Overlay: Add overlay annotations to Java & shared libraries

shared/regex/codeql/regex/HostnameRegexp.qll

@@ -2,6 +2,8 @@
  * Provides predicates for reasoning about regular expressions
  * that match URLs and hostname patterns.
  */
+overlay[local?]
+module;
 
 private import RegexTreeView
 

shared/regex/codeql/regex/MissingRegExpAnchor.qll

@@ -2,6 +2,8 @@
  * Provides predicates for reasoning about regular expressions
  * without anchors.
  */
+overlay[local?]
+module;
 
 private import RegexTreeView
 import HostnameRegexp as HostnameShared

shared/regex/codeql/regex/OverlyLargeRangeQuery.qll

@@ -1,6 +1,8 @@
 /**
  * Classes and predicates for working with suspicious character ranges.
  */
+overlay[local?]
+module;
 
 private import RegexTreeView
 

shared/regex/codeql/regex/RegexTreeView.qll

@@ -1,6 +1,8 @@
 /**
  * This file contains a `RegexTreeViewSig` module describing the syntax tree of regular expressions.
  */
+overlay[local?]
+module;
 
 /**
  * A signature describing the syntax tree of regular expressions.

shared/regex/codeql/regex/nfa/BadTagFilterQuery.qll

@@ -1,6 +1,8 @@
 /**
  * Provides predicates for reasoning about bad tag filter vulnerabilities.
  */
+overlay[local?]
+module;
 
 private import NfaUtils as NfaUtils
 private import RegexpMatching as RM

shared/regex/codeql/regex/nfa/ExponentialBackTracking.qll

@@ -61,6 +61,8 @@
  *   * Lastly we ensure that any state reached by repeating `n` copies of `w` has
  *     a suffix `x` (possible empty) that is most likely __not__ accepted.
  */
+overlay[local?]
+module;
 
 private import NfaUtils as NfaUtils
 private import codeql.regex.RegexTreeView

shared/regex/codeql/regex/nfa/NfaUtils.qll

@@ -1,6 +1,8 @@
 /**
  * A shared library for creating and reasoning about NFA's.
  */
+overlay[local?]
+module;
 
 private import codeql.regex.RegexTreeView
 private import codeql.util.Numbers

shared/regex/codeql/regex/nfa/RegexpMatching.qll

@@ -2,6 +2,8 @@
  * Provides predicates for reasoning about which strings are matched by a regular expression,
  * and for testing which capture groups are filled when a particular regexp matches a string.
  */
+overlay[local?]
+module;
 
 private import NfaUtils as NfaUtils
 private import codeql.regex.RegexTreeView

shared/regex/codeql/regex/nfa/SuperlinearBackTracking.qll

@@ -34,6 +34,8 @@
  * It has the same suffix detection issue as the `js/redos` query, which can cause false positives.
  * It also doesn't find all transitions in the product automaton, which can cause false negatives.
  */
+overlay[local?]
+module;
 
 private import NfaUtils as NfaUtils
 private import codeql.regex.RegexTreeView
@@ -99,6 +101,7 @@ module Make<RegexTreeViewSig TreeImpl> {
     /**
      * Holds if the tuple `(r1, r2, r3)` might be on path from a start-state to an end-state in the product automaton.
      */
+    overlay[caller]
     pragma[inline]
     predicate isFeasibleTuple(State r1, State r2, State r3) {
       // The first element is either inside a repetition (or the start state itself)