Overlay: Add overlay annotations to Java & shared libraries

java/ql/lib/semmle/code/java/regex/RegexFlowConfigs.qll

@@ -1,6 +1,8 @@
 /**
  * Defines configurations and steps for handling regexes
  */
+overlay[local?]
+module;
 
 import java
 import semmle.code.java.dataflow.ExternalFlow

java/ql/lib/semmle/code/java/regex/RegexTreeView.qll

@@ -1,4 +1,6 @@
 /** Provides a class hierarchy corresponding to a parse tree of regular expressions. */
+overlay[local?]
+module;
 
 private import semmle.code.java.regex.regex as RE // importing under a namescape to avoid naming conflict for `Top`.
 private import codeql.regex.nfa.NfaUtils as NfaUtils

java/ql/lib/semmle/code/java/regex/regex.qll

@@ -1,6 +1,8 @@
 /**
  * Definitions for parsing regular expressions.
  */
+overlay[local?]
+module;
 
 import java
 private import RegexFlowConfigs