diff --git a/config/add-overlay-annotations.py b/config/add-overlay-annotations.py
new file mode 100644
index 000000000000..f93929d41c60
--- /dev/null
+++ b/config/add-overlay-annotations.py
@@ -0,0 +1,273 @@
+# This script is used to annotate .qll files without any existing overlay annotations
+# with overlay[local?] and overlay[caller] annotations. Maintenance of overlay annotations
+# in annotated files will be handled by QL-for-QL queries.
+
+# It will walk the directory tree and annotate most .qll files, skipping only
+# some specific cases (e.g., empty files, files that configure dataflow for queries).
+
+# The script takes a list of languages and processes the corresponding directories.
+# If the optional --check argument is provided, the script checks for missing annotations,
+# but does not modify any files.
+
+# Usage: python3 add-overlay-annotations.py [--check] <language1> <language2> ...
+
+# The script will modify the files in place and print the changes made.
+# The script is designed to be run from the root of the repository.
+
+#!/usr/bin/python3
+import sys
+import os
+from difflib import *
+
+
+def has_overlay_annotations(lines):
+    '''
+    Check whether the given lines contain any overlay[...] annotations.
+    '''
+    overlays = ["local", "local?", "global", "caller"]
+    annotations = [f"overlay[{t}]" for t in overlays]
+    return any(ann in line for ann in annotations for line in lines)
+
+
+def is_line_comment(line):
+    return line.startswith("//") or (line.startswith("/*") and line.endswith("*/"))
+
+
+def find_file_level_module_declaration(lines):
+    '''
+    Returns the index of the existing file-level module declaration if one
+    exists. Returns None otherwise.
+    '''
+    comment = False
+    for i, line in enumerate(lines):
+        trimmed = line.strip()
+
+        if is_line_comment(trimmed):
+            continue
+        elif trimmed.startswith("/*"):
+            comment = True
+        elif comment and trimmed.endswith("*/"):
+            comment = False
+        elif not comment and trimmed.endswith("module;"):
+            return i
+
+    return None
+
+
+def is_file_module_qldoc(i, lines):
+    '''
+    Assuming a qldoc ended on line i, determine if it belongs to the implicit
+    file-level module. If it is followed by another qldoc or imports, then it
+    does and if it is followed by any other non-empty, non-comment lines, then
+    we assume that is a declaration of some kind and the qldoc is attached to
+    that declaration.
+    '''
+    comment = False
+
+    for line in lines[i+1:]:
+        trimmed = line.strip()
+
+        if trimmed.startswith("import ") or trimmed.startswith("private import ") or trimmed.startswith("/**"):
+             return True
+        elif is_line_comment(trimmed) or not trimmed:
+             continue
+        elif trimmed.startswith("/*"):
+             comment = True
+        elif comment and trimmed.endswith("*/"):
+             comment = False
+        elif not comment and trimmed:
+             return False
+
+    return True
+
+
+def find_file_module_qldoc_declaration(lines):
+    '''
+    Returns the index of last line of the implicit file module qldoc if one
+    exists. Returns None otherwise.
+    '''
+
+    qldoc = False
+    comment = False
+    for i, line in enumerate(lines):
+        trimmed = line.strip()
+
+        if trimmed.startswith("//"):
+            continue
+        elif (qldoc or trimmed.startswith("/**")) and trimmed.endswith("*/"):
+            # a qldoc just ended; determine if it belongs to the implicit file module
+            if is_file_module_qldoc(i, lines):
+                return i
+            else:
+                return None
+        elif trimmed.startswith("/**"):
+            qldoc = True
+        elif trimmed.startswith("/*"):
+            comment = True
+        elif comment and trimmed.endswith("*/"):
+            comment = False
+        elif (not qldoc and not comment) and trimmed:
+            return None
+
+    return None
+
+
+def only_comments(lines):
+    '''
+    Returns true if the lines contain only comments and empty lines.
+    '''
+    comment = False
+
+    for line in lines:
+        trimmed = line.strip()
+
+        if not trimmed or is_line_comment(trimmed):
+            continue
+        elif trimmed.startswith("/*"):
+            comment = True
+        elif comment and trimmed.endswith("*/"):
+            comment = False
+        elif comment:
+            continue
+        elif trimmed:
+            return False
+
+    return True
+
+
+def insert_toplevel_maybe_local_annotation(filename, lines):
+    '''
+    Find a suitable place to insert an overlay[local?] annotation at the top of the file.
+    Returns a pair consisting of description and the modified lines or None if no overlay
+    annotation is necessary (e.g., for files that only contain comments).
+    '''
+    if only_comments(lines):
+        return None
+
+    i = find_file_level_module_declaration(lines)
+    if not i == None:
+        out_lines = lines[:i]
+        out_lines.append("overlay[local?]\n")
+        out_lines.extend(lines[i:])
+        return (f"Annotating \"{filename}\" via existing file-level module statement", out_lines)
+
+    i = find_file_module_qldoc_declaration(lines)
+    if not i == None:
+        out_lines = lines[:i+1]
+        out_lines.append("overlay[local?]\n")
+        out_lines.append("module;\n")
+        out_lines.extend(lines[i+1:])
+        return (f"Annotating \"{filename}\" which has a file-level module qldoc", out_lines)
+
+    out_lines = ["overlay[local?]\n", "module;\n", "\n"] + lines
+    return (f"Annotating \"{filename}\" without file-level module qldoc", out_lines)
+
+
+def insert_overlay_caller_annotations(lines):
+    '''
+    Mark pragma[inline] predicates as overlay[caller] if they are not declared private.
+    '''
+    out_lines = []
+    for i, line in enumerate(lines):
+        trimmed = line.strip()
+        if trimmed == "pragma[inline]":
+            if i + 1 < len(lines) and not "private" in lines[i+1]:
+                whitespace = line[0: line.find(trimmed)]
+                out_lines.append(f"{whitespace}overlay[caller]\n")
+        out_lines.append(line)
+    return out_lines
+
+
+def annotate_as_appropriate(filename, lines):
+    '''
+    Insert new overlay[...] annotations according to heuristics in files without existing
+    overlay annotations.
+
+    Returns None if no annotations are needed. Otherwise, returns a pair consisting of a
+    string describing the action taken and the modified content as a list of lines.
+    '''
+    if has_overlay_annotations(lines):
+        return None
+
+    # These simple heuristics filter out those .qll files that we no _not_ want to annotate
+    # as overlay[local?].  It is not clear that these heuristics are exactly what we want,
+    # but they seem to work well enough for now (as determined by speed and accuracy numbers).
+    if (filename.endswith("Test.qll") or
+        ((filename.endswith("Query.qll") or filename.endswith("Config.qll")) and
+         any("implements DataFlow::ConfigSig" in line for line in lines))):
+        return None
+    elif not any(line for line in lines if line.strip()):
+        return None
+
+    lines = insert_overlay_caller_annotations(lines)
+    return insert_toplevel_maybe_local_annotation(filename, lines)
+
+
+def process_single_file(write, filename):
+    '''
+    Process a single file, annotating it as appropriate.
+    If write is set, the changes are written back to the file.
+    Returns True if the file requires changes.
+    '''
+    old = [line for line in open(filename)]
+
+    annotate_result = annotate_as_appropriate(filename, old)
+    if annotate_result is None:
+        return False
+
+    if not write:
+        return True
+
+    new = annotate_result[1]
+
+    diff = context_diff(old, new, fromfile=filename, tofile=filename)
+    diff = [line for line in diff]
+    if diff:
+        print(annotate_result[0])
+        for line in diff:
+            print(line.rstrip())
+        with open(filename, "w") as out_file:
+            for line in new:
+                out_file.write(line)
+
+    return True
+
+
+if len(sys.argv) > 1 and sys.argv[1] == "--check":
+  check = True
+  langs = sys.argv[2:]
+else:
+  check = False
+  langs = sys.argv[1:]
+
+dirs = []
+for lang in langs:
+    if lang in ["cpp", "go", "csharp", "java", "javascript", "python", "ruby", "rust", "swift"]:
+        dirs.append(f"{lang}/ql/lib")
+    else:
+        raise Exception(f"Unknown language \"{lang}\".")
+
+if dirs:
+    dirs.append("shared")
+
+missingAnnotations = []
+
+for roots in dirs:
+    for dirpath, dirnames, filenames in os.walk(roots):
+        for filename in filenames:
+            if filename.endswith(".qll") and not dirpath.endswith("tutorial"):
+                path = os.path.join(dirpath, filename)
+                res = process_single_file(not check, path)
+                if check and res:
+                    missingAnnotations.append(path)
+
+
+if len(missingAnnotations) > 0:
+    print("The following files have no overlay annotations:")
+    for path in missingAnnotations[:10]:
+      print("- " + path)
+    if len(missingAnnotations) > 10:
+      print("and " + str(len(missingAnnotations) - 10) + " additional files.")
+    print()
+    print("Please manually add overlay annotations or use the config/add-overlay-annotations.py script to automatically add sensible default overlay annotations.")
+    exit(-1)