine"
+    });
+  }
+
+  return uniqueRelations(relations);
+}
+
+function generateSectionHandlerRelations(fileRecords) {
+  const projectAssemblyFileMap = buildProjectAssemblyFileMap(fileRecords);
+  const codeTypeFileMap = buildCodeTypeFileMap(fileRecords);
+  const relations = [];
+
+  for (const fileRecord of fileRecords) {
+    if (!fileRecord.path.toLowerCase().endsWith(".config")) {
+      continue;
+    }
+
+    for (const declaration of parseSectionHandlerDeclarations(fileRecord.content)) {
+      const note = `section_handler:${declaration.sectionName}`;
+
+      for (const targetFileId of projectAssemblyFileMap.get(declaration.normalizedAssemblyName) ?? []) {
+        relations.push({
+          from: fileRecord.id,
+          to: targetFileId,
+          note
+        });
+      }
+
+      for (const targetFileId of codeTypeFileMap.get(declaration.normalizedTypeName) ?? []) {
+        relations.push({
+          from: fileRecord.id,
+          to: targetFileId,
+          note
+        });
+      }
+    }
+  }
+
+  return uniqueRelations(relations.filter((relation) => relation.from !== relation.to));
+}
+
+function generateConfigTransformKeyRelations(fileRecords, chunkRecords) {
+  const fileIdByPath = new Map(fileRecords.map((record) => [toPosixPath(record.path), record.id]));
+  const chunkFileIdById = new Map(chunkRecords.map((chunk) => [chunk.id, chunk.file_id]));
+  const configChunkIdsByAlias = new Map();
+
+  for (const chunk of chunkRecords) {
+    if (isWindowChunkId(chunk.id) || String(chunk.language ?? "").toLowerCase() !== "config") {
+      continue;
+    }
+    for (const alias of configChunkAliases(chunk)) {
+      const existing = configChunkIdsByAlias.get(alias) ?? [];
+      configChunkIdsByAlias.set(alias, [...existing, chunk.id]);
+    }
+  }
+
+  const relations = [];
+  for (const fileRecord of fileRecords) {
+    const transform = parseConfigTransformTarget(fileRecord);
+    if (!transform) {
+      continue;
+    }
+
+    const targetFileId = fileIdByPath.get(transform.targetPath);
+    if (!targetFileId) {
+      continue;
+    }
+
+    for (const key of parseConfigKeyMap(fileRecord.content).keys()) {
+      for (const targetChunkId of configChunkIdsByAlias.get(key) ?? []) {
+        if (chunkFileIdById.get(targetChunkId) !== targetFileId) {
+          continue;
+        }
+        relations.push({
+          from: fileRecord.id,
+          to: targetChunkId,
+          note: `${key}:${transform.environment}`
+        });
+      }
+    }
+  }
+
+  return uniqueRelations(relations);
+}
+
+function parseConfigTransformTarget(fileRecord) {
+  const relPath = toPosixPath(String(fileRecord?.path ?? "").trim());
+  const lowerPath = relPath.toLowerCase();
+  if (!lowerPath.endsWith(".config")) {
+    return null;
+  }
+
+  const content = String(fileRecord?.content ?? "");
+  if (!/\bxdt:(?:transform|locator)\b/i.test(content) && !/\bxmlns:xdt=/i.test(content)) {
+    return null;
+  }
+
+  const dir = path.posix.dirname(relPath);
+  const baseName = path.posix.basename(relPath, ".config");
+  const match = baseName.match(/^(.+)\.([^.]+)$/);
+  if (!match) {
+    return null;
+  }
+
+  const baseStem = match[1]?.trim();
+  const environment = match[2]?.trim();
+  if (!baseStem || !environment) {
+    return null;
+  }
+
+  const targetPath = dir === "." ? `${baseStem}.config` : `${dir}/${baseStem}.config`;
+  return {
+    targetPath,
+    environment: normalizeToken(environment)
+  };
+}
+
+function generateConfigTransformRelations(fileRecords) {
+  const fileIdByPath = new Map(fileRecords.map((record) => [toPosixPath(record.path), record.id]));
+  const relations = [];
+  const seen = new Set();
+
+  for (const fileRecord of fileRecords) {
+    const transform = parseConfigTransformTarget(fileRecord);
+    if (!transform) {
+      continue;
+    }
+
+    const targetFileId = fileIdByPath.get(transform.targetPath);
+    if (!targetFileId || targetFileId === fileRecord.id) {
+      continue;
+    }
+
+    const key = relationKey(fileRecord.id, targetFileId, transform.environment);
+    if (seen.has(key)) {
+      continue;
+    }
+    seen.add(key);
+    relations.push({
+      from: fileRecord.id,
+      to: targetFileId,
+      note: transform.environment
+    });
+  }
+
+  relations.sort((a, b) => relationKey(a.from, a.to, a.note).localeCompare(relationKey(b.from, b.to, b.note)));
+  return relations;
+}
+
+function shouldExtractSqlReferences(filePath) {
+  return SQL_REFERENCE_SOURCE_EXTENSIONS.has(path.extname(filePath).toLowerCase());
+}
+
+function extractSqlObjectReferencesFromContent(content, filePath = "", sqlResourceReferenceMap = new Map()) {
+  const refs = new Set();
+  const ext = path.extname(filePath).toLowerCase();
+
+  if (ext === ".resx") {
+    for (const values of parseResxSqlReferenceMap(content).values()) {
+      for (const ref of values) {
+        refs.add(ref);
+      }
+    }
+  } else if (ext === ".settings") {
+    for (const values of parseSettingsSqlReferenceMap(content).values()) {
+      for (const ref of values) {
+        refs.add(ref);
+      }
+    }
+  }
+
+  for (const pattern of SQL_OBJECT_REFERENCE_PATTERNS) {
+    let match;
+    while ((match = pattern.exec(content)) !== null) {
+      for (const ref of extractSqlReferenceNamesFromString(match[1])) {
+        refs.add(ref);
+      }
+    }
+  }
+
+  if (sqlResourceReferenceMap.size > 0) {
+    for (const key of extractSqlResourceKeyReferences(content)) {
+      for (const ref of sqlResourceReferenceMap.get(key) ?? []) {
+        refs.add(ref);
+      }
+    }
+  }
+
+  return uniqueSorted([...refs]);
+}
+
+function decodeXmlEntities(value) {
+  return String(value)
+    .replace(/&quot;/g, '"')
+    .replace(/&apos;/g, "'")
+    .replace(/&lt;/g, "<")
+    .replace(/&gt;/g, ">")
+    .replace(/&amp;/g, "&");
+}
+
+function projectIdFor(filePath) {
+  return `project:${filePath}`;
+}
+
+function isProjectDefinitionFile(filePath) {
+  return PROJECT_DEFINITION_EXTENSIONS.has(path.extname(filePath).toLowerCase());
+}
+
+function resolveProjectRelativePath(baseFilePath, includePath) {
+  if (!includePath) {
+    return null;
+  }
+
+  const normalizedInclude = toPosixPath(decodeXmlEntities(includePath).trim().replace(/\\/g, "/"));
+  if (!normalizedInclude) {
+    return null;
+  }
+
+  const resolved = path.resolve(REPO_ROOT, path.dirname(baseFilePath), normalizedInclude);
+  const relPath = toPosixPath(path.relative(REPO_ROOT, resolved));
+  if (!relPath || relPath.startsWith("../")) {
+    return null;
+  }
+
+  return relPath;
+}
+
+function projectLanguageForExtension(ext) {
+  switch (ext) {
+    case ".vbproj":
+      return "vbnet";
+    case ".csproj":
+      return "csharp";
+    case ".fsproj":
+      return "fsharp";
+    case ".sln":
+      return "solution";
+    default:
+      return "dotnet";
+  }
+}
+
+function extractXmlTagValue(content, tagName) {
+  const match = content.match(new RegExp(`<${tagName}>([\\s\\S]*?)<\\/${tagName}>`, "i"));
+  return match ? decodeXmlEntities(match[1]).trim() : "";
+}
+
+function collectXmlIncludeValues(content, elementNames) {
+  const values = [];
+  const pattern = new RegExp(
+    `<(?:${elementNames.join("|")})\\b[^>]*\\bInclude="([^"]+)"[^>]*\\/?>`,
+    "gi"
+  );
+  let match;
+  while ((match = pattern.exec(content)) !== null) {
+    values.push(decodeXmlEntities(match[1]).trim());
+  }
+  return values;
+}
+
+function parseSolutionProject(fileRecord, indexedFileIds) {
+  const declaredMembers = [];
+  const referencesProjectRelations = [];
+  const includesFileRelations = [];
+  const fileRelationKeys = new Set();
+  const ext = path.extname(fileRecord.path).toLowerCase();
+  const fallbackName = path.basename(fileRecord.path, ext);
+  const projectPattern =
+    /^Project\([^)]*\)\s*=\s*"([^"]+)",\s*"([^"]+\.(?:vbproj|csproj|fsproj))",\s*"\{[^"]+\}"$/gim;
+
+  let match;
+  while ((match = projectPattern.exec(fileRecord.content)) !== null) {
+    const memberName = match[1].trim();
+    const memberPath = resolveProjectRelativePath(fileRecord.path, match[2]);
+    if (!memberPath) {
+      continue;
+    }
+    declaredMembers.push({ name: memberName, path: memberPath });
+    const targetId = projectIdFor(memberPath);
+    if (indexedFileIds.has(`file:${memberPath}`)) {
+      referencesProjectRelations.push({
+        from: projectIdFor(fileRecord.path),
+        to: targetId,
+        note: `solution_member:${memberName}`
+      });
+    }
+  }
+
+  for (const fileId of [`file:${fileRecord.path}`]) {
+    if (indexedFileIds.has(fileId) && !fileRelationKeys.has(fileId)) {
+      fileRelationKeys.add(fileId);
+      includesFileRelations.push({ from: projectIdFor(fileRecord.path), to: fileId });
+    }
+  }
+
+  const summaryParts = [`Solution ${fallbackName}`];
+  if (declaredMembers.length > 0) {
+    summaryParts.push(`Contains ${declaredMembers.length} project references`);
+  }
+
+  return {
+    project: {
+      id: projectIdFor(fileRecord.path),
+      path: fileRecord.path,
+      name: fallbackName,
+      kind: "solution",
+      language: projectLanguageForExtension(ext),
+      target_framework: "",
+      summary: `${summaryParts.join(". ")}.`,
+      file_count: includesFileRelations.length,
+      updated_at: fileRecord.updated_at,
+      source_of_truth: false,
+      trust_level: 78,
+      status: "active"
+    },
+    includesFileRelations,
+    referencesProjectRelations
+  };
+}
+
+function parseDotNetProject(fileRecord, indexedFileIds) {
+  const ext = path.extname(fileRecord.path).toLowerCase();
+  const fallbackName = path.basename(fileRecord.path, ext);
+  const assemblyName = extractXmlTagValue(fileRecord.content, "AssemblyName");
+  const rootNamespace = extractXmlTagValue(fileRecord.content, "RootNamespace");
+  const targetFrameworkRaw =
+    extractXmlTagValue(fileRecord.content, "TargetFramework") ||
+    extractXmlTagValue(fileRecord.content, "TargetFrameworkVersion") ||
+    extractXmlTagValue(fileRecord.content, "TargetFrameworks");
+  const targetFramework = targetFrameworkRaw.split(";")[0].trim();
+  const includeCandidates = collectXmlIncludeValues(fileRecord.content, [
+    "Compile",
+    "Content",
+    "EmbeddedResource",
+    "None",
+    "Page",
+    "ApplicationDefinition"
+  ]);
+  const projectReferenceCandidates = collectXmlIncludeValues(fileRecord.content, ["ProjectReference"]);
+  const includesFileRelations = [];
+  const referencesProjectRelations = [];
+  const fileRelationKeys = new Set();
+
+  const addFileRelation = (relPath) => {
+    const fileId = `file:${relPath}`;
+    if (!indexedFileIds.has(fileId) || fileRelationKeys.has(fileId)) {
+      return;
+    }
+    fileRelationKeys.add(fileId);
+    includesFileRelations.push({
+      from: projectIdFor(fileRecord.path),
+      to: fileId
+    });
+  };
+
+  addFileRelation(fileRecord.path);
+
+  for (const includePath of includeCandidates) {
+    const relPath = resolveProjectRelativePath(fileRecord.path, includePath);
+    if (!relPath) {
+      continue;
+    }
+    addFileRelation(relPath);
+  }
+
+  for (const includePath of projectReferenceCandidates) {
+    const relPath = resolveProjectRelativePath(fileRecord.path, includePath);
+    if (!relPath) {
+      continue;
+    }
+    const targetFileId = `file:${relPath}`;
+    if (!indexedFileIds.has(targetFileId)) {
+      continue;
+    }
+    referencesProjectRelations.push({
+      from: projectIdFor(fileRecord.path),
+      to: projectIdFor(relPath),
+      note: includePath
+    });
+  }
+
+  const summaryParts = [
+    `${projectLanguageForExtension(ext).toUpperCase()} project ${assemblyName || rootNamespace || fallbackName}`
+  ];
+  if (targetFramework) {
+    summaryParts.push(`Target framework ${targetFramework}`);
+  }
+  if (includesFileRelations.length > 1) {
+    summaryParts.push(`Includes ${includesFileRelations.length - 1} indexed project files`);
+  }
+  if (referencesProjectRelations.length > 0) {
+    summaryParts.push(`References ${referencesProjectRelations.length} projects`);
+  }
+
+  return {
+    project: {
+      id: projectIdFor(fileRecord.path),
+      path: fileRecord.path,
+      name: assemblyName || rootNamespace || fallbackName,
+      kind: "project",
+      language: projectLanguageForExtension(ext),
+      target_framework: targetFramework,
+      summary: `${summaryParts.join(". ")}.`,
+      file_count: includesFileRelations.length,
+      updated_at: fileRecord.updated_at,
+      source_of_truth: false,
+      trust_level: 80,
+      status: "active"
+    },
+    includesFileRelations,
+    referencesProjectRelations
+  };
+}
+
+function generateProjects(fileRecords) {
+  const indexedFileIds = new Set(fileRecords.map((record) => record.id));
+  const projectRecords = [];
+  const includesFileRelations = [];
+  const referencesProjectRelations = [];
+  const includeKeys = new Set();
+  const referenceKeys = new Set();
+
+  for (const fileRecord of fileRecords) {
+    if (!isProjectDefinitionFile(fileRecord.path)) {
+      continue;
+    }
+
+    const ext = path.extname(fileRecord.path).toLowerCase();
+    const parsed =
+      ext === ".sln"
+        ? parseSolutionProject(fileRecord, indexedFileIds)
+        : parseDotNetProject(fileRecord, indexedFileIds);
+
+    projectRecords.push(parsed.project);
+
+    for (const relation of parsed.includesFileRelations) {
+      const key = relationKey(relation.from, relation.to);
+      if (includeKeys.has(key)) {
+        continue;
+      }
+      includeKeys.add(key);
+      includesFileRelations.push(relation);
+    }
+
+    for (const relation of parsed.referencesProjectRelations) {
+      const key = relationKey(relation.from, relation.to, relation.note);
+      if (referenceKeys.has(key)) {
+        continue;
+      }
+      referenceKeys.add(key);
+      referencesProjectRelations.push(relation);
+    }
+  }
+
+  projectRecords.sort((a, b) => a.path.localeCompare(b.path));
+  includesFileRelations.sort((a, b) => relationKey(a.from, a.to).localeCompare(relationKey(b.from, b.to)));
+  referencesProjectRelations.sort((a, b) =>
+    relationKey(a.from, a.to, a.note).localeCompare(relationKey(b.from, b.to, b.note))
+  );
+
+  return {
+    projects: projectRecords,
+    includesFileRelations,
+    referencesProjectRelations
+  };
+}
+
+function removeChunkStateForFile(fileId, chunkRecordMap, definesRelationMap, callsRelationMap, importsRelationMap, callsSqlRelationMap) {
+  const removedChunkIds = new Set();
+
+  for (const [chunkId, chunkRecord] of chunkRecordMap.entries()) {
+    if (chunkRecord.file_id === fileId) {
+      removedChunkIds.add(chunkId);
+      chunkRecordMap.delete(chunkId);
+    }
+  }
+
+  if (removedChunkIds.size === 0) {
+    return;
+  }
+
+  for (const [key, relation] of definesRelationMap.entries()) {
+    if (relation.from === fileId || removedChunkIds.has(relation.to)) {
+      definesRelationMap.delete(key);
+    }
+  }
+
+  for (const [key, relation] of callsRelationMap.entries()) {
+    if (removedChunkIds.has(relation.from) || removedChunkIds.has(relation.to)) {
+      callsRelationMap.delete(key);
+    }
+  }
+
+  for (const [key, relation] of importsRelationMap.entries()) {
+    if (removedChunkIds.has(relation.from)) {
+      importsRelationMap.delete(key);
+    }
+  }
+
+  for (const [key, relation] of callsSqlRelationMap.entries()) {
+    if (relation.from === fileId || removedChunkIds.has(relation.to)) {
+      callsSqlRelationMap.delete(key);
+    }
+  }
+}
+
+function hydrateIncrementalChunkState(fileRecords) {
+  const fileIdSet = new Set(fileRecords.map((record) => record.id));
+  const chunkRecordMap = new Map();
+  const definesRelationMap = new Map();
+  const callsRelationMap = new Map();
+  const importsRelationMap = new Map();
+  const callsSqlRelationMap = new Map();
+
+  for (const record of readJsonlSafe(path.join(CACHE_DIR, "entities.chunk.jsonl"))) {
+    if (!record || typeof record !== "object") continue;
+    const chunkId = String(record.id ?? "");
+    const fileId = String(record.file_id ?? "");
+    if (!chunkId || !fileIdSet.has(fileId)) {
+      continue;
+    }
+    chunkRecordMap.set(chunkId, {
+      ...record,
+      id: chunkId,
+      file_id: fileId
+    });
+  }
+
+  const chunkIdSet = new Set(chunkRecordMap.keys());
+
+  for (const record of readJsonlSafe(path.join(CACHE_DIR, "relations.defines.jsonl"))) {
+    if (!record || typeof record !== "object") continue;
+    const from = String(record.from ?? "");
+    const to = String(record.to ?? "");
+    if (!fileIdSet.has(from) || !chunkIdSet.has(to)) {
+      continue;
+    }
+    definesRelationMap.set(relationKey(from, to), { from, to });
+  }
+
+  for (const record of readJsonlSafe(path.join(CACHE_DIR, "relations.calls.jsonl"))) {
+    if (!record || typeof record !== "object") continue;
+    const from = String(record.from ?? "");
+    const to = String(record.to ?? "");
+    const callType = String(record.call_type ?? "direct");
+    if (!chunkIdSet.has(from) || !chunkIdSet.has(to)) {
+      continue;
+    }
+    callsRelationMap.set(relationKey(from, to, callType), {
+      from,
+      to,
+      call_type: callType
+    });
+  }
+
+  for (const record of readJsonlSafe(path.join(CACHE_DIR, "relations.imports.jsonl"))) {
+    if (!record || typeof record !== "object") continue;
+    const from = String(record.from ?? "");
+    const to = String(record.to ?? "");
+    const importName = String(record.import_name ?? "");
+    if (!chunkIdSet.has(from) || !fileIdSet.has(to)) {
+      continue;
+    }
+    importsRelationMap.set(relationKey(from, to, importName), {
+      from,
+      to,
+      import_name: importName
+    });
   }
-  fs.writeFileSync(filePath, `${lines.join("\n")}\n`, "utf8");
-}
 
-function readJsonlSafe(filePath) {
-  if (!fs.existsSync(filePath)) {
-    return [];
+  for (const record of readJsonlSafe(path.join(CACHE_DIR, "relations.calls_sql.jsonl"))) {
+    if (!record || typeof record !== "object") continue;
+    const from = String(record.from ?? "");
+    const to = String(record.to ?? "");
+    const note = String(record.note ?? "");
+    if (!fileIdSet.has(from) || !chunkIdSet.has(to)) {
+      continue;
+    }
+    callsSqlRelationMap.set(relationKey(from, to, note), {
+      from,
+      to,
+      note
+    });
   }
 
-  return fs
-    .readFileSync(filePath, "utf8")
-    .split(/\r?\n/)
-    .map((line) => line.trim())
-    .filter(Boolean)
-    .map((line) => {
-      try {
-        return JSON.parse(line);
-      } catch {
-        return null;
-      }
-    })
-    .filter((record) => record !== null);
+  return {
+    chunkRecordMap,
+    definesRelationMap,
+    callsRelationMap,
+    importsRelationMap,
+    callsSqlRelationMap
+  };
 }
 
 function normalizeRuleTokens(ruleRecord) {
@@ -559,6 +2070,198 @@ function chunkIdFor(filePath, chunk) {
   return `chunk:${filePath}:${chunk.name}:${startLine}-${endLine}`;
 }
 
+function generateChunkDescription(chunk) {
+  const parts = [chunk.kind];
+  if (chunk.exported) parts.push("exported");
+  if (chunk.async) parts.push("async");
+  parts.push(chunk.signature);
+
+  if (typeof chunk.description === "string" && chunk.description.trim().length > 10) {
+    parts.push(normalizeWhitespace(chunk.description).slice(0, 200));
+  }
+
+  // Extract leading JSDoc/comment from body
+  // Match leading JSDoc (/** */), block (/* */) and line (//) comments
+  const commentMatch = chunk.body.match(/^(?:\s*(?:\/\*[\s\S]*?\*\/|\/\/[^\n]*)[\s\n]*)+/);
+  if (commentMatch) {
+    const cleaned = commentMatch[0]
+      .replace(/\/\*\*|\*\/|\*|\/\//g, "")
+      .replace(/\s+/g, " ").trim()
+      .slice(0, 200);
+    if (cleaned.length > 10) parts.push(cleaned);
+  }
+
+  return parts.join(". ") + ".";
+}
+
+function generateModuleSummary(dir, files, exportNames, repoRoot = REPO_ROOT) {
+  // Check for README.md in directory
+  const readmePath = path.join(repoRoot, dir, "README.md");
+  if (fs.existsSync(readmePath)) {
+    try {
+      const content = fs.readFileSync(readmePath, "utf8");
+      // Skip first heading line, take first 300 chars
+      const lines = content.split(/\r?\n/);
+      const startIdx = lines.findIndex(l => !l.startsWith("#") && l.trim().length > 0);
+      if (startIdx >= 0) {
+        const excerpt = lines.slice(startIdx).join(" ").trim().slice(0, 300);
+        if (excerpt.length > 20) return excerpt;
+      }
+    } catch {
+      // fall through to auto-generated summary
+    }
+  }
+
+  const name = path.basename(dir);
+  const codeFiles = files.filter(f => f.kind === "CODE");
+  const docFiles = files.filter(f => f.kind !== "CODE");
+
+  const parts = [`Module ${name}`];
+  parts.push(`Contains ${files.length} files (${codeFiles.length} code, ${docFiles.length} docs)`);
+
+  // Detect common file extension pattern
+  const exts = new Set(codeFiles.map(f => path.extname(f.path).toLowerCase()));
+  if (exts.size === 1) {
+    const ext = [...exts][0];
+    const extNames = { ".ts": "TypeScript", ".js": "JavaScript", ".mjs": "JavaScript (ESM)", ".tsx": "TypeScript React" };
+    if (extNames[ext]) parts.push(`${extNames[ext]} source files`);
+  }
+
+  if (exportNames.length > 0) {
+    parts.push(`Key exports: ${exportNames.slice(0, 5).join(", ")}`);
+  }
+
+  return parts.join(". ") + ".";
+}
+
+function generateModules(fileRecords, chunkRecords) {
+  const dirFiles = new Map();
+  const dirChunks = new Map();
+  const fileById = new Map(fileRecords.map(f => [f.id, f]));
+
+  for (const file of fileRecords) {
+    const dir = path.dirname(file.path);
+    if (!dirFiles.has(dir)) dirFiles.set(dir, []);
+    dirFiles.get(dir).push(file);
+  }
+
+  for (const chunk of chunkRecords) {
+    if (!chunk.exported || isWindowChunkId(chunk.id)) continue;
+    const file = fileById.get(chunk.file_id);
+    if (!file) continue;
+    const dir = path.dirname(file.path);
+    if (!dirChunks.has(dir)) dirChunks.set(dir, []);
+    dirChunks.get(dir).push(chunk);
+  }
+
+  const modules = [];
+  const containsRelations = [];
+  const containsModuleRelations = [];
+  const exportsRelations = [];
+
+  const MIN_MODULE_FILES = 2;
+
+  for (const [dir, files] of dirFiles) {
+    if (files.length < MIN_MODULE_FILES) continue;
+
+    const exports = dirChunks.get(dir) || [];
+    const exportNames = [...new Set(exports.slice(0, 20).map(c => c.name))];
+    const moduleId = `module:${dir}`;
+
+    modules.push({
+      id: moduleId,
+      path: dir,
+      name: path.basename(dir),
+      summary: generateModuleSummary(dir, files, exportNames),
+      file_count: files.length,
+      exported_symbols: exportNames.join(", "),
+      updated_at: files.reduce((latest, f) => f.updated_at > latest ? f.updated_at : latest, ""),
+      source_of_truth: false,
+      trust_level: 75,
+      status: "active"
+    });
+
+    // CONTAINS: Module -> File
+    for (const file of files) {
+      containsRelations.push({ from: moduleId, to: file.id });
+    }
+
+    // EXPORTS: Module -> Chunk
+    for (const chunk of exports) {
+      exportsRelations.push({ from: moduleId, to: chunk.id });
+    }
+  }
+
+  // CONTAINS_MODULE: parent Module -> child Module
+  const moduleDirs = new Set(modules.map(m => m.path));
+  for (const dir of moduleDirs) {
+    const parent = path.dirname(dir);
+    if (parent !== dir && moduleDirs.has(parent)) {
+      containsModuleRelations.push({
+        from: `module:${parent}`,
+        to: `module:${dir}`
+      });
+    }
+  }
+
+  return { modules, containsRelations, containsModuleRelations, exportsRelations };
+}
+
+function isWindowChunkId(chunkId) {
+  return typeof chunkId === "string" && chunkId.includes(":window:");
+}
+
+function splitChunkIntoWindows(chunkRecord, options) {
+  const { windowLines, overlapLines, splitMinLines, maxWindows, chunkBody } = options;
+  const sourceBody = typeof chunkBody === "string" ? chunkBody : chunkRecord.body;
+  const lines = sourceBody.split(/\r?\n/);
+  const totalLines = lines.length;
+  if (totalLines < splitMinLines || totalLines <= windowLines) {
+    return [];
+  }
+
+  const windows = [];
+  const safeOverlap = Math.max(0, Math.min(overlapLines, windowLines - 1));
+  let start = 0;
+  let windowIndex = 1;
+
+  while (start < totalLines && windows.length < maxWindows) {
+    const isLastAllowedWindow = windows.length + 1 >= maxWindows;
+    const end = isLastAllowedWindow ? totalLines : Math.min(totalLines, start + windowLines);
+    const windowStartLine = chunkRecord.start_line + start;
+    const windowEndLine = chunkRecord.start_line + Math.max(0, end - 1);
+    const windowBody = lines.slice(start, end).join("\n");
+    const persistedBody = isLastAllowedWindow ? windowBody : windowBody.slice(0, MAX_BODY_CHARS);
+    windows.push({
+      id: `${chunkRecord.id}:window:${windowIndex}:${windowStartLine}-${windowEndLine}`,
+      file_id: chunkRecord.file_id,
+      name: `${chunkRecord.name}#window${windowIndex}`,
+      kind: chunkRecord.kind,
+      signature: `${chunkRecord.signature} [window ${windowIndex}]`,
+      body: persistedBody,
+      description: chunkRecord.description || "",
+      start_line: windowStartLine,
+      end_line: windowEndLine,
+      language: chunkRecord.language,
+      exported: chunkRecord.exported || false,
+      checksum: checksum(Buffer.from(windowBody)),
+      updated_at: chunkRecord.updated_at,
+      trust_level: chunkRecord.trust_level,
+      status: chunkRecord.status,
+      source_of_truth: chunkRecord.source_of_truth
+    });
+
+    if (end >= totalLines) {
+      break;
+    }
+
+    start = end - safeOverlap;
+    windowIndex += 1;
+  }
+
+  return windows;
+}
+
 function main() {
   const { mode, verbose } = parseArgs(process.argv);
   const configPath = path.join(CONTEXT_DIR, "config.yaml");
@@ -582,6 +2285,25 @@ function main() {
 
   const rules = parseRules(fs.readFileSync(rulesPath, "utf8"));
   const { candidates, incrementalMode, deletedRelPaths } = collectCandidateFiles(sourcePaths, mode);
+  const chunkWindowLines = parsePositiveIntegerEnv(
+    "CORTEX_CHUNK_WINDOW_LINES",
+    DEFAULT_CHUNK_WINDOW_LINES
+  );
+  const chunkOverlapLines = Math.max(
+    0,
+    Math.min(
+      chunkWindowLines - 1,
+      parseNonNegativeIntegerEnv("CORTEX_CHUNK_OVERLAP_LINES", DEFAULT_CHUNK_OVERLAP_LINES)
+    )
+  );
+  const chunkSplitMinLines = Math.max(
+    chunkWindowLines + 1,
+    parsePositiveIntegerEnv("CORTEX_CHUNK_SPLIT_MIN_LINES", DEFAULT_CHUNK_SPLIT_MIN_LINES)
+  );
+  const chunkMaxWindows = parsePositiveIntegerEnv(
+    "CORTEX_CHUNK_MAX_WINDOWS",
+    DEFAULT_CHUNK_MAX_WINDOWS
+  );
 
   const fileRecordMap = new Map();
   const adrRecordMap = new Map();
@@ -715,23 +2437,70 @@ function main() {
 
   const fileRecords = [...fileRecordMap.values()].sort((a, b) => a.path.localeCompare(b.path));
   const adrRecords = [...adrRecordMap.values()].sort((a, b) => a.path.localeCompare(b.path));
+  const indexedFileIds = new Set(fileRecords.map((record) => record.id));
+  const changedFileIds = new Set(
+    [...candidates].map((absolutePath) => `file:${toPosixPath(path.relative(REPO_ROOT, absolutePath))}`)
+  );
+
+  const {
+    chunkRecordMap,
+    definesRelationMap,
+    callsRelationMap,
+    importsRelationMap,
+    callsSqlRelationMap
+  } = incrementalMode
+    ? hydrateIncrementalChunkState(fileRecords)
+    : {
+        chunkRecordMap: new Map(),
+        definesRelationMap: new Map(),
+        callsRelationMap: new Map(),
+        importsRelationMap: new Map(),
+        callsSqlRelationMap: new Map()
+      };
 
-  // Extract chunks from code files
-  const chunkRecords = [];
-  const definesRelations = [];
-  const callsRelations = [];
-  const importsRelations = [];
+  const cachedChunkFileIds = new Set(
+    [...chunkRecordMap.values()].map((record) => String(record.file_id ?? "")).filter(Boolean)
+  );
+  const cachedSqlReferenceFileIds = new Set(
+    [...callsSqlRelationMap.values()].map((record) => String(record.from ?? "")).filter(Boolean)
+  );
+  const usesConfigKeyRelationMap = new Map();
+  const usesResourceKeyRelationMap = new Map();
+  const usesSettingKeyRelationMap = new Map();
+
+  // Extract chunks from changed or uncached code files
+  let windowedChunkCount = 0;
+  const sqlChunkIdsByAlias = new Map();
+  const configChunkIdsByAlias = new Map();
+  const resourceChunkIdsByAlias = new Map();
+  const settingChunkIdsByAlias = new Map();
+  const deferredSqlCallEdges = [];
 
   for (const fileRecord of fileRecords) {
-    if (fileRecord.kind !== "CODE") continue;
-
     const ext = path.extname(fileRecord.path).toLowerCase();
-    const supportedForChunking = [".js", ".mjs", ".cjs", ".ts"].includes(ext);
-    if (!supportedForChunking) continue;
+    const parser = getChunkParserForExtension(ext);
+    const isStructuredNonCodeChunk = STRUCTURED_NON_CODE_CHUNK_EXTENSIONS.has(ext);
+    if (fileRecord.kind !== "CODE" && !isStructuredNonCodeChunk) continue;
+    if (!parser) continue;
+    if (typeof parser.isAvailable === "function" && !parser.isAvailable()) continue;
+
+    const shouldParseFile =
+      !incrementalMode || changedFileIds.has(fileRecord.id) || !cachedChunkFileIds.has(fileRecord.id);
+    if (!shouldParseFile) {
+      continue;
+    }
+
+    removeChunkStateForFile(
+      fileRecord.id,
+      chunkRecordMap,
+      definesRelationMap,
+      callsRelationMap,
+      importsRelationMap,
+      callsSqlRelationMap
+    );
 
     try {
-      const language = ext === ".ts" ? "typescript" : "javascript";
-      const parseResult = parseCode(fileRecord.content, fileRecord.path, language);
+      const parseResult = parser.parse(fileRecord.content, fileRecord.path, parser.language);
 
       if (parseResult.errors.length > 0 && verbose) {
         console.log(`[ingest] parse errors in ${fileRecord.path}:`, parseResult.errors[0].message);
@@ -747,6 +2516,51 @@ function main() {
           chunkIdsByName.set(chunk.name, []);
         }
         chunkIdsByName.get(chunk.name).push(chunkId);
+        if (parser.language === "sql") {
+          for (const alias of sqlChunkAliases(chunk.name)) {
+            if (!sqlChunkIdsByAlias.has(alias)) {
+              sqlChunkIdsByAlias.set(alias, []);
+            }
+            sqlChunkIdsByAlias.get(alias).push(chunkId);
+          }
+          deferredSqlCallEdges.push({
+            chunkId,
+            calls: Array.isArray(chunk.calls) ? chunk.calls : []
+          });
+        } else if (parser.language === "config") {
+          for (const alias of configChunkAliases(chunk)) {
+            if (!configChunkIdsByAlias.has(alias)) {
+              configChunkIdsByAlias.set(alias, []);
+            }
+            configChunkIdsByAlias.get(alias).push(chunkId);
+          }
+          deferredSqlCallEdges.push({
+            chunkId,
+            calls: Array.isArray(chunk.calls) ? chunk.calls : []
+          });
+        } else if (parser.language === "resource") {
+          for (const alias of namedEntryChunkAliases(chunk)) {
+            if (!resourceChunkIdsByAlias.has(alias)) {
+              resourceChunkIdsByAlias.set(alias, []);
+            }
+            resourceChunkIdsByAlias.get(alias).push(chunkId);
+          }
+          deferredSqlCallEdges.push({
+            chunkId,
+            calls: Array.isArray(chunk.calls) ? chunk.calls : []
+          });
+        } else if (parser.language === "settings") {
+          for (const alias of namedEntryChunkAliases(chunk)) {
+            if (!settingChunkIdsByAlias.has(alias)) {
+              settingChunkIdsByAlias.set(alias, []);
+            }
+            settingChunkIdsByAlias.get(alias).push(chunkId);
+          }
+          deferredSqlCallEdges.push({
+            chunkId,
+            calls: Array.isArray(chunk.calls) ? chunk.calls : []
+          });
+        }
 
         const chunkRecord = {
           id: chunkId,
@@ -754,35 +2568,59 @@ function main() {
           name: chunk.name,
           kind: chunk.kind,
           signature: chunk.signature,
-          body: chunk.body.slice(0, 12000), // Limit chunk body size
+          body: chunk.body.slice(0, MAX_BODY_CHARS), // Limit chunk body size
+          description: generateChunkDescription(chunk),
           start_line: chunk.startLine,
           end_line: chunk.endLine,
           language: chunk.language,
+          exported: Boolean(chunk.exported),
           checksum: checksum(Buffer.from(chunk.body)),
           updated_at: fileRecord.updated_at,
-          trust_level: fileRecord.trust_level
+          trust_level: fileRecord.trust_level,
+          status:
+            typeof fileRecord.status === "string" && fileRecord.status.trim().length > 0
+              ? fileRecord.status
+              : "active",
+          source_of_truth: Boolean(fileRecord.source_of_truth)
         };
-        chunkRecords.push(chunkRecord);
+        chunkRecordMap.set(chunkId, chunkRecord);
 
         // DEFINES relation: File -> Chunk
-        definesRelations.push({
+        definesRelationMap.set(relationKey(fileRecord.id, chunkId), {
           from: fileRecord.id,
           to: chunkId
         });
 
+        const windows = splitChunkIntoWindows(chunkRecord, {
+          windowLines: chunkWindowLines,
+          overlapLines: chunkOverlapLines,
+          splitMinLines: chunkSplitMinLines,
+          maxWindows: chunkMaxWindows,
+          chunkBody: chunk.body
+        });
+        if (windows.length > 0) {
+          windowedChunkCount += windows.length;
+          for (const windowChunk of windows) {
+            chunkRecordMap.set(windowChunk.id, windowChunk);
+            definesRelationMap.set(relationKey(fileRecord.id, windowChunk.id), {
+              from: fileRecord.id,
+              to: windowChunk.id
+            });
+          }
+        }
+
         // IMPORTS relations: Chunk -> File
         for (const importPath of chunk.imports || []) {
-          // Normalize relative imports to absolute paths
-          if (importPath.startsWith(".")) {
-            const dirName = path.dirname(fileRecord.path);
-            const resolvedImport = path.posix.normalize(path.posix.join(dirName, importPath));
-            const targetFileId = `file:${resolvedImport}`;
-            importsRelations.push({
-              from: chunkId,
-              to: targetFileId,
-              import_name: importPath
-            });
+          const targetFileId = resolveRelativeImportTargetId(fileRecord.path, importPath, indexedFileIds);
+          if (!targetFileId) {
+            continue;
           }
+
+          importsRelationMap.set(relationKey(chunkId, targetFileId, importPath), {
+            from: chunkId,
+            to: targetFileId,
+            import_name: importPath
+          });
         }
       }
 
@@ -797,7 +2635,7 @@ function main() {
               continue;
             }
             seenCallEdges.add(callKey);
-            callsRelations.push({
+            callsRelationMap.set(relationKey(chunkId, targetChunkId, "direct"), {
               from: chunkId,
               to: targetChunkId,
               call_type: "direct"
@@ -812,13 +2650,194 @@ function main() {
     }
   }
 
+  const chunkRecords = [...chunkRecordMap.values()].sort((a, b) => String(a.id).localeCompare(String(b.id)));
+
   // Filter CALLS relations to only valid targets (chunks that actually exist)
   const chunkIdSet = new Set(chunkRecords.map(c => c.id));
-  const validCallsRelations = callsRelations.filter(rel => chunkIdSet.has(rel.to));
+  const validDefinesRelations = [...definesRelationMap.values()].filter(
+    (rel) => indexedFileIds.has(rel.from) && chunkIdSet.has(rel.to)
+  );
+  const totalCallsRelations = callsRelationMap.size;
+  for (const edge of deferredSqlCallEdges) {
+    for (const calledName of edge.calls) {
+      for (const alias of sqlChunkAliases(calledName)) {
+        const targetChunkIds = sqlChunkIdsByAlias.get(alias) || [];
+        for (const targetChunkId of targetChunkIds) {
+          if (targetChunkId === edge.chunkId) {
+            continue;
+          }
+          callsRelationMap.set(relationKey(edge.chunkId, targetChunkId, "sql_reference"), {
+            from: edge.chunkId,
+            to: targetChunkId,
+            call_type: "sql_reference"
+          });
+        }
+      }
+    }
+  }
+  const validCallsRelations = [...callsRelationMap.values()].filter(
+    (rel) => chunkIdSet.has(rel.from) && chunkIdSet.has(rel.to)
+  );
+  const validImportsRelations = [...importsRelationMap.values()].filter(
+    (rel) => chunkIdSet.has(rel.from) && indexedFileIds.has(rel.to)
+  );
+  const sqlDefinitionsChanged =
+    incrementalMode &&
+    fileRecords.some(
+      (fileRecord) =>
+        changedFileIds.has(fileRecord.id) && path.extname(fileRecord.path).toLowerCase() === ".sql"
+    );
+  const sqlResourceReferenceMap = buildSqlResourceReferenceMap(fileRecords);
+  for (const fileRecord of fileRecords) {
+    if (!shouldExtractSqlReferences(fileRecord.path)) {
+      continue;
+    }
+
+    const shouldAnalyzeFile =
+      !incrementalMode ||
+      sqlDefinitionsChanged ||
+      changedFileIds.has(fileRecord.id) ||
+      !cachedSqlReferenceFileIds.has(fileRecord.id);
+    if (!shouldAnalyzeFile) {
+      continue;
+    }
+
+    for (const [key, relation] of callsSqlRelationMap.entries()) {
+      if (relation.from === fileRecord.id) {
+        callsSqlRelationMap.delete(key);
+      }
+    }
+
+    for (const refName of extractSqlObjectReferencesFromContent(
+      fileRecord.content,
+      fileRecord.path,
+      sqlResourceReferenceMap
+    )) {
+      for (const alias of sqlChunkAliases(refName)) {
+        const targetChunkIds = sqlChunkIdsByAlias.get(alias) || [];
+        for (const targetChunkId of targetChunkIds) {
+          callsSqlRelationMap.set(relationKey(fileRecord.id, targetChunkId, refName), {
+            from: fileRecord.id,
+            to: targetChunkId,
+            note: refName
+          });
+        }
+      }
+    }
+  }
+  const validCallsSqlRelations = [...callsSqlRelationMap.values()].filter(
+    (rel) => indexedFileIds.has(rel.from) && chunkIdSet.has(rel.to)
+  );
+  for (const fileRecord of fileRecords) {
+    if (!shouldExtractNamedResourceReferences(fileRecord.path)) {
+      continue;
+    }
+
+    for (const key of extractSqlResourceKeyReferences(fileRecord.content)) {
+      for (const targetChunkId of resourceChunkIdsByAlias.get(key) ?? []) {
+        usesResourceKeyRelationMap.set(relationKey(fileRecord.id, targetChunkId, key), {
+          from: fileRecord.id,
+          to: targetChunkId,
+          note: key
+        });
+      }
+      for (const targetChunkId of settingChunkIdsByAlias.get(key) ?? []) {
+        usesSettingKeyRelationMap.set(relationKey(fileRecord.id, targetChunkId, key), {
+          from: fileRecord.id,
+          to: targetChunkId,
+          note: key
+        });
+      }
+    }
+
+    for (const key of extractConfigKeyReferences(fileRecord.content)) {
+      for (const targetChunkId of configChunkIdsByAlias.get(key) ?? []) {
+        usesConfigKeyRelationMap.set(relationKey(fileRecord.id, targetChunkId, key), {
+          from: fileRecord.id,
+          to: targetChunkId,
+          note: key
+        });
+      }
+    }
+  }
+  for (const relation of generateConfigTransformKeyRelations(fileRecords, chunkRecords)) {
+    usesConfigKeyRelationMap.set(relationKey(relation.from, relation.to, relation.note), relation);
+  }
+  const validUsesConfigKeyRelations = [...usesConfigKeyRelationMap.values()].filter(
+    (rel) => indexedFileIds.has(rel.from) && chunkIdSet.has(rel.to)
+  );
+  const validUsesResourceKeyRelations = [...usesResourceKeyRelationMap.values()].filter(
+    (rel) => indexedFileIds.has(rel.from) && chunkIdSet.has(rel.to)
+  );
+  const validUsesSettingKeyRelations = [...usesSettingKeyRelationMap.values()].filter(
+    (rel) => indexedFileIds.has(rel.from) && chunkIdSet.has(rel.to)
+  );
 
   if (verbose && chunkRecords.length > 0) {
     console.log(`[ingest] extracted ${chunkRecords.length} chunks from ${fileRecords.filter(f => f.kind === "CODE").length} code files`);
-    console.log(`[ingest] ${validCallsRelations.length} call relations (${callsRelations.length - validCallsRelations.length} filtered)`);
+    if (windowedChunkCount > 0) {
+      console.log(
+        `[ingest] overlap windows added=${windowedChunkCount} (window_lines=${chunkWindowLines}, overlap_lines=${chunkOverlapLines}, max_windows=${chunkMaxWindows})`
+      );
+    }
+    console.log(`[ingest] ${validCallsRelations.length} call relations (${totalCallsRelations - validCallsRelations.length} filtered)`);
+    if (validCallsSqlRelations.length > 0) {
+      console.log(`[ingest] sql call links=${validCallsSqlRelations.length}`);
+    }
+    if (validUsesConfigKeyRelations.length > 0) {
+      console.log(`[ingest] uses_config_key=${validUsesConfigKeyRelations.length}`);
+    }
+    if (validUsesResourceKeyRelations.length > 0 || validUsesSettingKeyRelations.length > 0) {
+      console.log(
+        `[ingest] uses_resource_key=${validUsesResourceKeyRelations.length} uses_setting_key=${validUsesSettingKeyRelations.length}`
+      );
+    }
+  }
+
+  // Generate Module entities and relations
+  const moduleResult = generateModules(fileRecords, chunkRecords);
+  const moduleRecords = moduleResult.modules;
+  const moduleContainsRelations = moduleResult.containsRelations;
+  const moduleContainsModuleRelations = moduleResult.containsModuleRelations;
+  const moduleExportsRelations = moduleResult.exportsRelations;
+  const projectResult = generateProjects(fileRecords);
+  const projectRecords = projectResult.projects;
+  const projectIncludesFileRelations = projectResult.includesFileRelations;
+  const projectReferencesProjectRelations = projectResult.referencesProjectRelations;
+  const namedResourceRelationResult = generateNamedResourceRelations(fileRecords);
+  const usesResourceRelations = namedResourceRelationResult.usesResourceRelations;
+  const usesSettingRelations = namedResourceRelationResult.usesSettingRelations;
+  const configIncludeRelations = generateConfigIncludeRelations(fileRecords);
+  const machineConfigRelations = generateMachineConfigRelations(fileRecords);
+  const sectionHandlerRelations = generateSectionHandlerRelations(fileRecords);
+  const usesConfigRelations = uniqueRelations([
+    ...namedResourceRelationResult.usesConfigRelations,
+    ...configIncludeRelations,
+    ...machineConfigRelations,
+    ...sectionHandlerRelations
+  ]);
+  const configTransformRelations = generateConfigTransformRelations(fileRecords);
+
+  if (verbose && moduleRecords.length > 0) {
+    console.log(`[ingest] modules=${moduleRecords.length} contains=${moduleContainsRelations.length} contains_module=${moduleContainsModuleRelations.length} exports=${moduleExportsRelations.length}`);
+  }
+  if (verbose && projectRecords.length > 0) {
+    console.log(
+      `[ingest] projects=${projectRecords.length} includes_file=${projectIncludesFileRelations.length} references_project=${projectReferencesProjectRelations.length}`
+    );
+  }
+  if (
+    verbose &&
+    (
+      usesResourceRelations.length > 0 ||
+      usesSettingRelations.length > 0 ||
+      usesConfigRelations.length > 0 ||
+      configTransformRelations.length > 0
+    )
+  ) {
+    console.log(
+      `[ingest] uses_resource=${usesResourceRelations.length} uses_setting=${usesSettingRelations.length} uses_config=${usesConfigRelations.length} transforms_config=${configTransformRelations.length}`
+    );
   }
 
   const ruleRecords = rules.map((rule) => ({
@@ -920,9 +2939,27 @@ function main() {
   writeJsonl(path.join(CACHE_DIR, "relations.supersedes.jsonl"), supersedesRelations);
   writeJsonl(path.join(CACHE_DIR, "relations.constrains.jsonl"), constrainsRelations);
   writeJsonl(path.join(CACHE_DIR, "relations.implements.jsonl"), implementsRelations);
-  writeJsonl(path.join(CACHE_DIR, "relations.defines.jsonl"), definesRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.defines.jsonl"), validDefinesRelations);
   writeJsonl(path.join(CACHE_DIR, "relations.calls.jsonl"), validCallsRelations);
-  writeJsonl(path.join(CACHE_DIR, "relations.imports.jsonl"), importsRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.imports.jsonl"), validImportsRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.calls_sql.jsonl"), validCallsSqlRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.uses_config_key.jsonl"), validUsesConfigKeyRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.uses_resource_key.jsonl"), validUsesResourceKeyRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.uses_setting_key.jsonl"), validUsesSettingKeyRelations);
+  writeJsonl(path.join(CACHE_DIR, "entities.module.jsonl"), moduleRecords);
+  writeJsonl(path.join(CACHE_DIR, "relations.contains.jsonl"), moduleContainsRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.contains_module.jsonl"), moduleContainsModuleRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.exports.jsonl"), moduleExportsRelations);
+  writeJsonl(path.join(CACHE_DIR, "entities.project.jsonl"), projectRecords);
+  writeJsonl(path.join(CACHE_DIR, "relations.includes_file.jsonl"), projectIncludesFileRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.uses_resource.jsonl"), usesResourceRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.uses_setting.jsonl"), usesSettingRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.uses_config.jsonl"), usesConfigRelations);
+  writeJsonl(path.join(CACHE_DIR, "relations.transforms_config.jsonl"), configTransformRelations);
+  writeJsonl(
+    path.join(CACHE_DIR, "relations.references_project.jsonl"),
+    projectReferencesProjectRelations
+  );
 
   writeTsv(
     path.join(DB_IMPORT_DIR, "file_nodes.tsv"),
@@ -1055,7 +3092,7 @@ function main() {
   writeTsv(
     path.join(DB_IMPORT_DIR, "defines_rel.tsv"),
     ["from", "to"],
-    definesRelations.map((record) => [record.from, record.to])
+    validDefinesRelations.map((record) => [record.from, record.to])
   );
 
   writeTsv(
@@ -1067,7 +3104,99 @@ function main() {
   writeTsv(
     path.join(DB_IMPORT_DIR, "imports_rel.tsv"),
     ["from", "to", "import_name"],
-    importsRelations.map((record) => [record.from, record.to, record.import_name])
+    validImportsRelations.map((record) => [record.from, record.to, record.import_name])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "calls_sql_rel.tsv"),
+    ["from", "to", "note"],
+    validCallsSqlRelations.map((record) => [record.from, record.to, record.note])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "uses_config_key_rel.tsv"),
+    ["from", "to", "note"],
+    validUsesConfigKeyRelations.map((record) => [record.from, record.to, record.note])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "uses_resource_key_rel.tsv"),
+    ["from", "to", "note"],
+    validUsesResourceKeyRelations.map((record) => [record.from, record.to, record.note])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "uses_setting_key_rel.tsv"),
+    ["from", "to", "note"],
+    validUsesSettingKeyRelations.map((record) => [record.from, record.to, record.note])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "project_nodes.tsv"),
+    [
+      "id",
+      "path",
+      "name",
+      "kind",
+      "language",
+      "target_framework",
+      "summary",
+      "file_count",
+      "updated_at",
+      "source_of_truth",
+      "trust_level",
+      "status"
+    ],
+    projectRecords.map((record) => [
+      record.id,
+      record.path,
+      record.name,
+      record.kind,
+      record.language,
+      record.target_framework,
+      record.summary,
+      record.file_count,
+      record.updated_at,
+      record.source_of_truth,
+      record.trust_level,
+      record.status
+    ])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "includes_file_rel.tsv"),
+    ["from", "to"],
+    projectIncludesFileRelations.map((record) => [record.from, record.to])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "references_project_rel.tsv"),
+    ["from", "to", "note"],
+    projectReferencesProjectRelations.map((record) => [record.from, record.to, record.note])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "uses_resource_rel.tsv"),
+    ["from", "to", "note"],
+    usesResourceRelations.map((record) => [record.from, record.to, record.note])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "uses_setting_rel.tsv"),
+    ["from", "to", "note"],
+    usesSettingRelations.map((record) => [record.from, record.to, record.note])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "uses_config_rel.tsv"),
+    ["from", "to", "note"],
+    usesConfigRelations.map((record) => [record.from, record.to, record.note])
+  );
+
+  writeTsv(
+    path.join(DB_IMPORT_DIR, "transforms_config_rel.tsv"),
+    ["from", "to", "note"],
+    configTransformRelations.map((record) => [record.from, record.to, record.note])
   );
 
   const manifest = {
@@ -1082,9 +3211,24 @@ function main() {
       relations_constrains: constrainsRelations.length,
       relations_implements: implementsRelations.length,
       relations_supersedes: supersedesRelations.length,
-      relations_defines: definesRelations.length,
+      relations_defines: validDefinesRelations.length,
       relations_calls: validCallsRelations.length,
-      relations_imports: importsRelations.length
+      relations_imports: validImportsRelations.length,
+      relations_calls_sql: validCallsSqlRelations.length,
+      relations_uses_config_key: validUsesConfigKeyRelations.length,
+      relations_uses_resource_key: validUsesResourceKeyRelations.length,
+      relations_uses_setting_key: validUsesSettingKeyRelations.length,
+      modules: moduleRecords.length,
+      relations_contains: moduleContainsRelations.length,
+      relations_contains_module: moduleContainsModuleRelations.length,
+      relations_exports: moduleExportsRelations.length,
+      projects: projectRecords.length,
+      relations_includes_file: projectIncludesFileRelations.length,
+      relations_references_project: projectReferencesProjectRelations.length,
+      relations_uses_resource: usesResourceRelations.length,
+      relations_uses_setting: usesSettingRelations.length,
+      relations_uses_config: usesConfigRelations.length,
+      relations_transforms_config: configTransformRelations.length
     },
     skipped,
     incremental_mode: incrementalMode,
@@ -1107,7 +3251,10 @@ function main() {
     `[ingest] rels constrains=${manifest.counts.relations_constrains} implements=${manifest.counts.relations_implements} supersedes=${manifest.counts.relations_supersedes}`
   );
   console.log(
-    `[ingest] rels defines=${manifest.counts.relations_defines} calls=${manifest.counts.relations_calls} imports=${manifest.counts.relations_imports}`
+    `[ingest] rels defines=${manifest.counts.relations_defines} calls=${manifest.counts.relations_calls} imports=${manifest.counts.relations_imports} calls_sql=${manifest.counts.relations_calls_sql} uses_config_key=${manifest.counts.relations_uses_config_key} uses_resource_key=${manifest.counts.relations_uses_resource_key} uses_setting_key=${manifest.counts.relations_uses_setting_key}`
+  );
+  console.log(
+    `[ingest] rels contains=${manifest.counts.relations_contains} contains_module=${manifest.counts.relations_contains_module} exports=${manifest.counts.relations_exports} includes_file=${manifest.counts.relations_includes_file} references_project=${manifest.counts.relations_references_project} uses_resource=${manifest.counts.relations_uses_resource} uses_setting=${manifest.counts.relations_uses_setting} uses_config=${manifest.counts.relations_uses_config} transforms_config=${manifest.counts.relations_transforms_config}`
   );
   console.log(
     `[ingest] skipped unsupported=${skipped.unsupported} too_large=${skipped.tooLarge} binary=${skipped.binary}`
@@ -1115,4 +3262,25 @@ function main() {
   console.log(`[ingest] wrote cache + db import files under .context/`);
 }
 
-main();
+const isMainModule = process.argv[1] && path.resolve(process.argv[1]) === path.resolve(__filename);
+if (isMainModule) {
+  main();
+}
+
+export {
+  buildSqlResourceReferenceMap,
+  detectKind,
+  extractSqlObjectReferencesFromContent,
+  generateChunkDescription,
+  generateConfigIncludeRelations,
+  generateConfigTransformKeyRelations,
+  generateMachineConfigRelations,
+  generateConfigTransformRelations,
+  generateModuleSummary,
+  generateModules,
+  generateNamedResourceRelations,
+  generateProjects,
+  generateSectionHandlerRelations,
+  getChunkParserForExtension,
+  resolveRelativeImportTargetId
+};