Include diff-edidted files in overlay changes.

lib/analyze-action.js

@@ -27720,15 +27720,15 @@ var require_pattern = __commonJS({
     exports2.removeDuplicateSlashes = removeDuplicateSlashes;
     function partitionAbsoluteAndRelative(patterns) {
       const absolute = [];
-      const relative2 = [];
+      const relative3 = [];
       for (const pattern of patterns) {
         if (isAbsolute2(pattern)) {
           absolute.push(pattern);
         } else {
-          relative2.push(pattern);
+          relative3.push(pattern);
         }
       }
-      return [absolute, relative2];
+      return [absolute, relative3];
     }
     exports2.partitionAbsoluteAndRelative = partitionAbsoluteAndRelative;
     function isAbsolute2(pattern) {
@@ -80536,8 +80536,8 @@ var require_follow_redirects = __commonJS({
       }
       return parsed;
     }
-    function resolveUrl(relative2, base) {
-      return useNativeURL ? new URL2(relative2, base) : parseUrl(url2.resolve(base, relative2));
+    function resolveUrl(relative3, base) {
+      return useNativeURL ? new URL2(relative3, base) : parseUrl(url2.resolve(base, relative3));
     }
     function validateUrl(input) {
       if (/^\[/.test(input.hostname) && !/^\[[:0-9a-f]+\]$/i.test(input.hostname)) {
@@ -90922,8 +90922,38 @@ async function writeOverlayChangesFile(config, sourceRoot, logger) {
   const baseFileOids = await readBaseDatabaseOidsFile(config, logger);
   const overlayFileOids = await getFileOidsUnderPath(sourceRoot);
   const changedFiles = computeChangedFiles(baseFileOids, overlayFileOids);
+  const originalCount = changedFiles.length;
+  let forcedAddedCount = 0;
+  try {
+    const forced = getForcedOverlayFilesFromDiff(logger);
+    if (forced.size > 0) {
+      const existing = new Set(changedFiles);
+      for (const f of forced) {
+        if (!existing.has(f)) {
+          if (overlayFileOids[f] !== void 0 || fs6.existsSync(path7.join(sourceRoot, f))) {
+            existing.add(f);
+            changedFiles.push(f);
+            forcedAddedCount++;
+          }
+        }
+      }
+      if (forcedAddedCount > 0) {
+        logger.debug(
+          `Force-included ${forcedAddedCount} file(s) from diff ranges into overlay: ${changedFiles.slice(-forcedAddedCount).join(", ")}`
+        );
+      } else {
+        logger.debug(
+          "All diff range files were already present in natural overlay changes (or none applicable)."
+        );
+      }
+    }
+  } catch (e) {
+    logger.debug(
+      `Failed while attempting to force-include diff range files in overlay: ${e.message || e}`
+    );
+  }
   logger.info(
-    `Found ${changedFiles.length} changed file(s) under ${sourceRoot}.`
+    `Found ${originalCount} natural changed file(s); force-added ${forcedAddedCount}; total ${changedFiles.length} under ${sourceRoot}.`
   );
   const changedFilesJson = JSON.stringify({ changes: changedFiles });
   const overlayChangesFile = path7.join(
@@ -90950,6 +90980,23 @@ function computeChangedFiles(baseFileOids, overlayFileOids) {
   }
   return changes;
 }
+function getForcedOverlayFilesFromDiff(logger) {
+  const forced = /* @__PURE__ */ new Set();
+  const diffRanges = readDiffRangesJsonFile(logger);
+  if (!diffRanges || diffRanges.length === 0) {
+    return forced;
+  }
+  const checkoutPath = getRequiredInput("checkout_path");
+  for (const r of diffRanges) {
+    const absPath = r.path;
+    if (!absPath) continue;
+    let rel = path7.relative(checkoutPath, absPath);
+    if (!rel || rel.startsWith("..")) continue;
+    rel = rel.split(path7.sep).join("/");
+    forced.add(rel);
+  }
+  return forced;
+}
 var CACHE_VERSION = 1;
 var CACHE_PREFIX = "codeql-overlay-base-database";
 var MAX_CACHE_OPERATION_MS = 6e5;

lib/init-action-post.js

@@ -27720,15 +27720,15 @@ var require_pattern = __commonJS({
     exports2.removeDuplicateSlashes = removeDuplicateSlashes;
     function partitionAbsoluteAndRelative(patterns) {
       const absolute = [];
-      const relative2 = [];
+      const relative3 = [];
       for (const pattern of patterns) {
         if (isAbsolute2(pattern)) {
           absolute.push(pattern);
         } else {
-          relative2.push(pattern);
+          relative3.push(pattern);
         }
       }
-      return [absolute, relative2];
+      return [absolute, relative3];
     }
     exports2.partitionAbsoluteAndRelative = partitionAbsoluteAndRelative;
     function isAbsolute2(pattern) {
@@ -80536,8 +80536,8 @@ var require_follow_redirects = __commonJS({
       }
       return parsed;
     }
-    function resolveUrl(relative2, base) {
-      return useNativeURL ? new URL2(relative2, base) : parseUrl(url2.resolve(base, relative2));
+    function resolveUrl(relative3, base) {
+      return useNativeURL ? new URL2(relative3, base) : parseUrl(url2.resolve(base, relative3));
     }
     function validateUrl(input) {
       if (/^\[/.test(input.hostname) && !/^\[[:0-9a-f]+\]$/i.test(input.hostname)) {
@@ -84278,8 +84278,8 @@ var require_readdir_glob = __commonJS({
           useStat = true;
         }
         const filename = dir + "/" + name;
-        const relative2 = filename.slice(1);
-        const absolute = path19 + "/" + relative2;
+        const relative3 = filename.slice(1);
+        const absolute = path19 + "/" + relative3;
         let stats = null;
         if (useStat || followSymlinks) {
           stats = await stat(absolute, followSymlinks);
@@ -84291,12 +84291,12 @@ var require_readdir_glob = __commonJS({
           stats = { isDirectory: () => false };
         }
         if (stats.isDirectory()) {
-          if (!shouldSkip(relative2)) {
-            yield { relative: relative2, absolute, stats };
+          if (!shouldSkip(relative3)) {
+            yield { relative: relative3, absolute, stats };
             yield* exploreWalkAsync(filename, path19, followSymlinks, useStat, shouldSkip, false);
           }
         } else {
-          yield { relative: relative2, absolute, stats };
+          yield { relative: relative3, absolute, stats };
         }
       }
     }
@@ -84366,11 +84366,11 @@ var require_readdir_glob = __commonJS({
         }
         setTimeout(() => this._next(), 0);
       }
-      _shouldSkipDirectory(relative2) {
-        return this.skipMatchers.some((m) => m.match(relative2));
+      _shouldSkipDirectory(relative3) {
+        return this.skipMatchers.some((m) => m.match(relative3));
       }
-      _fileMatches(relative2, isDirectory2) {
-        const file = relative2 + (isDirectory2 ? "/" : "");
+      _fileMatches(relative3, isDirectory2) {
+        const file = relative3 + (isDirectory2 ? "/" : "");
         return (this.matchers.length === 0 || this.matchers.some((m) => m.match(file))) && !this.ignoreMatchers.some((m) => m.match(file)) && (!this.options.nodir || !isDirectory2);
       }
       _next() {
@@ -84379,16 +84379,16 @@ var require_readdir_glob = __commonJS({
             if (!obj.done) {
               const isDirectory2 = obj.value.stats.isDirectory();
               if (this._fileMatches(obj.value.relative, isDirectory2)) {
-                let relative2 = obj.value.relative;
+                let relative3 = obj.value.relative;
                 let absolute = obj.value.absolute;
                 if (this.options.mark && isDirectory2) {
-                  relative2 += "/";
+                  relative3 += "/";
                   absolute += "/";
                 }
                 if (this.options.stat) {
-                  this.emit("match", { relative: relative2, absolute, stat: obj.value.stats });
+                  this.emit("match", { relative: relative3, absolute, stat: obj.value.stats });
                 } else {
-                  this.emit("match", { relative: relative2, absolute });
+                  this.emit("match", { relative: relative3, absolute });
                 }
               }
               this._next(this.iterator);
@@ -89873,8 +89873,8 @@ var require_primordials = __commonJS({
       ArrayPrototypeIndexOf(self2, el) {
         return self2.indexOf(el);
       },
-      ArrayPrototypeJoin(self2, sep5) {
-        return self2.join(sep5);
+      ArrayPrototypeJoin(self2, sep6) {
+        return self2.join(sep6);
       },
       ArrayPrototypeMap(self2, fn) {
         return self2.map(fn);
@@ -101761,7 +101761,7 @@ var require_commonjs16 = __commonJS({
        *
        * @internal
        */
-      constructor(cwd = process.cwd(), pathImpl, sep5, { nocase, childrenCacheSize = 16 * 1024, fs: fs20 = defaultFS } = {}) {
+      constructor(cwd = process.cwd(), pathImpl, sep6, { nocase, childrenCacheSize = 16 * 1024, fs: fs20 = defaultFS } = {}) {
         this.#fs = fsFromOption(fs20);
         if (cwd instanceof URL || cwd.startsWith("file://")) {
           cwd = (0, node_url_1.fileURLToPath)(cwd);
@@ -101772,7 +101772,7 @@ var require_commonjs16 = __commonJS({
         this.#resolveCache = new ResolveCache();
         this.#resolvePosixCache = new ResolveCache();
         this.#children = new ChildrenCache(childrenCacheSize);
-        const split = cwdPath.substring(this.rootPath.length).split(sep5);
+        const split = cwdPath.substring(this.rootPath.length).split(sep6);
         if (split.length === 1 && !split[0]) {
           split.pop();
         }
@@ -102615,10 +102615,10 @@ var require_ignore2 = __commonJS({
       ignored(p) {
         const fullpath = p.fullpath();
         const fullpaths = `${fullpath}/`;
-        const relative2 = p.relative() || ".";
-        const relatives = `${relative2}/`;
+        const relative3 = p.relative() || ".";
+        const relatives = `${relative3}/`;
         for (const m of this.relative) {
-          if (m.match(relative2) || m.match(relatives))
+          if (m.match(relative3) || m.match(relatives))
             return true;
         }
         for (const m of this.absolute) {
@@ -102629,9 +102629,9 @@ var require_ignore2 = __commonJS({
       }
       childrenIgnored(p) {
         const fullpath = p.fullpath() + "/";
-        const relative2 = (p.relative() || ".") + "/";
+        const relative3 = (p.relative() || ".") + "/";
         for (const m of this.relativeChildren) {
-          if (m.match(relative2))
+          if (m.match(relative3))
             return true;
         }
         for (const m of this.absoluteChildren) {
@@ -129189,8 +129189,38 @@ async function writeOverlayChangesFile(config, sourceRoot, logger) {
   const baseFileOids = await readBaseDatabaseOidsFile(config, logger);
   const overlayFileOids = await getFileOidsUnderPath(sourceRoot);
   const changedFiles = computeChangedFiles(baseFileOids, overlayFileOids);
+  const originalCount = changedFiles.length;
+  let forcedAddedCount = 0;
+  try {
+    const forced = getForcedOverlayFilesFromDiff(logger);
+    if (forced.size > 0) {
+      const existing = new Set(changedFiles);
+      for (const f of forced) {
+        if (!existing.has(f)) {
+          if (overlayFileOids[f] !== void 0 || fs6.existsSync(path7.join(sourceRoot, f))) {
+            existing.add(f);
+            changedFiles.push(f);
+            forcedAddedCount++;
+          }
+        }
+      }
+      if (forcedAddedCount > 0) {
+        logger.debug(
+          `Force-included ${forcedAddedCount} file(s) from diff ranges into overlay: ${changedFiles.slice(-forcedAddedCount).join(", ")}`
+        );
+      } else {
+        logger.debug(
+          "All diff range files were already present in natural overlay changes (or none applicable)."
+        );
+      }
+    }
+  } catch (e) {
+    logger.debug(
+      `Failed while attempting to force-include diff range files in overlay: ${e.message || e}`
+    );
+  }
   logger.info(
-    `Found ${changedFiles.length} changed file(s) under ${sourceRoot}.`
+    `Found ${originalCount} natural changed file(s); force-added ${forcedAddedCount}; total ${changedFiles.length} under ${sourceRoot}.`
   );
   const changedFilesJson = JSON.stringify({ changes: changedFiles });
   const overlayChangesFile = path7.join(
@@ -129217,6 +129247,23 @@ function computeChangedFiles(baseFileOids, overlayFileOids) {
   }
   return changes;
 }
+function getForcedOverlayFilesFromDiff(logger) {
+  const forced = /* @__PURE__ */ new Set();
+  const diffRanges = readDiffRangesJsonFile(logger);
+  if (!diffRanges || diffRanges.length === 0) {
+    return forced;
+  }
+  const checkoutPath = getRequiredInput("checkout_path");
+  for (const r of diffRanges) {
+    const absPath = r.path;
+    if (!absPath) continue;
+    let rel = path7.relative(checkoutPath, absPath);
+    if (!rel || rel.startsWith("..")) continue;
+    rel = rel.split(path7.sep).join("/");
+    forced.add(rel);
+  }
+  return forced;
+}
 
 // src/tools-features.ts
 var semver3 = __toESM(require_semver2());

lib/init-action.js

@@ -29628,15 +29628,15 @@ var require_pattern = __commonJS({
     exports2.removeDuplicateSlashes = removeDuplicateSlashes;
     function partitionAbsoluteAndRelative(patterns) {
       const absolute = [];
-      const relative2 = [];
+      const relative3 = [];
       for (const pattern of patterns) {
         if (isAbsolute3(pattern)) {
           absolute.push(pattern);
         } else {
-          relative2.push(pattern);
+          relative3.push(pattern);
         }
       }
-      return [absolute, relative2];
+      return [absolute, relative3];
     }
     exports2.partitionAbsoluteAndRelative = partitionAbsoluteAndRelative;
     function isAbsolute3(pattern) {
@@ -81633,8 +81633,8 @@ var require_follow_redirects = __commonJS({
       }
       return parsed;
     }
-    function resolveUrl(relative2, base) {
-      return useNativeURL ? new URL2(relative2, base) : parseUrl(url.resolve(base, relative2));
+    function resolveUrl(relative3, base) {
+      return useNativeURL ? new URL2(relative3, base) : parseUrl(url.resolve(base, relative3));
     }
     function validateUrl(input) {
       if (/^\[/.test(input.hostname) && !/^\[[:0-9a-f]+\]$/i.test(input.hostname)) {
@@ -86812,8 +86812,38 @@ async function writeOverlayChangesFile(config, sourceRoot, logger) {
   const baseFileOids = await readBaseDatabaseOidsFile(config, logger);
   const overlayFileOids = await getFileOidsUnderPath(sourceRoot);
   const changedFiles = computeChangedFiles(baseFileOids, overlayFileOids);
+  const originalCount = changedFiles.length;
+  let forcedAddedCount = 0;
+  try {
+    const forced = getForcedOverlayFilesFromDiff(logger);
+    if (forced.size > 0) {
+      const existing = new Set(changedFiles);
+      for (const f of forced) {
+        if (!existing.has(f)) {
+          if (overlayFileOids[f] !== void 0 || fs6.existsSync(path8.join(sourceRoot, f))) {
+            existing.add(f);
+            changedFiles.push(f);
+            forcedAddedCount++;
+          }
+        }
+      }
+      if (forcedAddedCount > 0) {
+        logger.debug(
+          `Force-included ${forcedAddedCount} file(s) from diff ranges into overlay: ${changedFiles.slice(-forcedAddedCount).join(", ")}`
+        );
+      } else {
+        logger.debug(
+          "All diff range files were already present in natural overlay changes (or none applicable)."
+        );
+      }
+    }
+  } catch (e) {
+    logger.debug(
+      `Failed while attempting to force-include diff range files in overlay: ${e.message || e}`
+    );
+  }
   logger.info(
-    `Found ${changedFiles.length} changed file(s) under ${sourceRoot}.`
+    `Found ${originalCount} natural changed file(s); force-added ${forcedAddedCount}; total ${changedFiles.length} under ${sourceRoot}.`
   );
   const changedFilesJson = JSON.stringify({ changes: changedFiles });
   const overlayChangesFile = path8.join(
@@ -86840,6 +86870,23 @@ function computeChangedFiles(baseFileOids, overlayFileOids) {
   }
   return changes;
 }
+function getForcedOverlayFilesFromDiff(logger) {
+  const forced = /* @__PURE__ */ new Set();
+  const diffRanges = readDiffRangesJsonFile(logger);
+  if (!diffRanges || diffRanges.length === 0) {
+    return forced;
+  }
+  const checkoutPath = getRequiredInput("checkout_path");
+  for (const r of diffRanges) {
+    const absPath = r.path;
+    if (!absPath) continue;
+    let rel = path8.relative(checkoutPath, absPath);
+    if (!rel || rel.startsWith("..")) continue;
+    rel = rel.split(path8.sep).join("/");
+    forced.add(rel);
+  }
+  return forced;
+}
 var CACHE_VERSION = 1;
 var CACHE_PREFIX = "codeql-overlay-base-database";
 var MAX_CACHE_OPERATION_MS = 6e5;
@@ -87455,6 +87502,19 @@ function writeDiffRangesJsonFile(logger, ranges) {
 ${jsonContents}`
   );
 }
+function readDiffRangesJsonFile(logger) {
+  const jsonFilePath = getDiffRangesJsonFilePath();
+  if (!fs8.existsSync(jsonFilePath)) {
+    logger.debug(`Diff ranges JSON file does not exist at ${jsonFilePath}`);
+    return void 0;
+  }
+  const jsonContents = fs8.readFileSync(jsonFilePath, "utf8");
+  logger.debug(
+    `Read pr-diff-range JSON file from ${jsonFilePath}:
+${jsonContents}`
+  );
+  return JSON.parse(jsonContents);
+}
 async function getPullRequestEditedDiffRanges(branches, logger) {
   const fileDiffs = await getFileDiffsWithBasehead(branches, logger);
   if (fileDiffs === void 0) {

lib/upload-lib.js

@@ -29017,15 +29017,15 @@ var require_pattern = __commonJS({
     exports2.removeDuplicateSlashes = removeDuplicateSlashes;
     function partitionAbsoluteAndRelative(patterns) {
       const absolute = [];
-      const relative2 = [];
+      const relative3 = [];
       for (const pattern of patterns) {
         if (isAbsolute2(pattern)) {
           absolute.push(pattern);
         } else {
-          relative2.push(pattern);
+          relative3.push(pattern);
         }
       }
-      return [absolute, relative2];
+      return [absolute, relative3];
     }
     exports2.partitionAbsoluteAndRelative = partitionAbsoluteAndRelative;
     function isAbsolute2(pattern) {
@@ -81833,8 +81833,8 @@ var require_follow_redirects = __commonJS({
       }
       return parsed;
     }
-    function resolveUrl(relative2, base) {
-      return useNativeURL ? new URL2(relative2, base) : parseUrl(url2.resolve(base, relative2));
+    function resolveUrl(relative3, base) {
+      return useNativeURL ? new URL2(relative3, base) : parseUrl(url2.resolve(base, relative3));
     }
     function validateUrl(input) {
       if (/^\[/.test(input.hostname) && !/^\[[:0-9a-f]+\]$/i.test(input.hostname)) {
@@ -89293,8 +89293,38 @@ async function writeOverlayChangesFile(config, sourceRoot, logger) {
   const baseFileOids = await readBaseDatabaseOidsFile(config, logger);
   const overlayFileOids = await getFileOidsUnderPath(sourceRoot);
   const changedFiles = computeChangedFiles(baseFileOids, overlayFileOids);
+  const originalCount = changedFiles.length;
+  let forcedAddedCount = 0;
+  try {
+    const forced = getForcedOverlayFilesFromDiff(logger);
+    if (forced.size > 0) {
+      const existing = new Set(changedFiles);
+      for (const f of forced) {
+        if (!existing.has(f)) {
+          if (overlayFileOids[f] !== void 0 || fs5.existsSync(path7.join(sourceRoot, f))) {
+            existing.add(f);
+            changedFiles.push(f);
+            forcedAddedCount++;
+          }
+        }
+      }
+      if (forcedAddedCount > 0) {
+        logger.debug(
+          `Force-included ${forcedAddedCount} file(s) from diff ranges into overlay: ${changedFiles.slice(-forcedAddedCount).join(", ")}`
+        );
+      } else {
+        logger.debug(
+          "All diff range files were already present in natural overlay changes (or none applicable)."
+        );
+      }
+    }
+  } catch (e) {
+    logger.debug(
+      `Failed while attempting to force-include diff range files in overlay: ${e.message || e}`
+    );
+  }
   logger.info(
-    `Found ${changedFiles.length} changed file(s) under ${sourceRoot}.`
+    `Found ${originalCount} natural changed file(s); force-added ${forcedAddedCount}; total ${changedFiles.length} under ${sourceRoot}.`
   );
   const changedFilesJson = JSON.stringify({ changes: changedFiles });
   const overlayChangesFile = path7.join(
@@ -89321,6 +89351,23 @@ function computeChangedFiles(baseFileOids, overlayFileOids) {
   }
   return changes;
 }
+function getForcedOverlayFilesFromDiff(logger) {
+  const forced = /* @__PURE__ */ new Set();
+  const diffRanges = readDiffRangesJsonFile(logger);
+  if (!diffRanges || diffRanges.length === 0) {
+    return forced;
+  }
+  const checkoutPath = getRequiredInput("checkout_path");
+  for (const r of diffRanges) {
+    const absPath = r.path;
+    if (!absPath) continue;
+    let rel = path7.relative(checkoutPath, absPath);
+    if (!rel || rel.startsWith("..")) continue;
+    rel = rel.split(path7.sep).join("/");
+    forced.add(rel);
+  }
+  return forced;
+}
 
 // src/tools-features.ts
 var semver3 = __toESM(require_semver2());

lib/upload-sarif-action.js

@@ -27720,15 +27720,15 @@ var require_pattern = __commonJS({
     exports2.removeDuplicateSlashes = removeDuplicateSlashes;
     function partitionAbsoluteAndRelative(patterns) {
       const absolute = [];
-      const relative2 = [];
+      const relative3 = [];
       for (const pattern of patterns) {
         if (isAbsolute2(pattern)) {
           absolute.push(pattern);
         } else {
-          relative2.push(pattern);
+          relative3.push(pattern);
         }
       }
-      return [absolute, relative2];
+      return [absolute, relative3];
     }
     exports2.partitionAbsoluteAndRelative = partitionAbsoluteAndRelative;
     function isAbsolute2(pattern) {
@@ -81833,8 +81833,8 @@ var require_follow_redirects = __commonJS({
       }
       return parsed;
     }
-    function resolveUrl(relative2, base) {
-      return useNativeURL ? new URL2(relative2, base) : parseUrl(url2.resolve(base, relative2));
+    function resolveUrl(relative3, base) {
+      return useNativeURL ? new URL2(relative3, base) : parseUrl(url2.resolve(base, relative3));
     }
     function validateUrl(input) {
       if (/^\[/.test(input.hostname) && !/^\[[:0-9a-f]+\]$/i.test(input.hostname)) {
@@ -88949,8 +88949,8 @@ function wrapApiConfigurationError(e) {
 }
 
 // src/feature-flags.ts
-var fs6 = __toESM(require("fs"));
-var path8 = __toESM(require("path"));
+var fs7 = __toESM(require("fs"));
+var path9 = __toESM(require("path"));
 var semver3 = __toESM(require_semver2());
 
 // src/defaults.json
@@ -88958,8 +88958,8 @@ var bundleVersion = "codeql-bundle-v2.23.2";
 var cliVersion = "2.23.2";
 
 // src/overlay-database-utils.ts
-var fs5 = __toESM(require("fs"));
-var path7 = __toESM(require("path"));
+var fs6 = __toESM(require("fs"));
+var path8 = __toESM(require("path"));
 var actionsCache = __toESM(require_cache3());
 
 // src/git-utils.ts
@@ -89159,6 +89159,26 @@ async function isAnalyzingDefaultBranch() {
   return currentRef === defaultBranch;
 }
 
+// src/diff-informed-analysis-utils.ts
+var fs5 = __toESM(require("fs"));
+var path7 = __toESM(require("path"));
+function getDiffRangesJsonFilePath() {
+  return path7.join(getTemporaryDirectory(), "pr-diff-range.json");
+}
+function readDiffRangesJsonFile(logger) {
+  const jsonFilePath = getDiffRangesJsonFilePath();
+  if (!fs5.existsSync(jsonFilePath)) {
+    logger.debug(`Diff ranges JSON file does not exist at ${jsonFilePath}`);
+    return void 0;
+  }
+  const jsonContents = fs5.readFileSync(jsonFilePath, "utf8");
+  logger.debug(
+    `Read pr-diff-range JSON file from ${jsonFilePath}:
+${jsonContents}`
+  );
+  return JSON.parse(jsonContents);
+}
+
 // src/logging.ts
 var core7 = __toESM(require_core());
 function getActionsLogger() {
@@ -89184,12 +89204,12 @@ async function writeBaseDatabaseOidsFile(config, sourceRoot) {
   const gitFileOids = await getFileOidsUnderPath(sourceRoot);
   const gitFileOidsJson = JSON.stringify(gitFileOids);
   const baseDatabaseOidsFilePath = getBaseDatabaseOidsFilePath(config);
-  await fs5.promises.writeFile(baseDatabaseOidsFilePath, gitFileOidsJson);
+  await fs6.promises.writeFile(baseDatabaseOidsFilePath, gitFileOidsJson);
 }
 async function readBaseDatabaseOidsFile(config, logger) {
   const baseDatabaseOidsFilePath = getBaseDatabaseOidsFilePath(config);
   try {
-    const contents = await fs5.promises.readFile(
+    const contents = await fs6.promises.readFile(
       baseDatabaseOidsFilePath,
       "utf-8"
     );
@@ -89202,24 +89222,54 @@ async function readBaseDatabaseOidsFile(config, logger) {
   }
 }
 function getBaseDatabaseOidsFilePath(config) {
-  return path7.join(config.dbLocation, "base-database-oids.json");
+  return path8.join(config.dbLocation, "base-database-oids.json");
 }
 async function writeOverlayChangesFile(config, sourceRoot, logger) {
   const baseFileOids = await readBaseDatabaseOidsFile(config, logger);
   const overlayFileOids = await getFileOidsUnderPath(sourceRoot);
   const changedFiles = computeChangedFiles(baseFileOids, overlayFileOids);
+  const originalCount = changedFiles.length;
+  let forcedAddedCount = 0;
+  try {
+    const forced = getForcedOverlayFilesFromDiff(logger);
+    if (forced.size > 0) {
+      const existing = new Set(changedFiles);
+      for (const f of forced) {
+        if (!existing.has(f)) {
+          if (overlayFileOids[f] !== void 0 || fs6.existsSync(path8.join(sourceRoot, f))) {
+            existing.add(f);
+            changedFiles.push(f);
+            forcedAddedCount++;
+          }
+        }
+      }
+      if (forcedAddedCount > 0) {
+        logger.debug(
+          `Force-included ${forcedAddedCount} file(s) from diff ranges into overlay: ${changedFiles.slice(-forcedAddedCount).join(", ")}`
+        );
+      } else {
+        logger.debug(
+          "All diff range files were already present in natural overlay changes (or none applicable)."
+        );
+      }
+    }
+  } catch (e) {
+    logger.debug(
+      `Failed while attempting to force-include diff range files in overlay: ${e.message || e}`
+    );
+  }
   logger.info(
-    `Found ${changedFiles.length} changed file(s) under ${sourceRoot}.`
+    `Found ${originalCount} natural changed file(s); force-added ${forcedAddedCount}; total ${changedFiles.length} under ${sourceRoot}.`
   );
   const changedFilesJson = JSON.stringify({ changes: changedFiles });
-  const overlayChangesFile = path7.join(
+  const overlayChangesFile = path8.join(
     getTemporaryDirectory(),
     "overlay-changes.json"
   );
   logger.debug(
     `Writing overlay changed files to ${overlayChangesFile}: ${changedFilesJson}`
   );
-  await fs5.promises.writeFile(overlayChangesFile, changedFilesJson);
+  await fs6.promises.writeFile(overlayChangesFile, changedFilesJson);
   return overlayChangesFile;
 }
 function computeChangedFiles(baseFileOids, overlayFileOids) {
@@ -89236,6 +89286,23 @@ function computeChangedFiles(baseFileOids, overlayFileOids) {
   }
   return changes;
 }
+function getForcedOverlayFilesFromDiff(logger) {
+  const forced = /* @__PURE__ */ new Set();
+  const diffRanges = readDiffRangesJsonFile(logger);
+  if (!diffRanges || diffRanges.length === 0) {
+    return forced;
+  }
+  const checkoutPath = getRequiredInput("checkout_path");
+  for (const r of diffRanges) {
+    const absPath = r.path;
+    if (!absPath) continue;
+    let rel = path8.relative(checkoutPath, absPath);
+    if (!rel || rel.startsWith("..")) continue;
+    rel = rel.split(path8.sep).join("/");
+    forced.add(rel);
+  }
+  return forced;
+}
 
 // src/tools-features.ts
 var semver2 = __toESM(require_semver2());
@@ -89428,7 +89495,7 @@ var Features = class {
     this.gitHubFeatureFlags = new GitHubFeatureFlags(
       gitHubVersion,
       repositoryNwo,
-      path8.join(tempDir, FEATURE_FLAGS_FILE_NAME),
+      path9.join(tempDir, FEATURE_FLAGS_FILE_NAME),
       logger
     );
   }
@@ -89607,12 +89674,12 @@ var GitHubFeatureFlags = class {
   }
   async readLocalFlags() {
     try {
-      if (fs6.existsSync(this.featureFlagsFile)) {
+      if (fs7.existsSync(this.featureFlagsFile)) {
         this.logger.debug(
           `Loading feature flags from ${this.featureFlagsFile}`
         );
         return JSON.parse(
-          fs6.readFileSync(this.featureFlagsFile, "utf8")
+          fs7.readFileSync(this.featureFlagsFile, "utf8")
         );
       }
     } catch (e) {
@@ -89625,7 +89692,7 @@ var GitHubFeatureFlags = class {
   async writeLocalFlags(flags) {
     try {
       this.logger.debug(`Writing feature flags to ${this.featureFlagsFile}`);
-      fs6.writeFileSync(this.featureFlagsFile, JSON.stringify(flags));
+      fs7.writeFileSync(this.featureFlagsFile, JSON.stringify(flags));
     } catch (e) {
       this.logger.warning(
         `Error writing cached feature flags file ${this.featureFlagsFile}: ${e}.`
@@ -89706,26 +89773,6 @@ var PACK_IDENTIFIER_PATTERN = (function() {
   return new RegExp(`^${component}/${component}$`);
 })();
 
-// src/diff-informed-analysis-utils.ts
-var fs7 = __toESM(require("fs"));
-var path9 = __toESM(require("path"));
-function getDiffRangesJsonFilePath() {
-  return path9.join(getTemporaryDirectory(), "pr-diff-range.json");
-}
-function readDiffRangesJsonFile(logger) {
-  const jsonFilePath = getDiffRangesJsonFilePath();
-  if (!fs7.existsSync(jsonFilePath)) {
-    logger.debug(`Diff ranges JSON file does not exist at ${jsonFilePath}`);
-    return void 0;
-  }
-  const jsonContents = fs7.readFileSync(jsonFilePath, "utf8");
-  logger.debug(
-    `Read pr-diff-range JSON file from ${jsonFilePath}:
-${jsonContents}`
-  );
-  return JSON.parse(jsonContents);
-}
-
 // src/trap-caching.ts
 var actionsCache2 = __toESM(require_cache3());
 

src/overlay-database-utils.ts

@@ -9,6 +9,7 @@ import { getAutomationID } from "./api-client";
 import { type CodeQL } from "./codeql";
 import { type Config } from "./config-utils";
 import { getCommitOid, getFileOidsUnderPath } from "./git-utils";
+import { readDiffRangesJsonFile } from "./diff-informed-analysis-utils";
 import { Logger, withGroupAsync } from "./logging";
 import {
   isInTestMode,
@@ -121,8 +122,43 @@ export async function writeOverlayChangesFile(
   const baseFileOids = await readBaseDatabaseOidsFile(config, logger);
   const overlayFileOids = await getFileOidsUnderPath(sourceRoot);
   const changedFiles = computeChangedFiles(baseFileOids, overlayFileOids);
+
+  // Augment changed files with any files that appear in the precomputed PR diff ranges.
+  // This ensures overlay analysis always includes every file with at least one edited range.
+  const originalCount = changedFiles.length;
+  let extraAddedCount = 0;
+  try {
+    const diffChangedFiles = getFilesFromDiff(logger);
+    if (diffChangedFiles.size > 0) {
+      const existing = new Set(changedFiles);
+      for (const f of diffChangedFiles) {
+        if (!existing.has(f)) {
+          // Only include if file still exists (added/modified) — skip deleted files that might appear in diff.
+          if (overlayFileOids[f] !== undefined || fs.existsSync(path.join(sourceRoot, f))) {
+            existing.add(f);
+            changedFiles.push(f);
+            extraAddedCount++;
+          }
+        }
+      }
+      if (extraAddedCount > 0) {
+        logger.debug(
+          `Added ${extraAddedCount} file(s) from PR diff ranges into overlay: ${changedFiles.slice(-extraAddedCount).join(", ")}`,
+        );
+      } else {
+        logger.debug(
+          "All diff range files were already present in the diff from the base database.",
+        );
+      }
+    }
+  } catch (e) {
+    logger.debug(
+      `Failed while attempting to add diff range files in overlay: ${(e as any).message || e}`,
+    );
+  }
+
   logger.info(
-    `Found ${changedFiles.length} changed file(s) under ${sourceRoot}.`,
+    `Found ${originalCount} natural changed file(s); added from diff ${extraAddedCount}; total ${changedFiles.length} under ${sourceRoot}.`,
   );
 
   const changedFilesJson = JSON.stringify({ changes: changedFiles });
@@ -155,6 +191,22 @@ function computeChangedFiles(
   return changes;
 }
 
+/**
+ * Derive the set of repository-relative file paths that have at least one edited range
+ * in the precomputed diff ranges JSON. Returns an empty set if no JSON exists.
+ */
+function getFilesFromDiff(logger: Logger): Set<string> {
+  const forced = new Set<string>();
+  const diffRanges = readDiffRangesJsonFile(logger);
+  if (!diffRanges || diffRanges.length === 0) {
+    return forced;
+  }
+  for (const r of diffRanges) {
+    forced.add(r.path);
+  }
+  return forced;
+}
+
 // Constants for database caching
 const CACHE_VERSION = 1;
 const CACHE_PREFIX = "codeql-overlay-base-database";